Project description:The purpose of this experiment was to compared the transcriptome of hepatocyte-like cells (HLCs) generated in vitro and adult primary human hepatocytes (PHHs). HLCs were differentiated from either hESCs or hIPSCs using previously established protocols (Hannah et al 2013; Segeritz et al 2018). Undifferentiated hIPSCs were used as control to confirm differentiation status. PHHs were commercially sourced as well as freshly isolated from donors.
Project description:In vitro challenge of primary hepatocytes, with the Infectious pancreatic necrosis (IPN) virus. Cells from were infected at MOI 0.1 with two different isolates of IPNV: V1244 and Vir410/2018. V1244 represents classical IPNV that is affected by the IPN-QTL, while Vir410/2018 is the QTL-insensitive or recent isolate, rIPNV in short.
Project description:A wheat × T. timopheevii pre-breeding population was analyzed using Genotyping-by-sequencing (GBS) combined with a skim-seq pipeline to identify and characterize T. timopheevii introgressions. Read coverage analysis based on a combined T. aestivum–T. timopheevii reference genome enabled high-resolution detection of major chromosomal introgressions and copy-number changes. Sequencing reads were aligned to this combined assembly, and chromosome identity and physical position could be extracted. An \"in silico wheat × T. timopheevii hybrid\" reference genome was constructed by combining the reference sequences of the donor and the recipient species. To identify wheat-T. timopheevii introgressions, we combined the Chinese Spring reference genome (IWGSC RefSeq v1.0) (IWGSC, 2018) with the draft genome assembly of T. timopheevii (GCA_963921465.1) (Grewal et al., 2024). During the assembly process, unique identifiers were assigned to all chromosomes or pseudomolecules to maintain distinctiveness. Prior to alignment, the Illumina short reads from 42 lines, along with the previously described control genotypes, were demultiplexed and adapter-trimmed with Stacks v2.68 (Rochette et al., 2019). The processed paired-end reads were then mapped separately to the combined reference genome using HISAT v2.1.0 (Kim et el., 2019) with the – no-spliced-alignment and – no-unal parameters. Following alignment, concordant unique reads were retrieved by filtering the sequence alignment map (SAM) outputs for the YT:Z:CP and NH:i:1 tags.
Project description:We conducted two iron-temperature bioassay incubation experiments during the austral summer of 2018-2019 in the Weddell Sea, Southern Ocean. The first bioassay (BA1) was initiated on December 28th, 2018, approximately 560 km away from the ice edge at 65°S 0.038°E. The second bioassay (BA2) was initiated on January 9th, 2019, approximately 70 km from the ice edge at 70.15°S 11.02°W (Figure 1A). For both bioassays, we collected sea water at 20 m depth using a custom-built ultraclean CTD sampling system – “Titan” (De Baar et al. 2008). We chose this depth to minimize light shock when the microbial community was brought on deck, and to prevent trace metal contamination from the ship. After recovery, Titan was moved into a dedicated, temperature-controlled, trace-metal-clean (TMC) laboratory container where the sea water was used for initial (T0) sampling, and to fill triplicate, 20 L, TMC cubitainers for each iron-temperature treatment. The treatment matrix including four iron-temperature conditions: low iron – low temperature, high iron – low temperature, low iron – high temperature, high iron – high temperature. We did not add any iron to the low iron treatments. We supplemented the high iron treatments with a naturally occurring but rare isotope of 57Fe, which allowed us to differentiate between the added iron and iron already present in the water (mainly 56Fe). For this, we made a 40 µM 57FeCl3 stock solution in 0.1 M trace-metal grade HCl, then added 1 mL of this stock to each of the high iron cubitainers. This resulted in an initial dissolved 57Fe concentration of 2 nM in the high iron treatments. We then sealed the cubitainers and placed them inside temperature-controlled deck incubators where the low temperature treatments were incubated under in situ temperature, and the high temperature treatments were incubated under in situ + 2 °C (Table S1).
Project description:Rotaviruses (RVs) account for severe diarrhea in children and young animals globally. In the current study, the fecal samples of diarrheic calves from a beef farm in Inner Mongolia were screened for RVA by ELISA and RT- PCR, followed by culture of three positive RVA samples in the MA-104 cell line. After 10 blind passages, cytopathic effects (CPE) appeared as detachment, granulation, and clustering of the inoculated cells. The virus isolates were identified by RT-PCR (VP6 gene RVA) and ESI-LC-MS/MS for whole protein sequencing. The protein sequences demonstrated the presence of two strains from species A rotavirus and one RVB strain; RVA/Cow-tc/ CHN/35333/2019/G6P[5] was mixed with one RVB strain (RVB/Cow-tc/CHN/35334/2019/G5P[3]) in two samples, and RVA/Cow-tc/CHN/10927/2019/G8P[7] was found in one sample. They are of genotype constellations (G6-P[5]-I2-R2-C2-M2-A3-N2-T6-E2-H3), (G8-P[7]-I5-R1-C1- M2-A1-N1-T1-E1-H1), and (G5-P[3]-I3-R5- C5-A5-N4-H5), respectively. Besides, phylogenetic analysis of the obtained sequences demonstrated viral evolution.
Project description:From January 1, 2018 to December 31, 2018, there were 19 patients (from four hemodialysis centers) undergoing failing arteriovenous fistula (AVF) that were resistant to endovascular therapy with extensive fistula aneurysmal change (n=4), diffuse stenosis (n=13) or poor skin condition of the forearm (n=2). While 13 of them manifested good size and quality of the outflow vein (>10 cm long, >6 mm in diameter and <6 mm under the skin, BF >600 ml/min) to create of a new AVF upstream. They have been provided with an end-to-side anastomosis of the outflow vein with the more proximal inflow artery, together with ligation of the failing downstream AVF. During the operation, the small segment adjacent to the distal healthy access was exercised for the control access (CA) sample. Until December 31, 2019, 5 of 13 patients had suffered failing AVF again, followed by the excision of segment of high-grade stenosis for the failing access (FA) samples.