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opencc-zeroMar 2023View details →

Data for: Optimal inference of molecular interaction dynamics in FRET microscopy

Intensity-based time-lapse fluorescence resonance energy transfer (FRET) microscopy has been a major tool for investigating cellular processes, converting otherwise unobservable molecular interactions into fluorescence time series. However, inferring the molecular interaction dynamics from the observables remains a challenging inverse problem, particularly when measurement noise and photobleaching are nonnegligible—a common situation in single-cell analysis. The conventional approach is to process the time-series data algebraically, but such methods inevitably accumulate the measurement noise and reduce the signal-to-noise ratio (SNR), limiting the scope of FRET microscopy. Here, we introduce an alternative probabilistic approach, B-FRET, generally applicable to standard 3-cube FRET-imaging data. Based on filtering theory, B-FRET implements a statistically optimal way to infer molecular interactions and thus drastically improves the SNR. We validate B-FRET using simulated data and then apply it to real data, including the notoriously noisy in vivo FRET time series from individual bacterial cells to reveal signaling dynamics otherwise hidden in the noise.

opencc-by-4.0Apr 2023View details →

Molecular Simulation Data Associated with the Manuscript "Function and dynamics of the intrinsically disordered carboxyl terminus of β2 adrenergic receptor"

Molecular Simulation Data Associated with the Manuscript "Function and dynamics of the intrinsically disordered carboxyl terminus of β2 adrenergic receptor" by Jie Heng, Yunfei Hu, Guillermo Pérez-Hernández, Asuka Inoue, Jiawei Zhao, Xiuyan Ma, Xiaoou Sun, Kouki Kawakami, Tatsuya Ikuta, Jienv Ding, Yujie Yang, Lujia Zhang, Sijia Peng, Xiaogang Niu, Hongwei Li, Ramon Guixà-González, Changwen Jin, Peter W. Hildebrand, Chunlai Chen & Brian K. Kobilka Nature Communications 2023, <a href="https://doi.org/10.1038/s41467-023-37233-1">https://doi.org/10.1038/s41467-023-37233-1</a> The representative molecular dynamics (MD) trajectories shown in the Supplementary Fig. 8, Variable contacts of the β2AR CT can be 3D visualized in the browser in the following link: <ul> <li><a href="https://proteinformatics.uni-leipzig.de/mdsrv.html?load=file://base/B2CT/variants.ngl"> https://proteinformatics.uni-leipzig.de/mdsrv.html?load=file://base/B2CT/variants.ngl</a></li> </ul>

opencc-by-4.0Mar 2023View details →

EMD data for the paper "Impact of ad-hoc post-processing parameters on the lubricant viscosity calculated with equilibrium molecular dynamics simulations"

This archive contains the post-processing data obtained from EMD simulations of 2,2,4-Trimethylhexane lubricant molecule under various operating conditions. The EMD simulations were performed using LAMMPS with COMPASS force field. (See manuscript and README for details.)

opencc-by-4.0Dec 2023View details →

Multi-omic integration of DNA methylation and gene expression data reveals molecular vulnerabilities in glioblastoma (processed data)

Glioblastoma multiforme (GBM) is one of the most aggressive types of cancer and exhibits profound genetic and epigenetic heterogeneity, making the development of an effective treatment a major challenge. The recent incorporation of molecular features into the diagnosis of GBM patients has led to an improved categorisation into various tumour subtypes with different prognoses and disease management. In this work, we have exploited the benefits of genome-wide multi-omic approaches to identify potential molecular vulnerabilities existing in GBM patients. Integration of gene expression and DNA methylation data from both bulk GBM and patient-derived GBM stem cell lines has revealed the presence of major sources of GBM variability, pinpointing subtype-specific tumour vulnerabilities amenable to pharmacological interventions. In this sense, inhibition of the AP1, SMAD3 and RUNX1 / RUNX2 pathways, in combination or not with the chemotherapeutic agent temozolomide, led to the subtype-specific impairment of tumour growth, particularly in the context of the aggressive, mesenchymal-like subtype. These results emphasize the involvement of these molecular pathways in the development of GBM and have potential implications for the development of personalized therapeutic approaches.

opencc-by-4.0Apr 2023View details →

Data for: Approaches for handling missing values and their impacts on biological inferences: a molecular rate case study

These data files are associated with the manuscript entitled: "Approaches for handling missing values and their impacts on biological inferences: a molecular rate case study" by Jacqueline A. May, Zeny Feng, and Sarah J. Adamowicz. This project entailed an evaluation of missing data handling approach on inferences using a molecular evolution case study. A target mixed-type dataset was first imputed using a real data-driven strategy for imputation method selection. Both trait-only (non-phylogenetic) and phylogenetic imputation methods were used to impute the dataset. Phylogenetic generalized least squares (PGLS) analyses were then applied to the complete-case and imputed datasets, specifying the traits as predictors and molecular evolutionary rates as the response variable. Those traits that associate significantly with molecular rates were identified and PGLS models compared to determine how the approach for handling missing data impacts biological inferences and conclusions. The files stored here are the trees built for phylogenetic imputation (RAxML tree and ultrametric tree versions) and the corresponding GenBank accession numbers.

opencc-zeroMay 2023View details →

Data from: Controlled molecular arrangement of easily aggregated deoxycholate with layered double hydroxide

Deoxycholate (DA) is a natural emulsifying agent involved in the absorption of dietary lipids. Due to the facial distribution of hydrophobic-hydrophilic region, DA easily aggregates under ambient conditions, and this property hinders the practical application of DA in clinical application. In this study, we found that the molecular arrangement of DA molecules could be controlled by utilizing layered double hydroxide (LDH) under a specific reaction condition. The effect of reaction methods such as co-precipitation, ion exchange, and reconstruction on the molecular arrangement of DA was investigated by X-ray diffraction, Fourier-transform infrared spectroscopy, high-resolution transmission electron microscopy, and differential scanning calorimetry. It was demonstrated that the self-aggregation of DA molecules could be suppressed by the oriented arrangement of DA between the gallery space of LDH. The DA moiety was well stabilized in the LDH layers due to the electrostatic interaction between DA molecules and LDH layers. The most ordered arrangement of DA molecules was observed when DA was incorporated into LDH via a reconstruction method. The DA molecules arranged in LDH via reconstruction did not show significant exothermic nor endothermic behavior up to 400℃, showing that the DA moiety lost its intermolecular attraction in between LDH layers.

opencc-by-4.0Mar 2023View details →

Supplemetary Data for the article: Machine-learning identified molecular fragments responsible for infrared emission features of polycyclic aromatic hydrocarbons

This is a set of Supplementary materials for the article 'Machine-learning identified molecular fragments responsible for infrared emission features of polycyclic aromatic hydrocarbons', by Meng et al. Supplementary_Data_I.pdf contains an extensive table spanning 36 pages that lists the top-10 molecular fragments accountable for the spectral bands between 2.761 and 1172.745 μm. To access this table, hyperlinks within the document can be used for navigation. Supplementary_Data_II.pdf comprises a large table that encompasses 10,691 pages, including the top-100 molecular fragments responsible for the spectral bands between 2.761 and 1172.745 μm. Navigation through the hyperlinks enables access to this table. Supplementary_Data_III.csv encompasses the chemical formulas, number of unpaired valence electrons, spin multiplicities, xyz data, and SMILES strings of the PAHs carrying the additional spectra. Supplementary_data_IV.zip includes the input and output datasets along with the ML code. The code script is written in Python 3.7, and is supported by the following libraries: sklearn, json, numpy, and pandas. Supplementary_Information.pdf contains the evidence supporting the choice of the cutoff radius, as well as the figures of the count of the molecules in the dataset, the FI with changing datasets and hyperparameters, of cross-validation, and of UIE bands and emission features of four SH PAHs. Importance of three carbon skeleton fragments for bands in different intervals is also demonstrated.

opencc-byDec 2020View details →

Data supporting Mixed-anion mixed-cation perovskite (FAPbI3)0.875(MAPbBr3)0.125: an ab initio molecular dynamics study

Data of a molecular dynamics simulation of the mixed cation and mixed halide perovskite (FAPbI3)0.875(MAPbBr3)0.125 , as well as the end compounds FAPbI3 and MAPbBr3. Related article:  J. Mater. Chem. A, 2022,10, 9592-9603, <a href="https://doi.org/10.1039/D1TA10860C">https://doi.org/10.1039/D1TA10860C</a> arXiv:2112.09795 [cond-mat.mtrl-sci] arXiv: 2112.09795 <a href="https://doi.org/10.48550/arXiv.2112.09795">https://doi.org/10.48550/arXiv.2112.09795</a>

opencc-by-nc-sa-4.0Jun 2023View details →

Molecular in situ monitoring of the pH-triggered response in adaptive polymers by two-dimensional Raman micro-correlation-spectroscopy - Raw Data

Raw data for publication Molecular in situ monitoring of the pH-triggered response in adaptive polymers by two-dimensional Raman micro-correlation-spectroscopy

Data for: Magnetic-field-assisted molecular beam epitaxy: Engineering of Fe3O4 ultrathin films on MgO(111)

Molecular beam epitaxy is widely used for engineering low-dimensional materials. Here, we present a novel extension of the capabilities of this method by assisting epitaxial growth with the presence of an external magnetic field (MF). MF-assisted epitaxial growth was implemented under ultra-high vacuum conditions thanks to specialized sample holders for generating in-plane or out-of-plane MF and dedicated manipulator stations with heating and cooling options. The significant impact of MF on the magnetic properties was shown for ultra-thin epitaxial magnetite films grown on MgO(111). Using in situ and ex situ characterization methods, scanning tunneling microscopy, conversion electron Mössbauer spectroscopy, and the magneto-optic Kerr effect, we showed that the in-plane MF applied during the reactive deposition of 10 nm Fe3O4(111)/MgO(111) heterostructures influenced the growth morphology of the magnetite films, which affects both in-plane and out-of-plane characteristics of the magnetization process. The observed changes are explained in terms of modification of the effective magnetic anisotropy.

Data from: Quantum computation of frequency-domain molecular response properties using a three-qubit iToffoli gate

The quantum computation of molecular response properties on near-term quantum hardware is a topic of substantial interest. Computing these properties directly in the frequency domain is desirable, but the circuits require large depth if the typical hardware gate set consisting of single- and two-qubit gates is used. Here, we report the application of a high-fidelity multipartite gate, the iToffoli gate, to the computation of frequency-domain response properties of diatomic molecules. The iToffoli gate enables a ~50% reduction in circuit depth and ~40% reduction in circuit execution time compared to the traditional gate set. We show that the molecular properties obtained with the iToffoli gate exhibit comparable or better agreement with theory than those obtained with the native CZ gates. Our work is among the first demonstrations of the practical usage of a native multi-qubit gate in quantum simulation, with diverse potential applications to near-term quantum computation.

Data for: A unique C-terminal domain contributes to the molecular function of restorer-of-fertility proteins in plant mitochondria

Restorer-of-fertility (Rf) genes have practical applications in hybrid seed production as a means to control self-pollination. They encode pentatricopeptide repeat (PPR) proteins that are targeted to mitochondria where they specifically bind to transcripts that induce cytoplasmic male sterility and repress their expression. We have identified a unique domain, RfCTD (Restorer-of-fertility C-terminal domain), which discriminates Restorer-of-fertility-like (RFL) proteins from hundreds of PPR proteins encoded in plant genomes. Using the sequence of this domain from hundreds of plant species, we have constructed a sequence profile that can quickly and accurately identify RfCTD sequences in plant genomes or transcriptomes. This data set contains PPR genes identified in 213 plant genomes (as summarised in accompanying table).

Data for dating in the dark: Elevated substitution rates in cave cockroaches (Blattodea: Nocticolidae) have negative impacts on molecular date estimates

Rates of nucleotide substitution vary substantially across the Tree of Life, with potentially confounding effects on phylogenetic and evolutionary analyses. A large acceleration in mitochondrial substitution rate occurs in the cockroach family Nocticolidae, which predominantly inhabit subterranean environments. To evaluate the impacts of this among-lineage rate heterogeneity on estimates of phylogenetic relationships and evolutionary timescales, we analysed nuclear ultraconserved elements (UCEs) and mitochondrial genomes from nocticolids and other cockroaches. Substitution rates were substantially elevated in nocticolid lineages compared with other cockroaches, especially in mitochondrial protein-coding genes. This disparity in evolutionary rates is likely to have led to different evolutionary relationships being supported by mitochondrial genomes and UCE loci. Furthermore, analyses using relaxed-clock models inferred much deeper divergence times compared with a flexible local clock. Our phylogenetic analysis of UCEs, which is the first genome-scale study to include all nine major cockroach families, unites Corydiidae and Nocticolidae and places Anaplectidae as the sister lineage to the rest of Blattoidea. We uncover an extraordinary level of genetic divergence in Nocticolidae, including two highly distinct clades that separated ~115 million years ago despite both containing representatives of the genus Nocticola. The results of our study highlight the potential impacts of high among-lineage rate variation on estimates of phylogenetic relationships and evolutionary timescales.

Data from: Dissecting molecular evolution of class 1 integron gene cassettes and their bacterial hosts in suburban creeks via epicPCR

Horizontal gene transfer (HGT) of class 1 integrons plays a key role in the dissemination of antimicrobial resistance (AMR) with clinical consequences worldwide. Class 1 integrons in clinical pathogens are commonly associated with AMR genes and embedded in mobile genetic elements. Over time, these mobile class 1 integrons have spread to diverse environmental bacterial hosts via HGT. We applied a single-cell fusion PCR-based technique to link class 1 integron gene cassette arrays to the phylogenetic markers in their bacterial hosts. Class 1 integrons and associated gene cassettes were detected in Alpha- and Gammaproteobacteria hosts from freshwater samples from two creeks in suburban Sydney. Molecular and bioinformatic characterisations of altered gene cassettes generated new insights into mechanisms that contribute to the evolution of class 1 integron gene cassettes. Here, we present experimental and bioinformatic evidence for key signatures of molecular evolution of gene cassettes, including the gain of a regulatory 5'-untranslated region (5'-UTR), the loss of attC recombination sites between adjacent gene cassettes, and the invasion of a 5'-UTR by an insertion sequence (IS) element. Notably, our experimental testing of a new variant of the aminoglycoside adenylyltransferase encoding aadA11 gene cassette demonstrated that the gain of 5'-UTR contributed to a 3-fold increase in the minimum inhibitory concentration of streptomycin relative to the ancestral reference gene cassette. Understanding these signatures of molecular evolution allows us to explain their effects on AMR phenotypes and offers the potential to better predict evolutionary trajectories of class 1 integrons.

opencc-zeroAug 2023View details →

Supporting information for: Integrating morphological, molecular, and cytogenetic data for F2 sea turtle hybrids diagnosis revealed balanced chromosomal sets

Hybridization could be considered part of the evolutionary history of many species. The hybridization among sea turtle species on the Brazilian coast is atypical and occurs where nesting areas and reproductive seasons overlap. Integrated analysis of morphology and genetics is still scarce, and there is no evidence of the parental chromosome set distribution in sea turtle interspecific hybrids. In this study, chromosome markers previously established for pure sea turtle species were combined with morphological and molecular analyses aiming to recognize genetic composition and chromosome sets in possible interspecific hybrids initially identified by mixed morphology. The data showed that one hybrid could be an F2 individual among Caretta caretta × Eretmochelys imbricata × Chelonia mydas, and another is resulting from backcross between C. caretta × Lepidochelys olivacea. Native alleles of different parental lineages were reported in the hybrids, and, despite this, it was verified that the hybrid chromosome sets were still balanced. Thus, how sea turtle hybridism can affect genetic features in the long term is a concern, as the implications of the crossing-over in hybrid chromosomal sets and the effects on genetic function are still unpredictable.

opencc-by-4.0Jul 2023View details →

Supporting data for:"An accurate and efficient SAXS/SANS implementation including solvation layer effects suitable for restrained Molecular Dynamics simulations."

PLUMED_NEST_REPO.zip contains the plumed.dat file and the template PDB used to perform the metainference MD simulations of Gelsolin and UP1-RNA, with and without the Solvation Layer Contribution. TRAJECTORIES.zip contains the Gelsolin and UP1-RNA trajectories and additional data generated with GROMACS. In details: -Gelsolin. Production Molecular Dynamics Parameter file (production.mdp), a topology file (topol.top), and 3 folders: TPRs (with 10 TPR files -one for each replica-), TRJ_SLC_OFF (with data from simulations without Solvation Layer Contribution), and TRJ_SLC_ON (with data from simulations with Solvation Layer Contribution). The last two contain an index file, a trajectory obtained from the concatenation of the 10 replicas (concat.xtc), and a template PDB file. -UP1-RNA. TPR file (md.tpr) and 2 folders: TRJ_SLC_OFF (with data from simulations without solvent correction), and TRJ_SLC_ON (with data from simulations with solvent correction). Each folder contains an index file, a template PDB file and a trajectory file (trj.xtc)

opencc-zeroAug 2023View details →

Molecular data of the Sphagnum cuspidatum complex relative to taxonomy

The use of species as a concept is an important metric for assessing biological diversity and ecosystem function. However, delimiting species based on morphological characters can be difficult, especially in aquatic plants that exhibit high levels of variation and overlap. The Sphagnum cuspidatum complex, which includes plants that dominate peatland hollows close to or at the water table, provides an example of challenges in species delimitation. Microscopic characters that have been used to define taxa and the possibility that these characters may simply be phenoplastic responses to variation in water availability make species delimitation in this group especially difficult. In particular, the use of leaf shape and serration, which have been used to separate species in the complex, have resulted in divergent taxonomic treatments. Using a combination of high-resolution population genomic data (RADseq) and a robust morphological assessment of plants representing the focal species, we provide evidence to evaluate putative species in this complex. Our results are broadly relevant to other aquatic groups where leaf shape and marginal teeth are used to distinguish species.

opencc-by-4.0Oct 2022View details →

Data supplement for "Molecular motors enhance microtubule lattice plasticity" Lecompte, William; John, Karin

This dataset contains the data and source files for figures 2 (a-e), 3(a-d), 4(b,c,e) and Supplementary figures 5, 7(a-e), 8 and 9(a-c) in the following publication:    W. Lecompte and K. John   "Molecular motors enhance microtubule lattice plasticity"   published in 2023 in PRX Life (ArXiv https://arxiv.org/abs/2209.09161)   Please follow the instructions given in 'Readme.txt'.

opencc-by-4.0Sep 2023View details →

Data for "Absolute binding free energy calculation based on the fragment molecular orbital method and its application in designing novel SHP-2 allosteric inhibitors"

Data for publication "Absolute binding free energy calculation based on the fragment molecular orbital method and its application in designing novel SHP-2 allosteric inhibitors".All structures of complex and input files for FMO , FMO/SMD , FMO/PCM , and COSMO calculation are provided .