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opencc-zeroOct 2023View details →

Nutrient conditions mediate mycorrhizal effects on biomass production and cell wall chemistry in poplar

Large-scale biofuel production from lignocellulosic feedstock is limited by the financial and environmental costs associated with growing and processing lignocellulosic material and the resilience of these plants to environmental stress. Symbiotic associations with arbuscular (AM) and ectomycorrhizal (EM) fungi represent a potential strategy for expanding feedstock production while reducing nutrient inputs. Comparing AM and EM effects on wood production and chemical composition is a necessary step in developing biofuel feedstocks. Here, we assessed the productivity, biomass allocation and secondary cell wall (SCW) composition of greenhouse-grown Populus tremuloidesMichx. inoculated with either AM or EM fungi. Given the long-term goal of reducing nutrient inputs for biofuel production, we further tested the effects of nutrient availability and nitrogen: phosphorus stoichiometry on mycorrhizal responses. Associations with both AM and EM fungi increased plant biomass by 14–74% depending on the nutrient conditions but had minimal effects on SCW composition. Mycorrhizal plants, especially those inoculated with EM fungi, also allocated a greater portion of their biomass to roots, which could be beneficial in the field where plants are likely to experience both water and nutrient stress. Leaf nutrient content was weakly but positively correlated with wood production in mycorrhizal plants. Surprisingly, phosphorus played a larger role in EM plants compared with AM plants. Relative nitrogen and phosphorus availability were correlated with shifts in SCW composition. For AM associations, the benefit of increased wood biomass may be partially offset by increased lignin content, a trait that affects downstream processing of lignocellulosic tissue for biofuels. By comparing AM and EM effects on the productivity and chemical composition of lignocellulosic tissue, this work links broad functional diversity in mycorrhizal associations to key biofuel traits and highlights the importance of considering both biotic and abiotic factors when developing strategies for sustainable biofuel production.

Identification of a small molecule Tim-3 inhibitor to potentiate T cell-mediated antitumor immunotherapy in preclinical models

T cell immunoglobulin and mucin-containing molecule 3 (Tim-3), expressed in dysfunctional and exhausted T cells, has been widely acknowledged as a promising immune checkpoint target for tumor immunotherapy. Here, using a strategy combining virtual and functional screening, we identified a compound named ML-T7 that targets the FG-CC' cleft of Tim-3, a highly conserved binding site of phosphatidylserine (PtdSer) and carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1). ML-T7 enhanced the survival and antitumor activity of primary CD8+ cytotoxic T lymphocytes (CTLs) and human chimeric antigen receptor (CAR) T cells and reduced their exhaustion in vitro and in vivo. In addition, ML-T7 promoted NK cells' killing activity and DC antigen-presenting capacity, consistent with the reported activity of Tim-3. Notably, ML-T7 strengthened DCs' functions through both Tim-3 and Tim-4, consistent with the hypothesis that Tim-4 contains a similar FG-CC' loop. Intraperitoneal dosing of ML-T7 showed comparable tumor inhibitory effects to Tim-3 blocking antibody. ML-T7 reduced syngeneic tumor progression in both wildtype and Tim-3 humanized mice and alleviated the immunosuppressive microenvironment. Furthermore, combined ML-T7 and anti-PD-1 therapy had greater therapeutic efficacy than monotherapy in mice, supporting further development of ML-T7 for tumor immunotherapy. Our study demonstrates a potential small molecule for selectively blocking Tim-3 and warrants further study.

opencc-by-4.0Dec 2023View details →

Targeted DNA-seq analysis was performed on sorted population of CD45+/CD34+ HSPCs from control or FLI-1 modified mRNA treated mPB after co-culture with vascular niche cells

Human mPB HSPCs were harvested isolated and transduced with either control or FLI-1 modified mRNA. HSPCs were introduced into co-culture with vascular niche ECs. Cultures were harvested and CD45+/CD34+ HSPCs were resoerted and processed for trageted DNA-seq analysis. Contains raw FASTQ sequencing files, unfiltered VCFs, and curated results in an excel.

Microchamber slide design for cell confinement during imaging- Tetrahymena rostrata timelapse data

We performed Imaging on a Nikon Ti2-E & Yokogawa CSU W1-SoRa microscope. The microscope was equipped with an ORCA-Fusion BT digital C-MOS camera. We used a 10× 0.45 Plan Apo Air  or a  Plan Apo λD 100x OIL OFN25 DIC N2 objective for differential interference contrast (DIC) imaging. More microscopy information is detailed in the metadata file associated with each .nd2 file. Tetrahymena rostrata was provided by Andrzej Kaczanowski, who isolated the cells from the small snail Cohlicopa lubrica near Warsaw. The cells were cultured in medium consisting 0.5% yeast extract and 0.5% of proteose peptone supplemented with 250 ug/ml streptomycin sulphate and 250 ug/ml penicillin G to maintain sterility.

Microchamber slide design for cell confinement during imaging- Colpoda steinii in 384 well or microwells

We performed Imaging on a Nikon Ti2-E & Yokogawa CSU W1-SoRa microscope. The microscope was equipped with an ORCA-Fusion BT digital C-MOS camera. We used a 10× 0.45 Plan Apo Air objective for differential interference contrast (DIC) imaging. More microscopy information is detailed in the metadata file associated with each .nd2 file. The repository contains timelapse series data at irregular intervals between the beginning of data collection and after two hours. Wells on a glass-bottom 384 well plate or microwells contained Colpoda steinii cells.

Cell size-dependent species sensitivity to nanoparticles underlies changes in phytoplankton diversity and productivity

Nanoparticle pollution has been shown to affect various organisms. However, the effects of nanoparticles on species interactions, and the role of species traits, such as body size, in modulating these effects, are not well understood. We addressed this issue using competing freshwater phytoplankton species exposed to copper oxide nanoparticles. Increasing nanoparticle concentration resulted in decreased phytoplankton species growth rates and community productivity (both abundance and biomass). Importantly, we consistently found that nanoparticles had greater negative effects on species with smaller cell sizes, such that nanoparticle pollution weakened the competitive dominance of smaller species and promoted species diversity. Moreover, nanoparticles reduced the growth rate differences and competitive ability differences of competing species, while having little effect on species niche differences. Consequently, nanoparticle pollution reduced the selection effect on phytoplankton community abundance but increased the selection effect on community biomass. Our results suggest cell size as a key functional trait to consider when predicting phytoplankton community structure and ecosystem functioning in the face of increasing nanopollution.

Microchamber slide design for cell confinement during imaging- early encystment

The data shows an early stage of Colpoda steinii encystment.We performed Imaging on a Nikon Ti2-E & Yokogawa CSU W1-SoRa microscope. The microscope was equipped with an ORCA-Fusion BT digital C-MOS camera. We used a 10× 0.45 Plan Apo Air objective for differential interference contrast (DIC) imaging. More microscopy information is detailed in the metadata file associated with each .nd2 files. The repository contains timelapse data.

Microchamber slide design for cell confinement during imaging- reanimation experiment

We dried slides with 1000 Colpoda steinii cysts per well over a weekend. We reanimated the slides with either 1 mM Tris pH 7.5 or hay medium + K. aerogenes (1ul of preculture + 1ml hay medium). We rehydrated the cells for 10 minutes in 1 mM Tris pH 7.5 on an orbital shaker (100 rpm). We washed the cells in 0.1% SDS for 10 minutes on the shaker. The cells were washed with 1 mM Tris three times for 1 minute before adding Tris or the experimental medium and imaging.Plate 1: TrisPlate 2: hay medium + K.a.At time point 26, active cells are visible in plate 2 at B6, C6, D6, E6. There were no reanimation events observed on the plate treated with Tris alone.

Phospho-seq: Integrated, multi-modal profiling of intracellular protein dynamics in single cells

Datasets to go along with the publication listed:full_object.rds: Brain Organoid Phospho-Seq dataset with ATAC, Protein and imputed RNA datarna_object.rds: Reference whole cell scRNA-Seq object on Brain organoidsmultiome_object.rds: Bridge dataset containing RNA and ATAC modalities for Brain organoidsmetacell_allnorm.rds: Metacell object for finding gene-peak-protein linkages in Brain organoid datasetfullobject_fragments.tsv.gz: fragment file to go with the full objectfullobject_fragments.tsv.gz.tbi:index file for the full object fragment filemultiome_fragments.tsv.gz: fragment file to go with the multiome objectmultiome_fragments.tsv.gz.tbi:index file for the multiome object fragment fileK562_Stem.rds : object corresponding to the pilot experiment including K562 cells and iPS cellsK562_stem_fragments.tsv.gz:  fragment file to go with the K562_stem objectK562_stem_fragments.tsv.gz.tbi: index file for the K562_stem object fragment fileretina.rds : object corresponding to the retinal organoid phospho-seq experimentretina_fragments.tsv.gz:  fragment file to go with the retina objectretina_fragments.tsv.gz.tbi: index file for the retina object fragment fileretina_multi.rds : object corresponding to the retinal organoid phospho-seq-multiome experimentretina_multi_fragments.tsv.gz:  fragment file to go with the retina_multi objectretina_multi_fragments.tsv.gz.tbi: index file for the retina_multi object fragment fileTo use the K562, multiome, retina and retina_multiome datasets provided, please use these lines of code to import the object into Signac/Seurat and change the fragment file path to the corresponding downloaded fragment file:obj <- readRDS("obj.rds") # remove fragment file information Fragments(obj) <- NULL # Update the path of the fragment file Fragments(obj) <- CreateFragmentObject(path = "download/obj_fragments.tsv.gz", cells = Cells(obj))To use the K562 and multiome datasets provided, please use these lines of code to import the object into Signac/Seurat and change the fragment file path to the corresponding downloaded fragment file:obj <- readRDS("obj.rds") # remove fragment file information Fragments(obj) <- NULL # Update the path of the fragment file Fragments(obj) <- CreateFragmentObject(path = "download/obj_fragments.tsv.gz", cells = Cells(obj))To use the "fullobject" dataset provided, please use these lines of code to import the object into Signac/Seurat and change the fragment file path to the corresponding downloaded fragment file: #load the stringr package library(stringr) #load the object obj <- readRDS("obj.rds") # remove fragment file information Fragments(obj) <- NULL #Remove unwanted residual information and rename cells obj@reductions$norm.adt.pca <- NULL obj@reductions$norm.pca <- NULL obj <- RenameCells(obj, new.names = str_remove(Cells(obj), "atac_")) # Update the path of the fragment file Fragments(obj) <- CreateFragmentObject(path = "download/obj_fragments.tsv.gz", cells = Cells(obj))

opencc-by-sa-4.0Nov 2023View details →

Automated bio-AFM generation of large mechanome data set and their analysis by machine learning to classify prostatic cell lines_Training base 100 PC3-GFP

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Dataset for the publication titlted "A computational mechanics model for producing molecular assembly using molecularly woven pantographs" in the journal Cell Reports Physical Science, authored by Byeonghwa Goh and Joonmyung Choi.

Dataset for the publication titlted "A computational mechanics model for producing molecular assembly using molecularly woven pantographs" in the journal Cell Reports Physical Science, authored by Byeonghwa Goh and Joonmyung Choi.

Sustained liver HBsAg loss and clonal T and B cell expansion upon therapeutic DNA vaccination require low HBsAg levels

C57BL/6 mice samples transduced with AAV-HBV, followed by treatment with siRNA+TxTv, control siRNA+TxVx or control siRNA+empty plasmid. 10x genomics (VDJ) was performed in liver IHIC.An rds object with the raw and normalised counts, the annotations is available.

Metabolomics of KP mouse LUAD cell lines

The goal of the experiment was to characterize the changes in metabolic pathway flux in these cells in response to HDAC and glutaminase inhibition. This dataset includes metabolomics of U-C13 glucose tracing (1h and 24h) and U-C13 glutamine (8h) of mouse LUAD cell lines with Kras overexpression and p53 knock-out (KP), carrying empty vector (EV) or overexpression of NRF2dNeh2 (NRF2) and treated with DMSO, Romidepsin or CB-839. 3 technical replicates were done per condition. The full methodology is described in the accompanying text file.

Interspecies chimerism with human embryonic stem cells generates functional human dopamine neurons at low efficiency

Interspecies chimeras offer great potential for regenerative medicine and creation of human disease models. Whether human pluripotent stem cell (hPSC) derived neurons in an interspecies chimera can differentiate into functional neurons and integrate into host neural circuity is not known. Here we show, using Engrailed 1 (En1) as a development niche that human naïve-like ES cells can incorporate into embryonic and adult mouse brains. Human-derived neurons including tyrosine hydroxylase (TH) positive neurons integrate into the mouse brain at low efficiency. These TH-positive neurons have electrophysiologic properties consistent with their human origin. Additionally, these human-derived neurons in the mouse brain accumulate pathologic phosphorylated α-synuclein in response to α-synuclein preformed fibrils. Optimization of human/mouse chimeras could be utilized to study human neuronal differentiation and human brain disorders.

Data from: Mouse gingival single cell transcriptomic atlas identified a novel fibroblast subpopulation activated to guide oral barrier immunity in periodontitis

Periodontitis, one of the most common non-communicable diseases, is characterized by chronic oral inflammation and uncontrolled tooth supporting alveolar bone resorption. Its underlying mechanism to initiate aberrant oral barrier immunity has yet to be delineated. Here, we report a unique fibroblast subpopulation activated to guide oral inflammation (AG fibroblasts) identified in a single-cell RNA sequencing gingival cell atlas constructed from the mouse periodontitis models. AG fibroblasts localized beneath the gingival epithelium and in the cervical periodontal ligament responded to the ligature placement and to the discrete topical application of Toll-like receptor stimulants to mouse maxillary tissue. The upregulated chemokines and ligands of AG fibroblasts linked to the putative receptors of neutrophils in the early stages of periodontitis. In the established chronic inflammation, neutrophils together with AG fibroblasts appeared to induce type 3 innate lymphoid cells (ILC3s) that were the primary source of interleukin-17 cytokines. The comparative analysis of Rag2-/- and Rag2gc-/- mice suggested that ILC3 contributed to the cervical alveolar bone resorption interfacing the gingival inflammation. We propose that the AG fibroblast–neutrophil–ILC3 axis as a previously unrecognized mechanism which could be involved in the complex interplay between oral barrier immune cells contributing to pathological inflammation in periodontitis.

A multiscale theory for spreading and migration of adhesion-reinforced mesenchymal cells

We present a chemomechanical whole-cell theory for the spreading and migration dynamics of mesenchymal cells that can actively reinforce their adhesion to an underlying viscoelastic substrate as a function of its stiffness. Our multiscale model couples the adhesion reinforcement effect at the subcellular scale with the nonlinear mechanics of the nucleus-cytoskeletal network complex at the cellular scale to explain the concurrent monotonic area-stiffness and non-monotonic speed-stiffness relationships observed in experiments: We consider that large cell spreading on stiff substrates flattens the nucleus, increasing the viscous drag force on it. The resulting force balance dictates a reduction in the migration speed on stiff substrates. We also reproduce the experimental influence of the substrate viscosity on the cell spreading area and migration speed by elucidating how the viscosity may either maintain adhesion reinforcement or prevent it depending on the substrate stiffness. Additionally, our model captures the experimental directed migration behavior of the adhesion-reinforced cells along a stiffness gradient, known as durotaxis, as well as up or down a viscosity gradient (viscotaxis or anti-viscotaxis), the cell moving towards an optimal viscosity in either case. Overall, our theory explains the intertwined mechanics of the cell spreading, migration speed and direction in the presence of the molecular adhesion reinforcement mechanism.

3D and multimodal X-ray microscopy reveals the impact of voids in CIGS solar cells

Data repository for the article "3D and multimodal X-ray microscopy reveals the impact of voids in CIGS solar cells"  DOI: 10.1002/advs.202301873

opencc-by-4.0Oct 2023View details →

ChromoPhyloGen: characterizing copy number alteration patterns in heterogeneous tumor cell populations at Single-Cell Resolution

The human liver cancer cell line Huh7 was obtained from the American Type Culture Collection (ATCC). Huh7 cells were cultivated in Dulbecco's Modified Eagle Medium (DMEM, Gibco, C11995), supplemented with 1% penicillin/streptomycin (Gibco, 15140122), and 10% fetal bovine serum (FBS, Excell, FSP500). Huh7 cell line was maintained under a 95% O2 and 5% CO2 humidified atmosphere in an incubator at 37˚C.  The scDNA-seq library was performed using the Chromium Single cell DNA Library & Gel Bead kit (10x Genomics, PN1000040) in combination with the Chromium instrument. The samples were processed on Chromium Single cell Chip C and D (10x Genomics, 1000022 and 1000042, respectively) according to the manufacturer's user guide and subsequently run on a thermocycler. The barcoded libraries were sequenced using the Novaseq 6000 300 cycle high-output flow cells. The scRNA-seq library was generated using the 10x Genomics Chromium Single Cell 3' & Gel Bead Kit v3 (10x Genomics, PN100075) in combination with the Chromium instrument. The samples were processed on Chromium Single cell Chip B (10x Genomics,1000154) according to the manufacturer's protocol and subsequently run on a thermocycler. The 3' gene expression libraries were sequenced using the Novaseq 6000 300 cycle high-output flow cells.

opencc-by-4.0Jul 2023View details →

INFLAMeR: a machine learning algorithm based on large-scale perturbation screening identified new lncRNAs regulating differentiation and survival of leukaemia cells

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