Find research datasets worth reusing

opencc-by-4.0Nov 2024View details →

Putative mutations associated with tetracycline resistance detected in Treponema spp.- an analysis of 4,355 Spirochaetales genomes

Supplementary Table 1–4, , as well as multiple sequence alignment files for 16S rRNA, rpsC, and rpsJ loci, have been deposited. Additionally, the archive contains a <code>scripts.txt</code> file that includes all custom Bash scripts used for: <ul> <li> rRNA gene detection and quantification using Barrnap </li> <li> Genome quality assessment using CheckM </li> <li> Gene-by-gene schema creation, allele calling, and cgMLST extraction using chewBBACA </li> <li> GFF merging and wide-format transformation for summarizing rRNA copy number per genome </li> </ul> These materials are provided to ensure reproducibility of the analyses and to support further investigations into antimicrobial resistance in Spirochaetales.

opencc-by-4.0Oct 2024View details →

Memory B Cells and Their Transcriptomic Profiles Associated with Belimumab Resistance in Systemic Lupus Erythematosus in the Maintenance Phase

Normalized count of RNA sequences from systemic lupus erythematosus patients treated with belimumab. We collected blood samples from patients with systemic lupus erythematosus (n=44) before and approximately 3 and 6 months after treatment by belimumab, respectively. We also included healthy individuals (n=17). There were no missing samples in the before-treatment specimen for 44 patients; however, five samples were missing at the three-month time, and four were missing at the six-month time after treatment. Whole blood samples were stored in PAXgene tubes (QUIAGEN). RNA was extracted by PAXgene Blood RNA Kit (QUIAGEN). Library preparation was performed using TruSeq stranded Total RNA Library PrepKit with Ribo-Zero Globin Human. Sequencing was conducted by NovaSeq6000 in the 100-bp paired-end mode. Sequencing reads were trimmed using Trimmomatic ver. 0.36 (leading: 20, trailing: 20, slidingwindow: 4:15, minlen: 36) and aligned to hg38 reference genome using STAR (ver. 2.7.3a). Gene counts were generated by RSEM (ver. 1.3.1) using Homo_sapiens.GRCh38.95.gtf from the Ensembl database. Gene counts were normalized by size factor implemented in DESeq2 and converted to count per million (CPM), and log2(CPM+1) was calculated.  Sample names starting with 'R_' indicate responders, while those ending with '_NR' indicate non-responders. '0M' represents before treatment, '3M' represents three months after treatment, and '6M' represents six months after treatment. The numeric ID, excluding the last two characters, represents individual patients.   If you use this data, please cite Iwasaki et al. Front. Immunol., 04 February 2025 <a href="https://doi.org/10.3389/fimmu.2025.1506298">https://doi.org/10.3389/fimmu.2025.1506298</a>

opencc-zeroNov 2021View details →

Data from: The impact of long-term azithromycin on antibiotic resistance in HIV-associated chronic lung disease

Background: Selection for resistance to azithromycin (AZM) and other antibiotics such as tetracyclines and lincosamides remains a concern with long-term AZM use for treatment of chronic lung diseases (CLD). We investigated the impact of 48 weeks of AZM on the carriage and antibiotic resistance of common respiratory bacteria among children with HIV-associated CLD. Methods: Nasopharyngeal (NP) swabs and sputa were collected at baseline, 48 and 72 weeks from participants with HIV-associated CLD randomised to receive weekly AZM or placebo for 48 weeks and followed post-intervention until 72 weeks. The primary outcomes were prevalence and antibiotic resistance of Streptococcus pneumoniae (SP), Staphylococcus aureus (SA), Haemophilus influenzae (HI), and Moraxella catarrhalis (MC) at these timepoints. Mixed-effects logistic regression and Fisher's exact test were used to compare carriage and resistance respectively. Results: Of 347 (174 AZM, 173 placebo) participants (median age 15 years [IQR =13–18], females 49%),NP carriage was significantly lower in the AZM (n=159) compared to placebo (n=153) arm for SP (18% vs 41%, p<0.001), HI (7% vs 16%, p=0.01), and MC (4% vs 11%, p=0.02); SP resistance to AZM (62% [18/29] vs 13%[8/63], p<0.0001) or tetracycline (60%[18/29] vs 21%[13/63], p<0.0001) were higher in the AZM arm. Carriage of SA resistant to AZM (91% [31/34] vs 3% [1/31], p<0.0001), tetracycline (35% [12/34] vs 13% [4/31], p= 0.05) and clindamycin (79% [27/34] vs 3% [1/31], p<0.0001) was also significantly higher in the AZM arm and persisted at 72 weeks. Similar findings were observed for sputa. Conclusions: The persistence of antibiotic resistance and its clinical relevance for future infectious episodes requiring treatment needs further investigation.

opencc-by-4.0Mar 2022View details →

Insertion sequences and other mobile elements associated with antibiotic resistance genes in Enterococcus isolates from an inpatient with prolonged bacteremia.

Insertion sequences (ISs) and other transposable elements are associated with the mobilization of antibiotic resistance determinants and the modulation of pathogenic characteristics. In this work, we aimed to investigate the association between ISs and antibiotic resistance genes, and their role in dissemination and modification of the antibiotic resistant phenotype. To that end, we leveraged fully resolved Enterococcus faecium and Enterococcus faecalis genomes of isolates collected over five days from an inpatient with prolonged bacteremia. Isolates from both species harbored similar IS family content but showed significant species-dependent differences in copy number and arrangements of ISs throughout their replicons. Here, we describe two inter-specific IS-mediated recombination events and IS-mediated excision events in plasmids of E. faecium isolates. We also characterize a novel arrangement of the ISs in a Tn1546-like transposon in E. faecalis isolates likely implicated in a vancomycin genotype-phenotype discrepancy. Furthermore, an extended analysis revealed a novel association between daptomycin resistance mutations in liaSR genes and a putative composite transposon in E. faecium, offering a new paradigm for the study of daptomycin resistance and novel insights into the dissemination of daptomycin resistance. In conclusion, our study highlights the role ISs and other transposable elements play in the rapid adaptation and response to clinically relevant stresses such as aggressive antibiotic treatment in enterococci.

opencc-zeroJun 2022View details →

Microbiomes associated with avian malaria survival differ between susceptible Hawaiian honeycreepers and sympatric malaria-resistant introduced birds

Of the estimated 55 Hawaiian honeycreepers (subfamily Carduelinae) only 17 species remain, 9 of which the International Union for Conservation of Nature considers endangered. Among the most pressing threats to honeycreeper survival is avian malaria, caused by the introduced blood parasite Plasmodium relictum, which is increasing in distribution in Hawai`i as a result of climate change. Preventing further honeycreeper decline will require innovative conservation strategies that confront malaria from multiple angles. Research on mammals revealed strong connections between gut microbiome composition and malaria susceptibility, illuminating a potential novel approach to malaria control through the manipulation of gut microbiota. One honeycreeper species, Hawai`i `amakihi (Chlorodrepanis virens), persists in some areas of high malaria prevalence, indicating they have acquired some level of immunity. To investigate if avian host-specific microbes may be associated with malaria survival, we characterized cloacal microbiomes and malaria infection for 174 `amakihi and 172 malaria-resistant warbling white-eyes (Zosterops japonicus) from Hawai`i Island using 16S rRNA gene metabarcoding and qPCR. Neither microbial alpha nor beta diversity covaried with infection, but 149 microbes showed positive associations with malaria survivors. Among these were Escherichia and Lactobacillus spp., which appear to mitigate malaria severity in mammalian hosts, revealing promising candidates for future probiotic research for augmenting malaria immunity in sensitive endangered species.

opencc-by-4.0Aug 2022View details →

Data from: Unravelling cucumber resistance to several viruses via genome-wide association studies highlighted resistance hotspots and new QTLs

The mapping and introduction of sustainable resistance to viruses in crops is a major challenge in modern breeding, especially regarding vegetables. We hence assembled a panel of cucumber elite lines and landraces from different horticultural groups for testing with six virus species. We mapped 18 quantitative trait loci (QTL) with a multiloci genome wide association studies (GWAS), some of which have already been described in the literature. We detected two resistance hotspots, one on chromosome 5 for resistance to the cucumber mosaic virus (CMV), cucumber vein yellowing virus (CVYV), cucumber green mottle mosaic virus (CGMMV) and watermelon mosaic virus (WMV), colocalizing with the RDR1 gene, and another on chromosome 6 for resistance to the zucchini yellowing mosaic virus (ZYMV) and papaya ringspot virus (PRSV) close to the putative VPS4 gene location. We observed clear structuring of resistance among horticultural groups due to plant virus coevolution and modern breeding which have impacted linkage disequilibrium (LD) in resistance QTLs. The inclusion of genetic structure in GWAS models enhanced the GWAS accuracy in this study. The dissection of resistance hotspots by local LD and haplotype construction helped gain insight into the panel’s resistance introduction history. ZYMV and CMV resistance were both introduced from different donors in the panel, resulting in multiple resistant haplotypes at same locus for ZYMV, and in multiple resistant QTLs for CMV.

opencc-zeroMay 2024View details →

Data from: Insect hypovirulence-associated mycovirus confers entomopathogenic fungi with enhanced resistance against phytopathogens

Mycoviruses can alter the biological characteristics of host fungi including decreasing or enhancing virulence or pathogenicity of phytopathogens and entomopathogenic fungi (EPF). As an extensively used EPF, Beauveria bassiana could not only directly control pests, but also improve plant resistance against plant disease through endophytic colonization. However, most studies on the mycoviruses found in B. bassiana have focused on the effects of the viruses on the virulence of host fungi toward insect pests, with relatively few reports on the effects to the host fungi with regard to plant disease resistance in hosts. The present study investigated the effects of the mycovirus Beauveria bassiana chrysovirus 2 (BbCV2) virus infection on host biological characteristics, additionally, we evaluated antagonistic activity of BbCV2 against phytopathogenic fungi (Sclerotinia sclerotiorum and Botrytis cinerea) in vitro and their associated diseases both in in vitro leaves and in pot experiments. Our results showed that the mycovirus, BbCV2, enhanced the growth rate, spore production, and biomass of host fungi B. bassiana. BbCV2 virus infection enhanced the capacity of host fungi and their metabolic products to inhibit phytopathogenic fungi S. sclerotiorum and B. cinerea. BbCV2 virus infection reduced the contents of the two pathogens in tomato plants significantly, and in turn enhanced the plant resistance induced by host fungi colonization against the diseases caused by the two pathogens.

Figure 5 in Confirmation and differential metabolism associated with quinclorac resistance in smooth crabgrass (Digitorio ischoemum)

Figure 5. Amount of quinclorac (mg g−1 plant, mean ± SE) detected by liquid chromatography–diode array detector (DAD) in extracts of plants (aerial parts) from susceptible (SMT2) and two resistant (MSU1 and MSU2) Digitorio ischoemum populations, with previous application of 2 kg malathion ha−1 followed by 0.84 kg quinclorac ha−1 (QM), 0.84 kg quinclorac ha−1 (Q1X), no application of quinclorac or malathion (Q0X), and application of 2 kg malathion ha−1 alone (M), evaluated at 72 and 168 h after treatment (HAT). Means within an evaluation time and treatment with the same capital letter are not significantly different at the 5% level as determined by Fisher's protected least significant difference (LSD) test; means for the same population and evaluation time with the same letter are not significantly different at the 5% level as determined by the LSD test.

Figure 4. Specific glutathione S-transferase activity changes toward 1 in Confirmation and differential metabolism associated with quinclorac resistance in smooth crabgrass (Digitorio ischoemum)

Figure 4. Specific glutathione S-transferase activity changes toward 1-chloro-2,4- dinitrobenzene in Digitorio ischoemum tissues after (A) 0.84 kg quinclorac ha−1 or (B) 7.56 kg quinclorac ha−1. Data were expressed as a percentage change of the nontreated. Values are presented as mean ± SE. Error bars indicate the standard error of the mean. R, resistant; S, susceptible.

Figure 2 in Confirmation and differential metabolism associated with quinclorac resistance in smooth crabgrass (Digitorio ischoemum)

Figure 2. Aboveground dry mass of susceptible and resistant Digitorio ischoemum at 28 d after treatment. The D. ischoemum was at the 3-leaf stage of growth when herbicide was applied. Data were expressed as a percentage decrease of the mean dry mass of the nontreated control. Error bars show the standard error of the mean. R, resistant; S, susceptible.

Figure 1 in Confirmation and differential metabolism associated with quinclorac resistance in smooth crabgrass (Digitorio ischoemum)

Figure 1. Visual control of susceptible and resistant Digitorio ischoemum crabgrass at 28 d after treatment. The crabgrass was at the three-leaf stage of growth when herbicide was applied. Control was visually assessed on a 0%–100% scale (0% = no plant death; 100% = complete plant death). The data were normalized relative to the nontreated control. Error bars show the standard error of the mean. R, resistant; S, susceptible.

Figure 3 in Confirmation and differential metabolism associated with quinclorac resistance in smooth crabgrass (Digitorio ischoemum)

Figure 3. Cyanide content of susceptible and resistant Digitorio ischoemum at 3 d after treatment. Data were expressed as a percentage increase of the mean control. Error bars indicate the standard error of the mean. R, resistant; S, susceptible.

opencc-by-4.0Aug 2019View details →

Antiviral activity of HIV-1 integrase strand-transfer inhibitors against mutants with integrase resistance-associated mutations and their frequency in treatment-naïve individuals

The development of  resistance to human immunodeficiency virus 1 (HIV-1) integrase strand-transfer inhibitors (INSTI) has been documented; however, knowledge of the impact of pre-existing integrase (IN) mutations on INSTI resistance (INSTI-R) is still evolving. The frequency of HIV-1 IN mutations in 2177 treatment-naïve subjects was investigated, along with the INSTI susceptibility of site-directed mutant viruses containing major and minor INSTI-R mutations. Total 6 of 39 minor INSTI-R mutations (M50I, S119P/G/T/R, and E157Q) were found in >1% of IN-treatment-naïve subjects with no impact on INSTI susceptibility. When each combined with major INSTI-R mutation, M50I, S119P, and E157Q led to decreased susceptibility to elvitegravir but remained sensitive to  dolutegravir and bictegravir.

opencc-by-4.0Jun 2013View details →

Figure 1 in Cloning and characterization of ubiquitin ribosome fusion gene RpS27a, a deltamethrin-resistance-associated gene from diamondback moth (Plutella xylostella L.)

Figure 1. The nucleotide and deduced amino acid sequences of the P. xylostella RpS27a gene coding region. The deduced amino acid sequence is presented below the nucleotide sequence in a single letter. The nuclear localization signal sequence is shaded. The initial and termination codon are underlined. The stop codon is denoted with an asterisk.

opencc-by-4.0Jun 2013View details →

Figure 5. Phylogenetic relationship between P. xylostella RpS27a in Cloning and characterization of ubiquitin ribosome fusion gene RpS27a, a deltamethrin-resistance-associated gene from diamondback moth (Plutella xylostella L.)

Figure 5. Phylogenetic relationship between P. xylostella RpS27a and some other species. Corresponding GenBank accession numbers are: M. sexta: ACY95367.1; P. dardanus: CAH04128.1; Bombyx mori: NP_001091826.1; P. polytes: BAM18943.1; P. xuthus: BAM17728.1; S. frugiperda: AAL62473.1; D. plexippus: EHJ77179.1; A. yamamai: BAD05031.1; P. xylostella: JX437934; T. rubida: AER92457.1; D. melanogaster: NP_476778.1; A. aegypti: AAS79344.1; C. quinquefasciatus: XP_001844485.1.

opencc-by-4.0Jun 2013View details →

Figure 6 in Cloning and characterization of ubiquitin ribosome fusion gene RpS27a, a deltamethrin-resistance-associated gene from diamondback moth (Plutella xylostella L.)

Figure 6. mRNA level of RpS27a in DS-strain and DR-strain of P. xylostella. All values are expressed as means ± SD. DS-strain: deltamethrin-susceptible strain; DR-strain: deltamethrinresistant strain. *P <0.01.

opencc-by-4.0Sep 2018View details →

Pooled DNA sequencing to identify SNPs associated with a major QTL for bacterial wilt resistance in Italian ryegrass (Lolium multiflorum Lam.)

We used pooled DNA sequencing to characterize a major QTL for bacterial wilt resistance of Italian ryegrass and to develop inexpensive sequence-based markers to efficiently target resistance alleles for marker-assisted recurrent selection. From the mapping population segregating for the QTL, DNA of 44 of the most resistant and 44 of the most susceptible F1 individuals were pooled and sequenced using the Illumina HiSeq2000 platform. Allele frequencies of 18 x 106 single nucleotide polymorphisms (SNP) were determined in the resistant and susceptible pool. A total of 271 SNPs on 140 scaffold sequences of the reference parental genome showed significantly different allele frequencies in both pools. We converted 44 selected SNPs to KASP markers, genetically mapped these proximal to the major QTL and thus validated their association with bacterial wilt resistance.