Contributors: Saroj Chakraborty

Date: 2019-11-12

... Pediatric hypertension is recognized as an emerging global health concern. While new guidelines are developed for facilitating clinical management, the reasons for the prevalence of hypertension in children remain unknown. Genetics and environmental factors do not fully account for the growing incidence of pediatric hypertension. Because stable bacterial flora in early life are linked with health outcomes later in life, we hypothesized that reshaping of gut microbiota in early developmental stages of life affects blood pressure (BP) of pediatric subjects. To test this hypothesis, we administered amoxicillin, the most commonly prescribed pediatric antibiotic, to alter gut microbiota of young, genetically hypertensive rats (study 1) and dams during gestation and lactation to reshape microbiota of offspring (study 2). Reshaping of microbiota, with reductions in Firmicutes/Bacteriodetes ratio observed in Amoxicillin treated young rats and in dams. Amoxicillin treated rats also had lower blood pressure compared to the untreated rats. In the young rats treated with amoxicillin, the lowering effect on blood pressure persisted even after the antibiotics were discontinued. Similarly, the offspring from the dams treated with amoxicillin also showed lower systolic blood pressure compared to the control rats. Remarkably, in all cases, a decrease in BP was associated with lowering of Veillonellaceae, which are succinate-producing bacteria. Elevated plasma succinate is reported in hypertension. Accordingly, serum succinate was measured and found lower in animals treated with amoxicillin. Our results demonstrate a direct correlation between succinate-producing gut microbiota and early development of hypertension, and indicate that reshaping gut microbiota, especially by depleting succinate-producing microbiota early in life may have long-term benefits for hypertension-prone individuals.

Contributors: Mowei Zhou, Neha Malhan, Amirhossein Ahkami, Kristin Engbrecht, Gabriel Myers, Jeffery Dahlberg, Joy Hollingsworth, Julie Sievert, Robert Hutmacher, Mary Madera

Date: 2019-10-24

... This study explores the changes in histone modifications of Sorghum bicolor (L.) Moench through developmental stages and in response to drought stress in two genotypes. We analyzed the leaves of 48 plants using top-down mass spectrometry and identified 26 unique histone proteins and 677 unique histone proteoforms. This is the collection of processed data and scripts used for data processing.

Contributors: Timothy Jenkins, Laura Peachey, Nadim Ajami, Andrew MacDonald, Michael Hsieh, Paul Brindley, Cinzia Cantacessi, Gabriel Rinaldi

Date: 2019-10-23

... Raw 16S rRNA sequencing data from luminal contents from sections of the small (SI) and large intestines (LI) of 10 Swiss-Webster female mice (S+) that were infected with 200 S. mansoni cercariae and 10 age- and gender-matched mice that remained uninfected and were included as controls (S-). For each S+ and S- group, five mice were euthanised 28 days after infection (D28 p.i., i.e. before egg laying by sexually mature S. mansoni females had commenced). The remaining mice (n = 5 for each S+ and S-) were euthanised at day 50 p.i. (D50 p.i., corresponding with ongoing egg laying by sexually mature S. mansoni females). The experiment was carried out in duplicate and samples from both experiments (i.e. Exp. 1 & Exp. 2) pooled for further analysis. The data set includes four types of files: 1. Raw joined read files - 1 per sample (demultiplexed): e.g. Exp1_SI_S-_D50_1.fasta 2. Joined, quality filtered file containing reads from all samples and ready for OTU picking. The file was generated using Qiime: seqs.fna 3. Metadata file containing the relevant contextual information for each sample: Schisto_microbiome_Metadata.csv 4. OTU table created using Qiime including all of the taxonomic information: otu_table_mc2_w_tax_no_pynast_failures.biom

Contributors: Hiroki Ando

Date: 2019-09-15

... The data products derived and presented in the manuscript of "Venusian cloud distribution simulated by a general circulation model" to Journal of Geophysical Research - Planets. *.grd file is grads format file and *.ctl file is control file of grads data. The detail of the data is given by Sugimoto et al. (2014a and 2014b) and Takagi et al. (2018).

Contributors: Ilias Georgakopoulos Soares

Date: 2019-08-09

... The mechanisms that underpin how insertions or deletions (indels) become fixed in DNA have primarily been ascribed to replication-related and/or double-strand break (DSB)-related processes. We introduce a novel way to evaluate indels, orientating them relative to gene transcription. In so doing, we reveal a number of surprising findings: First, there is a transcriptional strand asymmetry in the distribution of mononucleotide repeat tracts in the reference human genome. Second, there is a strong transcriptional strand asymmetry of indels across 2,575 whole genome sequenced human cancers. We suggest that this is due to the activity of transcription-coupled nucleotide excision repair (TC-NER). Furthermore, TC-NER interacts with mismatch repair (MMR) under physiological conditions to produce strand bias. Finally, we show how insertions and deletions differ in their dependencies on these repair pathways. Our new analytical approach reveals new insights into the contribution of DNA repair towards indel mutagenesis in human cells.

Contributors: Juan_Gabriel Rueda-Bayona

Date: 2019-07-22

... the folder contains input and setup files of the article An Alternative Method to Determine Extreme Hydrodynamic Forces with Data Limitations for Offshore Engineering

Contributors: Daniel Huston

Date: 2019-07-03

... The following data relates to the manuscript "An identity crisis in the Indo-Pacific: molecular exploration of the genus Koseiria (Digenea: Enenteridae)." which was accepted by the International Journal for Parasitology on 3 July 2019.

Contributors: Keping Sun, Vu Dinh Thong, Kangkang Zhang, Jiang Feng, Hanbo Zhao, Lin Zhang, Tong Liu, YANYAN XIAO, Longru Jin, Gábor Csorba

Date: 2019-07-01

... Raw data sets, including mitochondrial sequences, nuclear sequences, microsatellite data and GBS data used in this study.

Contributors: Irene Barnes, Brenda Wingfield, Magrieta van der Nest, Michael Wingfield, Arista Fourie, Lieschen de Vos

Date: 2019-06-27

... This data provides the MinION genome sequence data for the two genomes used in linkage map and QTL analyses of Ceratocystis fimbriata and C. manginecans. The genomes consist of long sequence reads, obtained from MinION sequence data, to provide improved contig assemblies, and Illumina sequence data to improve base call quality. The dataset also provides a python script that was used to convert the VCF file obtained from GATK to a binary code of A and B; the format required for JoinMap software for linkage map construction.

Contributors: Arista Fourie

Date: 2019-06-25

... This data provides the MinION assembled genomes that were used in the article "QTL mapping of mycelial growth and aggressiveness to distinct hosts in Ceratocystis pathogens" by Fourie et al. 2019. These genomes contain MinION sequence reads as well as Illumina HiSeq sequence reads. The data also contains a python script that was used to convert the SNP data to binary data used for downstream analyses.