From 2c2ec2ab5ffff81ecc54f6f4985229671ecc71ff Mon Sep 17 00:00:00 2001 From: "github-actions[bot]" <41898282+github-actions[bot]@users.noreply.github.com> Date: Wed, 30 Oct 2024 13:30:00 +0100 Subject: [PATCH] Update citations (#1296) Co-authored-by: bgruening --- _bibliography/citations-eu.bib | 38 ++++++++++++++++++++++++++++++++-- 1 file changed, 36 insertions(+), 2 deletions(-) diff --git a/_bibliography/citations-eu.bib b/_bibliography/citations-eu.bib index 124e3808..2da8bd27 100644 --- a/_bibliography/citations-eu.bib +++ b/_bibliography/citations-eu.bib @@ -8246,13 +8246,14 @@ @misc{noauthor_importance_2020 year = {2020} } -@misc{noauthor_insights_nodate, +@misc{noauthor_insights_2024, abstract = {Explore millions of resources from scholarly journals, books, newspapers, videos and more, on the ProQuest Platform.}, keywords = {{\textgreater}UseGalaxy.eu}, language = {de}, title = {Insights {Into} the {Evolution} of {Chromatin} {Architecture} {Generated} by {Inversion} {Breakpoints} in {\textless}em{\textgreater}{Drosophila} pseudoobscura{\textless}/em{\textgreater} - {ProQuest}}, url = {https://www.proquest.com/openview/a035085b5068b9266b3ed76dea6fa720/1?pq-origsite=gscholar&cbl=18750&diss=y}, - urldate = {2024-10-27} + urldate = {2024-10-27}, + year = {2024} } @misc{noauthor_nutrients_2024, @@ -9602,6 +9603,23 @@ @article{reyes_characterization_2023 year = {2023} } +@article{richter_genome_2024, + abstract = {{\textless}p{\textgreater}{\textless}italic{\textgreater}Diplocarpon coronariae{\textless}/italic{\textgreater} is a fungal pathogen that is prevalent in low-input apple production. Over the past 15 years, it has become increasingly distributed in Europe. However, comprehensive insights into its biology and pathogenicity remain limited. One particular aspect is the rarity of the sexual morph of this pathogen, a phenomenon hitherto unobserved in Europe. {\textless}italic{\textgreater}Diplocarpon coronariae{\textless}/italic{\textgreater} reproduces through a heterothallic mating system requiring at least two different mating types for sexual reproduction. Genes determining the mating types are located on the mating-type locus. In this study, {\textless}italic{\textgreater}D. coronariae{\textless}/italic{\textgreater} strain DC1\_JKI from Dresden, Germany, was sequenced and used to unravel the structure of the mating type locus. Using short-read and long-read sequencing methods, the first gapless and near-complete telomere-to-telomere genome assembly of {\textless}italic{\textgreater}D. coronariae{\textless}/italic{\textgreater} was achieved. The assembled genome spans 51.2 Mbp and comprises 21 chromosome-scale contigs of high completeness. The generated genome sequence was used to {\textless}italic{\textgreater}in silico{\textless}/italic{\textgreater} elucidate the structure of the mating-type locus, identified as MAT1-2. Furthermore, an examination of MAT1-1 and MAT1-2 frequency across a diverse set of samples sourced from Europe and Asia revealed the exclusive presence of MAT1-2 in European samples, whereas both MAT loci were present in Asian counterparts. Our findings suggest an explanation for the absence of the sexual morph, potentially linked to the absence of the second mating idiomorph of {\textless}italic{\textgreater}D. coronariae{\textless}/italic{\textgreater} in European apple orchards.{\textless}/p{\textgreater}}, + author = {Richter, Sophie and Kind, Sabine and Oberhänsli, Thomas Wolfgang and Schneider, Michael and Nenasheva, Natalia and Hoff, Katharina and Keilwagen, Jens and Yeon, Il-Kweon and Philion, Vincent and Moriya, Shigeki and Flachowsky, Henryk and Patocchi, Andrea and Wöhner, Thomas Wolfgang}, + doi = {10.3389/fpls.2024.1437132}, + issn = {1664-462X}, + journal = {Frontiers in Plant Science}, + keywords = {{\textgreater}UseGalaxy.eu, Apple blotch, D. coronariae, Malus, Short reads, genome sequence, long reads, mating types}, + language = {English}, + month = {October}, + note = {Publisher: Frontiers}, + title = {Genome sequence of a {European} {Diplocarpon} coronariae strain and in silico structure of the mating-type locus}, + url = {https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2024.1437132/full}, + urldate = {2024-10-28}, + volume = {15}, + year = {2024} +} + @article{riediger_analysis_2020, author = {Riediger, Matthias and Spät, Philipp and Bilger, Raphael and Voigt, Karsten and Maček, Boris and Hess, Wolfgang R.}, doi = {10.1093/plcell/koaa017}, @@ -10590,6 +10608,22 @@ @article{singh_biophysical_2024 year = {2024} } +@article{singh_hemoglobin_2024, + abstract = {Aminocarb (AMC), a carbamate pesticide, due to its prevalent usage exhibits increased accumulation in the environment affecting both insects and humans. It enters the human body via food grains and be transported through bloodstream. AMC's chemical structure, containing specific molecular frameworks and functional groups, enables it to bind with proteins like albumin and hemoglobin. Given that molecules with similar architecture are known to bind with hemoglobin, we aimed to explore Aminocarb's binding capability and the potential mechanism or mode of its interaction with hemoglobin. Hb being a tetramer with a profound interface between amino acid chains offers multiple binding sites. It is therefore important to investigate the structural aspects of binding of AMC by employing various spectroscopic and in-silico methods. The surface of the α1 chain near the α1β2 interface emerges as the preferred binding site for AMC, primarily due to its conformational restrictions. In its bound state, AMC tends to maintain a relaxed conformation, closely resembling its globally optimized geometry, and resides in close proximity to the α1 chain via multiple hydrophobic contacts and water bridge as observed in molecular dynamics (MD) simulations. Fluorescence quenching experiments showed moderate binding strength (7.7×10⁴ L M⁻1 at 288 K, 7.8×10⁴ L M⁻1 at 298 K, 7.9×10⁴ L M⁻1 at 308 K) and spontaneous binding, driven by hydrophobic and van der Waals interactions, as indicated by enthalpy (0.80 – 0.91 kJ mol⁻1), entropy (0.0970 – 0.0974 kJ mol⁻1), and Gibbs free energy (-27.13 to - 29.08 kJ mol⁻1). Circular dichroism experiments reveal no major structural changes in Hb. Quantum chemical calculations and MD simulations reveal conformation-dependent energy differences, enhancing our understanding of AMC's binding mechanism to Hb.}, + author = {Singh, Shweta and Gopi, Priyanka and Sharma, Palak and Rani, Majji Sai Sudha and Pandya, Prateek and Ali, Mohd Sajid}, + doi = {10.1016/j.bbrc.2024.150896}, + issn = {0006-291X}, + journal = {Biochemical and Biophysical Research Communications}, + keywords = {{\textgreater}ChemicalToolbox, {\textgreater}UseGalaxy.eu, Aminocarb, Conformation, Fluorescence Spectroscopy, Hemoglobin, Molecular Dynamics, Quantum chemical calculations}, + month = {October}, + pages = {150896}, + shorttitle = {Hemoglobin {Targeting} {Potential} of {Aminocarb} {Pesticide}}, + title = {Hemoglobin {Targeting} {Potential} of {Aminocarb} {Pesticide}: {Investigation} into {Dynamics}, {Conformational} {Stability}, and {Energetics} in {Solvent} {Environment}}, + url = {https://www.sciencedirect.com/science/article/pii/S0006291X24014323}, + urldate = {2024-10-28}, + year = {2024} +} + @techreport{singh_identification_2022, abstract = {Abstract Approximately, 10\% of the world population is facing the challenge of food allergy in direct or indirect way. In this study, a genome-wide identification and annotation of the novel putative allergen from Almond is performed. Initially, the whole proteome of Almond (31,000 proteins) was scanned by Allergenonline, a publically available database of already reported allergens from different sources. The detailed analysis suggests that there are 430 putative allergens which reduced to 45 on motif-based screening using AllFam database. These predicted allergens are annotated for their function by using PFAM, GO databases and orthology analysis. To validate our prediction, we have used structural insights of allergen and antibody interactions for one of the predicted putative allergen protein, homologous to Pru ar 3.0101allergen from Apricot. The structure of putative allergen was modeled and molecular docking studies were performed against the antibody. The best docked conformation was subjected to molecular simulation studies to confirm the stable binding of these two molecules. This detailed analysis suggests that the identified allergen will show cross reactivity similar to Pru ar 3.0101 allergen from Apricot. This is one of the first report of identifying and annotating the homologous of Pru ar 3.0101 allergen in Almond.},