Tag: CCA
Breadth of SARS-CoV-2 neutralization and protection induced by a nanoparticle vaccine
Animals and immunizations The study protocol and all veterinarian procedures were approved by the Bioqual IACUC per a memorandum of understanding with the Duke IACUC, and were performed based on standard operating procedures. Macaques studied were housed and maintained in an Association for Assessment and Accreditation of Laboratory Animal Care-accredited…
Inferring and perturbing cell fate regulomes in human brain organoids
Experimental methods Stem cell and organoid culture We used six human iPS cell lines (Hoik1, Wibj2, Kucg2 from the HipSci resource47; 409B2 from the RIKEN BRC cell bank; 01F49i-N-B7 (B7) from Institute of Molecular and Clinical Ophthalmology Basel; and WTC from the Allen Institute) and three human ES cell lines (H1-PAX6YFP…
A Phase 3, Open-Label, Randomized Study of Futibatinib Versus Gemcitabine-Cisplatin Chemotherapy as First-Line Treatment of Patients with Advanced Cholangiocarcinoma Harboring FGFR2 Gene Rearrangements
Official Trial Title A phase 3, open-label, randomized study of futibatinib versus germcitabine-cisplatin chemotherapy as first-line treatment of patients with advanced cholagiocarcinoma harboring FGFR2 gene rearrangements (FOENIX-CCA3) Study Description The University of Virginia is participating in a global clinical research study for adults ages 18 years of age, and over…
Dynamic mechanisms of CRISPR interference by Escherichia coli CRISPR-Cas3
In vitro reconstitution of Escherichia coli CRISPR-Cas3 interference E. coli CRISPR-Cas3 is generally well-characterized type I CRISPR complexes in vitro and in vivo32,33,37,38. However, recombinant EcoCas3 protein is difficult to purify because of poor solubility and propensity to aggregate at 37 °C25,26,30,39. Co-expression of HtpG chaperon40 and/or low temperature growth at…
Live-seq enables temporal transcriptomic recording of single cells
Biological materials RAW264.7, 293T and HeLa cells were obtained from ATCC. RAW264.7 cells with Tnf-mCherry reporter and relA-GFP fusion protein (RAW-G9 clone) were kindly provided by I.D.C. Fraser (National Institutes of Health). The IBA cell line derived from the stromal vascular fraction of interscapular brown adipose tissue of young male…
between results of RNAseq and absence/presence of Type3 Secretion System
Correlation between two different datasets: between results of RNAseq and absence/presence of Type3 Secretion System 1 Dear All, I have a “How would you solve” kind of question. I have two sets of tables : 1. Log2FoldChange table and 2. Effectors Table. Firstly, the Log2FoldChange table was obtained by performing…
(Single-cell RNA seq; R – Seurat) Re-clustering after removing cells using SubsetData
(Single-cell RNA seq; R – Seurat) Re-clustering after removing cells using SubsetData 0 I have a question regarding re-clustering after removing cells using SubsetData (R – Seurat package). I am in the process of analyzing a relatively large single-cell dataset (16 separate samples of ~5-10k cells each). In our first…
C698R mutation in Lrsam1 gene impairs nerve regeneration in a CMT2P mouse model
Animal generation The Lrsam1C698R knock-in mice were generated on a C57Bl/6J background using the CRISPR/Cas9 technique. Briefly, single-cell zygotes from C57BL/6J mice were microinjected with mRNA encoding Cas9 and a guide sequence (5′-ACAGCAGCAGACGTGGCCAC-3′ at 20 ng/µl) to target the exon 26 of Lrsam1. A single stranded DNA oligo carrying the C698R mutation…
Single-cell analyses define a continuum of cell state and composition changes in the malignant transformation of polyps to colorectal cancer
Mapping molecular changes across malignant transformation We generated single-cell data for 81 samples collected from eight FAP and seven non-FAP donors (Fig. 1a and Supplementary Tables 1 and 2). For each tissue, we performed matched scATAC-seq and snRNA-seq (10x Genomics). We obtained high-quality single-cell chromatin accessibility profiles for 447,829 cells…
Helsinn Expands US R&D Capabilities on Heels of BridgeBio Licensing Deal
Helsinn Group is expanding its global research and development capacity with the launch of a new dedicated hub in the U.S. The new R&D facility is a product of Helsinn’s new licensing deal with BridgeBio and will operate under Helsinn Therapeutics (U.S.). It will be instrumental in furthering the company’s projected increase in clinical activities to…
tReasure: R-based GUI package analyzing tRNA expression profiles from small RNA sequencing data | BMC Bioinformatics
tReasure (tRNA Expression Analysis Software Utilizing R for Easy use) is a graphical user interface (GUI) tool for the analysis of tRNA expression profiles from deep-sequencing data of small RNAs (small RNA-seq) using R packages. The whole analysis workflow, including the uploading of FASTQ files of small RNA-seq, quantification of…
Solved 28) What structure below provides an “anticodon”?
Transcribed image text: 28) What structure below provides an “anticodon”? (2pts) OmicroRNA mRNA tRNA rRNA 29) Which of the following modifications is involved in the 3′ (three prime) end-processing of pre- (4pts) mRNA precursors in eukaryotic cells? Addition of a methlyguanosine cap Splicing out introns Addition of Poly-A tail Forming…
Metagenomics technology and microbial community diversity analysis methods
A large number of microorganisms in nature cannot be cultivated under laboratory conditions by pure culture methods, and the technical methods of traditional microbiology limit the research on environmental microorganisms. The rapid development of high-throughput omics technology has enabled humans to have an unprecedented understanding of the complex microbial communities…
Helsinn Group and BridgeBio Pharma Announce Update to Strategic Collaboration to Develop, Manufacture and Commercialize Infigratinib in Oncology Indications in the U.S.
Lugano, Switzerland and Palo Alto, CA – Helsinn Group (Helsinn), a fully integrated, global biopharma company with a diversified pipeline of innovative oncology assets and strong track-record of commercial execution, and BridgeBio Pharma, Inc. (Nasdaq: BBIO) (BridgeBio), a commercial-stage biopharmaceutical company that focuses on genetic diseases and cancers, announced an…
Identification of Hub Genes Associated with COPD Through Integrated Bi
Introduction Chronic obstructive pulmonary disease (COPD) will become the third leading cause of death worldwide.1,2 The incidence of COPD worldwide is 13.1%3 and is 13.7% in the Chinese population over 40 years of age.4 Emphysema is one of the most common phenotypes.1 Over the past few decades, we have conducted…
scrnaseq – Integrating scRNA-seq data using raw data
I believe when you say alignment, you mean aligning reads to a genome (sometimes to transcriptome) and count these to get count matrices. In the aforementioned paper, however, what is meant is “bringing different data sets to a level where they can be compared/integrated/…”. Basically scRNA-seq data are heavily prone…
The Evolving Treatment Landscape of Cholangiocarcinoma
Recent genomic profiling studies revealed that approximately 40% of patients with biliary tract cancers harbor actionable genomic mutations. The advances in the understanding and characterization of biliary tract cancers (BTCs), particularly intrahepatic cholangiocarcinoma (iCCA), and genomic profiling over the past decade have led to a rapid expansion of available treatment…
Summer Research Assistant/Associate, Center for Computational Biology
Tremendous opportunities for discovery have emerged in the biological sciences, requiring the combined power of theory, data analysis, and simulation. Researchers are being confronted by an explosion of information from genome sequencing, gene expression profiling, proteomics, electron microscopy and tomography, and multiple high-resolution imaging modalities both dynamic and static. The…
Mutational Analysis of Mitochondrial tRNA Genes
Introduction Diabetes is a very complex disease characterized by the presence of chronic hyperglycemia. Clinically, insulin-dependent type 1 and non-insulin-dependent type 2 are the main types of diabetes. Among them, type 2 diabetes mellitus (T2DM, [MIM125853]) is a common endocrine disorder affecting approximately 10% of adult population.1 In most cases,…
Gene mutation analysis in papillary thyroid carcinoma
Introduction Thyroid tumors are the most common malignant tumors of the endocrine system, and their incidence has been increasing in the recent decades. Currently, there are some target drugs that can effectively treat PTC, and next-generation sequencing (NGS) can be used for targeted therapy. In order to make better informed…
New frog on the block!
The worldwide scientific community is too often bombarded with bad news — from first time ever rains at the Greenland ice summit to the Intergovernmental Panel on Climate Change’s (IPCC) doomsday forecast, there is hardly ever a reason to celebrate. Yet for Bangladesh’s nature enthusiasts, there is cause to celebrate….
