Find research datasets worth reusing

opencc-by-4.0Jan 2023View details →

Data supplement for the paper "An integrated computational strategy to predict personalized cancer drug combinations by reversing drug resistance signatures"

This dataset contains the the following data created for the paper "An integrated computational strategy to predict personalized cancer drug combinations by reversing drug resistance signatures". Data listing: Cell line-specific drug resistance signatures (CDRSR) Patient-specific drug resistance signatures (CTR-DB)

opencc-by-4.0Jun 2023View details →

Molecular mapping of quantitative trait loci (QTL) for resistance to early blight in tomato

Molecular mapping of quantitative trait loci (QTL) for resistance to early blight in tomato (1135884)

opencc-by-4.0Mar 2023View details →

European Union Summary Report on Antimicrobial Resistance in Zoonotic and Indicator Bacteria from Humans, Animals and Food in 2020/2021

All tables produced for the European Union Summary Report on Antimicrobial Resistance in Zoonotic and Indicator Bacteria from Humans, Animals and Food in 2021: - Campylobacter - E. coli - MRSA - Salmonella - ESBL Annexes A to F are also included.

opencc-zeroMar 2023View details →

Dataset for: The redlegged earth mite draft genome provides new insights into pesticide resistance evolution and demography in its invasive Australian range

Data and analyses for Thia et al. "The redlegged earth mite draft genome provides new insights into pesticide resistance evolution and demography in its invasive Australian range" submitted to Journal of Evolutionary Biology. This repository comprises data and scripts used to replicate the analyses in this paper. The goals of this study were to: (1) assemble a draft reference genome for Halotydeus destructor; (2) perform a comparative analysis of acetylcholinesterase genes among different agricultural arthropod pests; (3) characterise the population genetic patterns among Australian H. destructor populations; and (4) perform demographic modelling to understand the evolutionary relationships between eastern and western populations of H. destructor in Australia.

opencc-zeroMar 2023View details →

Data for: Heavy metal pollution impacts soil bacterial community structure and antimicrobial resistance at the Birmingham 35th Avenue Superfund Site

The data in this archive are the results of a study on the impact of heavy metals (HMs) on the soil microbiota of an urban Superfund site in Alabama. HMs are known to modify bacterial communities both in the laboratory and in situ. Consequently, soils in HM-contaminated sites such as the U.S. Environmental Protection Agency (EPA) Superfund sites are predicted to have altered ecosystem functioning, with potential ramifications for the health of organisms, including humans, that live nearby. Further, several studies have shown that heavy metal-resistant (HMR) bacteria often also display antimicrobial resistance (AMR), and therefore HM-contaminated soils could potentially act as reservoirs that could disseminate AMR genes into human-associated pathogenic bacteria. To explore this possibility, topsoil samples were collected from six public locations in the zip code 35207 (the home of the North Birmingham 35th Avenue Superfund Site) and in six public areas in the neighboring zip code, 35214. 35027 soils had significantly elevated levels of the HMs As, Mn, Pb, and Zn, and sequencing of the V4 region of the bacterial 16S rRNA gene revealed that elevated HM concentrations correlated with reduced microbial diversity and altered community structure. While there was no difference between zip codes in the proportion of total culturable HMR bacteria, bacterial isolates with HMR almost always also exhibited AMR. Metagenomes inferred using PICRUSt2 also predicted significantly higher mean relative frequencies in 35207 for several AMR genes related to both specific and broad-spectrum AMR phenotypes. Together, these results support the hypothesis that chronic HM pollution alters the soil bacterial community structure in ecologically meaningful ways and may also select for bacteria with increased potential to contribute to AMR in human disease.

opencc-by-4.0Mar 2023View details →

Kinetic in support of "Pre-Steady-State Kinetic Characterization of an Antibiotic-Resistant Mutant of Staphylococcus aureus DNA Polymerase PolC"

These are KinTek Explorer mechanism files containing the data and analysis described in the manuscript "Pre-Steady-State Kinetic Characterization of an Antibiotic-Resistant Mutant of Staphylococcus aureus DNA Polymerase PolC" (bioRxiv 2022.10.04.510889; doi: https://doi.org/10.1101/2022.10.04.510889).

opencc-by-4.0Mar 2023View details →

Supplementary Material 7 including Salamandra salamandra occurrence data, topographic, geological and land cover data and node-based resistances

Supplementary material for the article "Habitat connectivity supports the local abundance of fire salamanders (Salamandra salamandra) but also the spread of Batrachochytrium salamandrivorans" by Bolte et al. (2023) published in Landscape Ecology (DOI: 10.1007/s10980-023-01636-8) This folder comprises a .shp file with fire salamander occurrences, topographic and land cover data (GeoTiff) from the northern Eifel region as well as the R Code used for the statistical analysis of salamander habitat suitability and connectivity.

opencc-by-4.0Apr 2023View details →

Resistive switching and role of interfaces in memristive devices based on amorphous NbOx grown by anodic oxidation - Dataset

This is the dataset of "Resistive switching and role of interfaces in memristive devices based on amorphous NbOx grown by anodic oxidation"

opencc-zeroMay 2023View details →

MHC class II genes mediate susceptibility and resistance to coronavirus infections in bats

Understanding the immunogenetic basis of coronavirus (CoV) susceptibility in major pathogen reservoirs, such as bats, is central to infer their zoonotic potential. Members of the cryptic Hipposideros bat species complex differ in CoV susceptibility, but the underlying mechanisms remain unclear. The genes of the major histocompatibility complex (MHC) are the best understood genetic basis of pathogen resistance, and differences in MHC diversity are one possible reason for asymmetrical infection patterns among closely related species. Here, we aimed to link asymmetries in observed CoV (CoV-229E, CoV-2B, and CoV-2Bbasal) susceptibility to immunogenetic differences amongst four Hipposideros bat species. From the 2,072 bats assigned to their respective species using the mtDNA cytochrome b gene, members of the most numerous and ubiquitous species, Hipposideros caffer D, were most infected with CoV-229E and SARS-related CoV-2B. Using a subset of 569 bats we determined that much of the existent allelic and functional (i.e., supertype) MHC DRB class II diversity originated from common ancestry. One MHC supertype shared amongst all species, ST12, was consistently linked to susceptibility with CoV-229E, which is closely related to the common cold agent HCoV-229E, and infected bats with ST12 had a lower body condition. The same MHC supertype was connected to resistance to CoV-2B, and bats with ST12 were less likely be co-infected with CoV-229E and CoV-2B. Our work suggests a role of immunogenetics in determining CoV susceptibility in bats. We advocate for the preservation of functional genetic and species diversity in reservoirs as means of mitigating the risk of disease spillover.

opencc-by-4.0May 2023View details →

FTIR dataset from the article "Resistance to Degradation of Silk Fibroin Hydrogels Exposed to Neuroinflammatory Environments"

The attached archive encounters the FTIR data used for the calculation of the β-sheet content of the silk fibroin hydrogels in the in-vitro experiments. Such data is used in main Figures 2c and 2d, 4a and 7a as well as Supplementary Figure 2a of the associated article.   The acquisition of the files has been performed as indicated below: <ul> <li>Equipment: Thermo Scientific™ Nicolet™ iS™ 5 Spectrometer (Thermofisher, United States)</li> <li>Acquisition Software: OMNIC 9.2.86 (Thermofisher, United States)</li> <li>Number of Scans: 64</li> <li>Data Spacing: 0.482 cm -1</li> </ul>   The files have been reported as raw complete spectrum including the absorbances in the wavenumbers from 600 to 1500 cm -1 in the format of “.SPA”. In the following lines, we provide examples of software to process and analyze the spectra files included in the database. <ul> <li>Python version 3.8 to 3.10 upon the availability of the “SpectroChemPy” (Travert and Christian, 2023) function.</li> <li>Matlab R2016a and newer upon the availability of the “LoadSpectra” (Oldenburg, 2023) function.</li> <li>OMNIC 9 (Thermofisher, United States).</li> <li>Essential FTIR (Operant LLC, United States).</li> </ul>   Provision of the data in other formats is available upon request. Inquiries may be directed to <a href="mailto:daniel.gonzalez@ctb.upm.es?subject=FTIR%20Samples%20Format">Daniel González-Nieto</a> or <a href="mailto:mahdi.yonesi@ctb.upm.es?subject=FTIR%20Samples%20Format">Mahdi Yonesi</a>. References: OLDENBURG, K. 2023. LoadSpectra. MATLAB Central File Exchange. TRAVERT, A. & CHRISTIAN, F. 2023. SpectroChemPy, a framework for processing, analyzing and modeling spectroscopic data for chemistry with Python. Github.

opencc-zeroMay 2023View details →

Sexual recombination and temporal gene flow maintain host resistance and genetic diversity

Infectious disease can threaten host populations. Hosts can rapidly evolve resistance during epidemics, with this evolution often modulated by fitness trade-offs (e.g., between resistance and fecundity). However, many organisms switch between asexual and sexual reproduction, and this shift in reproductive strategy can also alter how resistance in host populations persists through time. Recombination can shuffle alleles selected for during an asexual phase, uncoupling the combinations of alleles that facilitated resistance to parasites and altering the distribution of resistance phenotypes in populations. Furthermore, in host species that produce diapausing propagules (e.g., seeds, spores, or resting eggs) after sex, accumulation of propagules into and gene flow out of a germ bank introduce allele combinations from past populations. Thus, recombination and gene flow might shift populations away from the trait distribution reached after selection by parasites. To understand how recombination and gene flow alter host population resistance, we tracked the genotypic diversity and resistance distributions of two wild populations of cyclical parthenogens. In one population, resistance and genetic diversity increased after recombination whereas, in the other, recombination did not shift already high resistance and genetic diversity. In both lakes, resistance remained high after temporal gene flow. This observation surprised us: due to costs to resistance imposed by a fecundity-resistance trade-off, we expected that high population resistance would be a transient state that would be eroded through time by recombination and gene flow. Instead, low resistance was the transient state, while recombination and gene flow re-established or maintained high resistance to this virulent parasite. We propose this outcome may have been driven by the joint influence of fitness trade-offs, genetic slippage after recombination, and temporal gene flow via the egg bank.

opencc-by-4.0May 2023View details →

Long-read, chromosome-scale assembly of Vitis rotundifolia cv. Carlos and its unique resistance to Xylella fastidiosa subsp. fastidiosa.

We assembled and annotated a new, long-read genome assembly for ‘Carlos’, a cultivar of muscadine that exhibits tolerance, to build upon the existing genetic resources available for muscadine. We are awaiting release of the genome through NCBI, so we have made the assembly and annotations available here.

opencc-zeroMay 2023View details →

Multispecies coinfections and presence of antibiotics shape resistance and fitness costs in a pathogenic bacterium

Increasing antimicrobial resistance (AMR) poses a challenge for treatment of bacterial diseases. In real life, bacterial infections are typically embedded within complex multispecies communities and influenced by the environment, which can shape costs and benefits of AMR. However, knowledge of such interactions and their implications for AMR in vivo is limited. To address this knowledge gap, we investigated fitness-related traits of a pathogenic bacterium (Flavobacterium columnare) in its fish host, capturing the effects of bacterial antibiotic resistance, multispecies coinfections (metazoan fluke Diplostomum pseudospathaceum), and antibiotic exposure. We quantified real-time replication and virulence of sensitive and resistant bacteria and demonstrate that both bacteria can benefit from coinfection in terms of persistence and replication, depending on the coinfecting partner and antibiotic presence. We also show that antibiotics can benefit resistant bacteria by increasing bacterial replication under coinfection with flukes. These results emphasize the importance of diverse, inter-kingdom coinfection interactions and antibiotic exposure in shaping costs and benefits of AMR, supporting their role as significant contributors to the spread and long-term persistence of resistance.

opencc-by-4.0Jun 2023View details →

Personalized aerosolised bacteriophage treatment of a chronic lung infection due to multidrug-resistant Pseudomonas aeruginosa

Bacteriophage therapy has been suggested as an alternative or complementary strategy for the treatment of multidrug resistant (MDR) bacterial infections. Here, we report the favourable clinical evolution of a 41-year-old male patient with a Kartagener syndrome complicated by a life-threatening MDR Pseudomonas aeruginosa infection, who was treated successfully with iterative aerosolized phage treatments specifically directed against the patient’s isolate. We followed the longitudinal evolution of both phage and bacterial loads during and after phage administration in respiratory samples. Phage titres in consecutive sputum samples showed in patient phage replication. Phenotypic analysis and whole genome sequencing of sequential bacterial isolates revealed a clonal, but phenotypically diverse population of hypermutator strains. The MDR phenotype in the collected isolates was multifactorial and mainly due to spontaneous chromosomal mutations.  All isolates recovered after phage treatment remained phage susceptible. These results demonstrate that clinically significant improvement is achievable by personalised phage therapy even in the absence of complete eradication of P. aeruginosa lung colonization.

opencc-zeroJun 2023View details →

pH-dependence of the Plasmodium falciparum chloroquine resistance transporter is linked to the transport cycle

This file contains the original data underpinning the following study: The chloroquine resistance transporter, PfCRT, of the human malaria parasite Plasmodium falciparum displays a strong pH-sensitivity in the weakly acidic range. Consequently, PfCRT operates only at 60% of its maximal drug transport activity at the pH of 5.2 of the digestive vacuole, a proteolytic organelle from which PfCRT expels drugs that interfere with heme detoxification. Despite structural information, the molecular mechanism by which PfCRT senses pH changes has remained unclear. Here we show, by alanine-scanning mutagenesis and functional transport studies, that E207 plays a critical role in pH sensing. The E207A mutant displayed a pH-insensitive transport activity, while preserving drug substrate specificity. Replacement of E207 by Asp or His, but not by any other proteinogenic amino acid, reconstituted pH sensitivity. Molecular dynamics simulations and kinetics analyses suggest an allosteric binding model in which PfCRT can simultaneously accept both protons and chloroquine in a partial non-competitive manner, with increasing proton concentrations reducing the drug transport activity. Molecular dynamics simulations of the open-to-vacuole, the occluded and the open-to-cytosol conformation of PfCRT revealed a drastic relocation of E207 from a peripheral to an engaged location during the transport cycle, resulting in E207 forming a salt bridge with residue K80. We propose that the ionized carboxyl group of E207 acts as a hydrogen acceptor for interactions accelerating progression through the transport cycle and that the pH sensing is a by-product of this function.

opencc-by-4.0Jun 2023View details →

Ultrastructure of macromolecular assemblies contributing to bacterial spore resistance revealed by in situ cryo-electron tomography

Cryo-electron tomograms reconstructed from data acquired on FIBM/SEM lamellae of Bacillus subtilis sporangia. Excel files containing measurements of various cellular ultrastructures observed by cryo-electron tomography and transmission electron microcopy of resin sections of B. subtilis sporangia.

Figure 5 Nav kdr 1016 and 1534 in Genetic study in Aedes (Stegomyia) aegypti (Linnaeus, 1762) from Londrina (Paraná State, Brazil): an approach to population structure and pyrethroid resistance

Figure 5 Nav kdr 1016 and 1534 site allele frequencies in UEL. Collection site locations were distributed in the three regions of the campus.

Figure 4 in Genetic study in Aedes (Stegomyia) aegypti (Linnaeus, 1762) from Londrina (Paraná State, Brazil): an approach to population structure and pyrethroid resistance

Figure 4 Allele frequencies of Nav kdr 1016 and 1534 genotyping distributed in the five different regions of Londrina.

Figure 3 in Genetic study in Aedes (Stegomyia) aegypti (Linnaeus, 1762) from Londrina (Paraná State, Brazil): an approach to population structure and pyrethroid resistance

Figure 3 Haplotypic network obtained through specimens collected in UEL. The circles are proportional to the number of specimens observed in each haplotype.

Figure 2 in Genetic study in Aedes (Stegomyia) aegypti (Linnaeus, 1762) from Londrina (Paraná State, Brazil): an approach to population structure and pyrethroid resistance

Figure 2 Haplotype network observed in five regions of Londrina. The circles are proportional to the number of specimens observed in each haplotype. The haplotypes observed are in bold. The numbers represent nucleotide change positions.