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Tag: cDNA
Endogenous Coriobacteriaceae enriched by a high-fat diet promotes colorectal tumorigenesis through the CPT1A-ERK axis
Bacteria Strain Cori.ST1911 was isolated from fresh stool of 20-week-old C57/BL6J mice fed a HFD at the Animal Center of the West China Hospital of Sichuan University. Briefly, faecal particles were ground with a glass grinding rod and suspended in sterile phosphate-buffered saline (PBS). After gradient dilution, the suspension was…
Understanding the Impact of Temperate Bacteriophages on Their Lysogens Through Transcriptomics
This protocol enables the impact of prophages on their hosts to be revealed. Bacterial cultures are synchronized using conditions that best support the lysogenic state, limiting spontaneous induction. RT-qPCR unequivocally distinguishes prophage-restricted genes and those uncoupled from phage control from those that are expressed during the lytic replication cycle. Prophages…
csi-miR-96-5p delivered by Clonorchis sinensis extracellular vesicles promotes intrahepatic cholangiocarcinoma proliferation and migration via the ferroptosis-related PTEN/SLC7A11/GPX4 axis | Parasites & Vectors
Human tissue samples The preoperative diagnosis of CS mainly relies on stool microscopy, enzyme-linked immunosorbent assay, or endoscopy. Fresh liver and intrahepatic bile duct specimens were collected from ICC patients with (CS-ICC group) and without (NC-ICC group) CS infection during partial hepatectomy at the First Hospital of Jilin University. Tumor tissues…
Apoptosis-resistant megakaryocytes produce large and hyperreactive platelets in response to radiation injury | Military Medical Research
Animals C57BL/6-Tg (Pf4-icre) Q3Rsko/J (Pf4-Cre) mice were purchased from the Jackson Laboratory (Bar Harbor, ME, USA). B6;129-Tmem173tm1(flox)Smoc (Stingfl) mice were purchased from Shanghai Model Organisms Center, Inc. (Shanghai, China). C57BL/6J-Ifnar1em1(flox)Cya (Ifnar1fl) mice were purchased from Cyagen Biosciences (Guangzhou, China). Stingcko and Ifnar1cko mice were generated by crossing Pf4-Cre mice with…
Summary of Genomics and Transcriptomics – DNA sequencing I. Goal II. Methodology A. Sanger DNA
DNA sequencing I. Goal II. Methodology A. Sanger DNA sequencing ● Up to 900 base pairs ● Primer extension with labeled ddNTPs (radioactive or fluorescent) ● Prior knowledge on target needed ● Difficult to detect variation in mixtures ● High accuracy + still in use for genotyping When it is…
Molecular characterization of a tetra segmented ssDNA virus infecting Botrytis cinerea worldwide | Virology Journal
Analysis of the multisegmented nature of BcssDV1 genome B. cinerea field isolates were previously obtained from infected grapes of vineyards of Italy and Spain and their mycovirome was determined [8]. A new ssDNA virus (BcssDV1, Genbank accession no. MN625247) was discovered and characterized. The sequence previously characterized of BcssDV1 (from…
LncRNA/circRNA-mRNA networks in CARAS | JIR
Introduction Combined allergic rhinitis and asthma syndrome (CARAS), a new terminology introduced by the World Allergy Organization (WAO) in 2004, is an allergic reaction that occurs in the respiratory tract, including upper respiratory tract allergy (allergic rhinitis, AR) and lower respiratory tract allergy (asthma, AS).1,2 The incidence of AS in…
Potent latency reversal by Tat RNA-containing nanoparticle enables multi-omic analysis of the HIV-1 reservoir
Participants and blood collection A total of n = 23 HIV-1 seropositive individuals on stably suppressive ART were included in this study (Supplementary Table 1). Participants were recruited at Ghent University Hospital. 2/23 individuals are female, 21/23 are male; the limited representation of female individuals in our study is a direct reflection of…
Analysis of Gene Expression in Acinetobacter baumannii: RNA-Seq
BPS3101Assignment 6 1.A graduate student studying the pathogenic bacteriaAcinetobacter baumanniimade cDNA from planktonic cells and biofilm cells and performed RNA-Seq on both samples. She aligned her sequencing reads to a locus of theA. baumanniigenome as shown. a.)Which genes are on an operon together?Explain which data supports this? b.)What is the…
insideBIGDATA AI News Briefs Bulletin Board
Welcome insideBIGDATA AI News Briefs Bulletin Board, our timely new feature bringing you the latest industry insights and perspectives surrounding the field of AI including deep learning, large language models, generative AI, and transformers. We’re working tirelessly to dig up the most timely and curious tidbits underlying the day’s most…
Evidence of an intracellular creatine-sensing mechanism that modulates creatine biosynthesis via AGAT expression in human HAP1 cells
Cell lines and reagents HAP1 cells used to generate the reporter cells were grown from a frozen stock of HAP1 (C859) passage 6 purchased from Horizon Discovery LTD (Cambridge, UK). Iscove’s media (Ref: 098–150, Wisent) supplemented with 10% Fetal Bovine serum (Multicell) was used to grow HAP1 cells. All cells…
Supports Instinct MI300, Radeon 7000 GPUs, AI Additions
AMD’s ROCm 6.0 software stack and the full source code are now available to download & come with Instinct MI300 & Radeon 7000 GPU support. AMD’s ROCm 6.0 Software Stack Now Brings Support For Additional AI Libraries, Unlocks FP8 Performance At PyTorch, Adds Instinct MI300 & Radeon 7000 GPU Support…
Gadolinium Oxide Nanoparticles reinforce immune response
Boyi Yu,1– 4 Xuanyi Lu,5 Xianglong Feng,1– 4 Ting Zhao,1– 4 Jiaxin Li,1– 4 Yudie Lu,5 Fei Ye,1– 4 Xiongxiong Liu,1– 4 Xiaogang Zheng,1– 4 Zheyu Shen,5 Xiaodong Jin,1– 4 Weiqiang Chen,1– 4 Qiang Li1– 4 1Biomedical Center, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou, People’s Republic of…
AMD ROCm 6.0 Now Available To Download With MI300 Support, PyTorch FP8 & More AI
Show Your Support: This site is primarily supported by advertisements. Ads are what have allowed this site to be maintained on a daily basis for the past 19+ years. We do our best to ensure only clean, relevant ads are shown, when any nasty ads are detected, we work to…
A transcriptomic taxonomy of mouse brain-wide spinal projecting neurons
Animals All experimental procedures were performed in compliance with animal protocols approved by the Institutional Animal Care and Use Committee at Boston Children’s Hospital (Protocol no. 20-05-4165 R). Mice were provided with food and water ad libitum, housed on a 12-hour light/dark schedule (7 a.m.–7 p.m. light period) with no more than five mice…
A high-resolution transcriptomic and spatial atlas of cell types in the whole mouse brain
Mouse breeding and husbandry All experimental procedures related to the use of mice were approved by the Institutional Animal Care and Use Committee of the AIBS, in accordance with NIH guidelines. Mice were housed in a room with temperature (21–22 °C) and humidity (40–51%) control within the vivarium of the AIBS…
Chromosome-level genome assembly of the Asian spongy moths Lymantria dispar asiatica
Boukouvala, M. C. et al. Lymantria dispar (L.) (Lepidoptera: Erebidae): Current Status of Biology, Ecology, and Management in Europe with Notes from North America. Insects 13 (2022). Keena M. A., Richards, J. Y. Comparison of Survival and Development of Gypsy Moth Lymantria dispar L. (Lepidoptera: Erebidae) Populations from Different Geographic…
QIAseq miRNA 96 Index Kit IL UDI-B (96)
Gel-free miRNA Sample to Insight solution for differential expression analysis and novel discovery using next-generation sequencing Features Gel-free miRNA sequencing library prep from as little as 1 ng of total RNA Elimination of adapter dimers and unwanted RNA species resulting in the highest fidelity and most efficient data Integrated Unique…
Bioactive glycans in a microbiome-directed food for children with malnutrition
Collection and handling of biospecimens obtained from participants in the randomized controlled clinical study of the efficacy of MDCF-2 The human study entitled ‘Community-based clinical trial with microbiota-directed complementary foods (MDCFs) made of locally available food ingredients for the management of children with primary moderate acute malnutrition (MAM)’ was approved…
Comprehensive Review of Small Interfering RNAs (siRNAs)
Introduction Cancer, also called malignancy, is a group of diseases caused by the rapid multiplication and spread of malignant cells.1,2 According to statistics from the National Cancer Center, more than 100 types of cancer have been identified.3 The ability of malignant tumor cells to metastasize via the blood-lymphatic system and…
Generating a New sgRNA Vector, pGL3-U6-sgRNA-PGK-mRFP-T2A-PuroR, to Improve Base Editing
doi: 10.32371/jger/246146. Epub 2022 Dec 17. Affiliations Expand Affiliation 1 Center for Molecular and Cellular Biosciences, School of Biological, Environmental, and Earth Sciences, University of Southern Mississippi, Hattiesburg, Mississippi 39406, United States of America. Free PMC article Item in Clipboard Tolulope E Ayo et al. J Genome Ed Regul. 2022. Free…
Regulation of the ER-Resident Mannosidase EDEM2 in HEK293 Cells
Abstract EDEM2 plays an important role as the first enzyme that acts during mannose trimming of N-glycosylated proteins in the ERAD machinery. Although EDEM2 expression has been reported to be transcriptionally regulated by the IRE1-sXBP1 pathway, very little is known about how endogenous EDEM2 protein expression is regulated. In this…
Kinnex launch promises to revolutionize RNA research
RNA sequencing (RNA-seq) has become an indispensable tool for analyzing transcriptomes across all domains of life that can reveal insights about biology and disease. While the genome remains relatively constant for most species over brief time scales, the transcriptome –the sum total of expressed messenger RNA (mRNA) transcripts – varies…
Thyroid hormone-regulated chromatin landscape and transcriptional sensitivity of the pituitary gland
Mouse genetic models The ThrbHAB allele expresses TRβ proteins (TRβ1 and TRβ2) fused to a peptide with a hemagglutinin (HAx2) tag and a site for biotinylation by prokaryotic BirA ligase, modified from a published tag30. The tag was inserted at the endogenous Thrb gene by homologous recombination in W9.5 (129/Sv)…
Takara Bio USA Wins EU Opposition Hearing, Revoking Jumpcode Genomics’ NGS Library Enrichment Patent
Article content SAN JOSE, Calif. — Takara Bio USA, Inc. today announced that it has once again prevailed in its second patent dispute with Jumpcode Genomics, Inc. The latest result concerns Takara Bio USA’s challenge to the validity of Jumpcode’s granted European patent EP3102722. Following a hearing before the Opposition…
Next-generation sequencing emerges as innovative tool to detect orthopedic infections
December 11, 2023 6 min read Add topic to email alerts Receive an email when new articles are posted on Please provide your email address to receive an email when new articles are posted on . “ data-action=”subscribe”> Subscribe We were unable to process…
Takara Bio USA Wins EU Opposition Hearing, Revoking Jumpcode Genomics’ NGS Library Enrichment Patent
SAN JOSE, Calif., December 11, 2023–(BUSINESS WIRE)–Takara Bio USA, Inc. today announced that it has once again prevailed in its second patent dispute with Jumpcode Genomics, Inc. The latest result concerns Takara Bio USA’s challenge to the validity of Jumpcode’s granted European patent EP3102722. Following a hearing before the Opposition…
What is B-Cell Receptor Repertoire Sequencing?
What is BCR-seq? B cell receptor sequencing (BCR-seq) represents an advanced and rapid method for the exhaustive detection of target-amplified B-cell receptors (BCRs) through the integration of high-throughput sequencing technology and bioinformatics. By scrutinizing the abundance of each sequence, BCR-seq unveils the intricacies of B-cell-mediated humoral immune responses and the…
Origin and evolution of the triploid cultivated banana genome
Rouard, M. et al. Three new genome assemblies support a rapid radiation in Musa acuminata (wild banana). Genome Biol. Evol. 10, 3129–3140 (2018). CAS PubMed PubMed Central Google Scholar Langhe, E. D., Vrydaghs, L., Maret, P. D., Perrier, X. & Denham, T. Why bananas matter: an introduction to the history…
A naturally occurring polyacetylene isolated from carrots promotes health and delays signatures of aging
Cell culture conditions Unless otherwise stated, cells were cultured with DMEM (Sigma Aldrich; #D6429) and 4.5 g/l glucose, phenol red, 10% FBS, and 1% penicillin/streptomycin with pH 7.4 and were incubated at 37 °C, 5% CO2, and 95% relative humidity. Wild-type HepG2 (#300198), HEK293 (#300192), and MCF-7 (#300273) were derived from CLS…
SOCS2 inhibits hepatoblastoma metastasis via downregulation of the JAK2/STAT5 signal pathway
Weighted gene co-expression network analysis GSE131329 has comprehensive clinical data, and WGCNA was carried out with this expression profile. WGCNA is a systems biology method for characterizing gene association patterns between different samples, used to identify highly synergistic sets of genes and to screen for candidate biomarker genes or therapeutic…
Solved a. Describe how silencing RNA (siRNA) functions in
Transcribed image text: a. Describe how silencing RNA (siRNA) functions in the regulation of gene expression and how this can be used as a tool in genetic research. b. PCR has opened the door to analysis of ancient DNA taken from long-dead organisms. The most useful DNA fragments in such…
Phenotypic profiling of solute carriers characterizes serine transport in cancer
Cell culture All cell lines used in this study were cultured at 37 °C in 5% CO2 in a humidified incubator. Human cell lines were authenticated by STR profiling using Promega GenePrint 10 and tested for Mycoplasma using Mycoalert (Lonza). Other than HCT116 p21−/− (a gift of B. Vogelstein60) all cell…
Identification of the protein coding capability of coronavirus defective viral genomes by mass spectrometry | Virology Journal
In the current study, nanopore direct RNA sequencing and liquid chromatography-tandem mass spectrometry (LC–MS/MS) analysis were employed to examine whether DVGs can encode proteins in infected cells. With the protein databases generated by nanopore direct RNA sequencing, six DVG-encoded proteins were identified by LC–MS/MS based on the featured fusion peptides…
Illumina RNA Sequencing – SeqCenter, LLC
RNA, the intermediate stage in the flow of genetic information from DNA to protein, contains many systems of expression and regulation that can be studied through RNA sequencing. While whole genome sequencing reveals information at the DNA level, next generation RNA sequencing (RNA-seq) characterizes the transcriptome and provides additional context…
AMD Advancing AI Event Live Blog: Instinct MI300 Launch, Ryzen 8000 “Hawk Point” Expected
Refresh 2023-12-06T18:45:51.125Z (Image credit: AMD) Here are some of the specifications of AMD’s new Instinct MI300X platform. The system consists of eight MI300X accelerators in one system. It supports 400 GbE networking and has a monstrous 1.5TB of total HBM3 capacity. 2023-12-06T18:43:30.129Z (Image credit: AMD) The talk has turned to…
Strandedness of RNA-seq results
Strandedness of RNA-seq results 1 Hi all, I am not very familiar with bioinfo things as my background is more towards wetlab. I am analysing my dual RNA-seq results (host+pathogen RNA), and I am using HISAT2 (aligned to genome) + featurecounts pipeline. I am not sure why I only get…
Functional conservation of specialized ribosomes bearing genome-encoded variant rRNAs in Vibrio species
Fig 1. rrnI-dependent expression of HspA in V. vulnificus MO6-24/O strains. (A) Schematic representation of the allele-specific RT-PCR analysis analyzing the relative amounts of I-rRNA or G-rRNA. (B) The number of I-rRNA or G-rRNA amplicons and other rRNAs amplified from the cDNA of the MO6 WT, MO6+rrnG, and MO6+rrnI strains…
Identification and validation of key miRNAs for colon cancer
Introduction With nearly 2 million new cases and 1 million deaths worldwide in 2020, colorectal cancer is the third-most common cancer and the second leading cause of cancer-related deaths.1 According to data from the US Surveillance, Epidemiology and End Results program and the National Program of Cancer Registries program, the…
The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance
Cell line and growth assays Cell lines were grown in Roswell Park Memorial Institute-1640 medium (RPMI-1640) with 1% penicillin–streptomycin (10,000 U ml−1) and 10% FBS or in Iscove’s modified Dulbecco’s medium (IMDM) with 1% penicillin–streptomycin (10,000 U ml−1), l-glutamine (200 mM) and 10% FBS in a humidified incubator with 5% CO2 maintained at 37 °C. Drugs…
Antibody Production Companies: Re-shaping Life Sciences Together
(Photo : Michal Jarmoluk from Pixabay) Antibody production companies are essential in dealing with the growing demand for antibodies for life sciences, therapeutic, and diagnostic applications. Therefore, a number of service providers are specialized in offering various types of services regarding the complex production of antibodies. Many biotechnology companies rely…
500U | Taq DNA Polymerase, 5u/ul Anawa
Taq DNA Polymerase, 5u/ul Product information Taq DNA Polymerase (New Buffer!) Product Description: Taq DNA Polymerase is a thermosle DNA Polymerase isolated from a strain of Thermus sp. Taq has a half life of 3 hours at 95°C. Taq has high fidelity with an error frequency 10/10^6 (or 0.01/10^3) during…
kallisto index build difference according to version
kallisto index build difference according to version 0 Hi all, I’m trying to implement kallisto for a dataset of single-end RNA-seq data, And obviously started with building an index (The files were downloaded from ensembl). Homo_sapiens.GRCh37.ncrna.fa.gz Homo_sapiens.GRCh37.cdna.all.fa.gz using the command kallisto index -i index.idx Homo_sapiens.GRCh37.ncrna.fa.gz Homo_sapiens.GRCh37.cdna.all.fa.gz And although this wasn’t…
Characteristics of BMKS patient-, mother- and unrelated control-derived iPSCs.
For the analyses, data from two patient iPSC lines, two parent iPSC lines and two unrelated control iPSC lines were pooled. A) Relative TXNL4A mRNA expression levels for patient iPSCs compared to mother iPSCs and unrelated control iPSCs, determined using qPCR of cDNA from each cell line. Graphs were obtained…
Chapter 6 GGHH 2023 – notes – Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes
Chapter 6. Expression Quantitative Trait Loci (eQTL) Learning Outcomes Define an eQTL Summarise the methodology of RNAseq Understand the reason for expressing RNAseq outcomes as transcripts per million (TPM) Explain why patterns of H3K4me3 and H3K27ac can be used as markers of transcriptionally active genes Incorporate this data into a…
Association analysis of production traits of Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing
Tsudzuki, M. Mutations of Japanese quail (Coturnix japonica) and recent advances of molecular genetics for this species. J. Poult. Sci. 45, 159–179 (2008). CAS Google Scholar Recoquillay, J. et al. A medium density genetic map and QTL for behavioral and production traits in Japanese quail. BMC Genom. 16, 10 (2015)….
Alfalfa vein mottling virus, a novel potyvirid infecting Medicago sativa L. | Virology Journal
Plant material Five alfalfa plants (stems and leaves) were sampled from each of the four different fields, 10–15 acres in size, located in Yuma Country, Arizona, USA. Geographic coordinates of the alfalfa fields and the adjacent crops are shown in Table 1. Table 1 Geographic locations of alfalfa fields Total…
Salpa genome and developmental transcriptome analyses reveal molecular flexibility enabling reproductive success in a rapidly changing environment
Loeb, V. et al. Effects of sea-ice extent and krill or salp dominance on the Antarctic food web. Nature 387, 897–900 (1997). Article ADS CAS Google Scholar Atkinson, A., Siegel, V., Pakhomov, E. & Rothery, P. Long-term decline in krill stock and increase in salps within the Southern Ocean. Nature…
Two mitochondrial HMG-box proteins, Cim1 and Abf2, antagonistically regulate mtDNA copy number in Saccharomyces cerevisiae | Nucleic Acids Research
Abstract The mitochondrial genome, mtDNA, is present in multiple copies in cells and encodes essential subunits of oxidative phosphorylation complexes. mtDNA levels have to change in response to metabolic demands and copy number alterations are implicated in various diseases. The mitochondrial HMG-box proteins Abf2 in yeast and TFAM in mammals…
MSL2 ensures biallelic gene expression in mammals
Materials Animals All of the mice were kept in the animal facility of the Max Planck Institute of Immunobiology and Epigenetics. The mice were maintained under specific-pathogen-free conditions, with 2 to 5 mice housed in individually ventilated cages (Techniplast). The cages were equipped with bedding material, nesting material, a paper…
Precise base editing without unintended indels in human cells and mouse primary myoblasts
Base editors cause unintended indels at the target sites Several types of evolved base editors based on the CRISPR system have been developed for more accurate and efficient genome engineering21,37. Among these, AncBE4max and ABEmax were evolved by modifying codon usage, NLSs, and ancestral deaminase reconstructions21. These modifications greatly improve…
ESRP1 controls biogenesis and function of a large abundant multiexon circRNA | Nucleic Acids Research
Abstract While the majority of circRNAs are formed from infrequent back-splicing of exons from protein coding genes, some can be produced at quite high level and in a regulated manner. We describe the regulation, biogenesis and function of circDOCK1(2–27), a large, abundant circular RNA that is highly regulated during epithelial-mesenchymal…
Genome editing approaches with CRISPR/Cas9: the association of NOX4 expression in breast cancer patients and effectiveness evaluation of different strategies of CRISPR/Cas9 to knockout Nox4 in cancer cells | BMC Cancer
A. Bioinformatics analyzes Search strategy and study selection From April to June 2021, we read relevant and related publications in Medline, EMBASE, Web of Science, and Wanfang. The search term “NOX4” have been used. The articles that fit specified criteria were all added at once: (1) Participants were split into…
Global Gene Expression Research Report 2023: A $20.94 Billion Market by 2030
Company Logo Global Gene Expression Market Global Gene Expression Market Dublin, Nov. 28, 2023 (GLOBE NEWSWIRE) — The “Gene Expression Market Size, Share & Trends Analysis Report By Product (DNA Chip/Microarray, Kits & Reagents), By Technique (Promoter Analysis, RNA Exp.), By Capacity, By Process, By Application, And Segment Forecasts, 2023…
Optimized RT-qPCR and a novel normalization method for validating circulating miRNA biomarkers in ageing-related diseases
Reagents miRNeasy Serum/Plasma Advanced Kit (Qiagen, Hilden, Germany, # 217204); TaqMan® Advanced miRNA cDNA Synthesis Kit (Applied Biosystems, Bedford, MA, USA, #A28007); TaqMan® Fast Advanced Master Mix (Applied Biosystems, Bedford, MA, USA, # 4444556); TaqMan® Advanced miRNA Assays Single-tube assays (Applied Biosystems, Bedford, MA, USA, # A25576: 478293_mir, Spike-In cel-miR-39-3p;…
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data? 0 I have some cDNA data comparing various mutants to a control sample (each with 3+ replicates) that were obtained using a modified version of the direct cDNA sequencing kit (SQK-DCS109) from ONT. Due to the modified protocol,…
H101 for cervical cancer | DDDT
Introduction Patients with persistent, recurrent, or metastatic (P/R/M) cervical carcinoma respond poorly to treatment despite the best available therapeutic regimens, with a 5-year survival of 17%.1 Most of them are heavily pretreated with chemotherapy and/or radiotherapy, and many patients experience complications related to treatment or advanced disease, which exclude them…
Sol-Gel Technologies (NASDAQ:SLGL) vs. Oxford Nanopore Technologies (OTC:ONTTF) Head-To-Head Contrast
Oxford Nanopore Technologies (OTC:ONTTF – Get Free Report) and Sol-Gel Technologies (NASDAQ:SLGL – Get Free Report) are both medical companies, but which is the better business? We will compare the two businesses based on the strength of their analyst recommendations, risk, earnings, dividends, institutional ownership, profitability and valuation. Analyst Recommendations…
Gene of choice – RefSeq Accession: NM_ cDNA NM_ ACATTTGCTT CTGACACAAC TGTGTTCACT AGCAACCTCA
Gene of choice: HBB (hemoglobin subunit beta) located in chromosome11:5,225,464 – 5,227,071 which contains 1,608bp. RefSeq Accession: NM_00518 cDNA NM_000518 ACATTTGCTT CTGACACAAC TGTGTTCACT AGCAACCTCA AACAGACACC 50 ATGGTGCATC TGACTCCTGA GGAGAAGTCT GCCGTTACTG CCCTGTGGGG 100 CAAGGTGAAC GTGGATGAAG TTGGTGGTGA GGCCCTGGGC AGGCTGCTGG 150 TGGTCTACCC TTGGACCCAG AGGTTCTTTG AGTCCTTTGG GGATCTGTCC 200 ACTCCTGATG CTGTTATGGG CAACCCTAAG GTGAAGGCTC ATGGCAAGAA 250…
Molecular complexity of diffuse large B-cell lymphoma: a molecular perspective and therapeutic implications
Agarwal P, Kabir FM, DeInnocentes P, Bird RC (2012) Tumor suppressor gene p16/INK4A/CDKN2A and its role in cell cycle exit, differentiation, and determination of cell fate. Tumor Suppressor Genes 3(10):27882 Google Scholar Alaggio R, Amador C, Anagnostopoulos I, Attygalle AD, Araujo IBO, Berti E et al (2022) The 5th edition…
Biophysical properties of NaV1.5 channels from atrial-like and ventricular-like cardiomyocytes derived from human induced pluripotent stem cells
hiPSC cultures and cardiomyocyte differentiation The hiPSC lines CBRCULi001-A54 and CBRCULi008-A55 were generated from a 44-year-old male and 75-year-old female control lymphoblastoids, respectively, and they were reprogramed at the LOEX core facility (Quebec City, QC, Canada). All the work with hiPSCs were approved by CIUSSS de la Capitale-Nationale ethics committee (Project…
MinKNOW software installation doubt for MinION Nanopore sequencing
MinKNOW software installation doubt for MinION Nanopore sequencing 0 Hi good people, Recently in lab we have received a Nanopore MinION device and currently trying to figure out installation and other details. I am seeking a few suggestions from users and experts. The running machine spec is AMD Ryzen 9…
Immune-privileged tissues formed from immunologically cloaked mouse embryonic stem cells survive long term in allogeneic hosts
Mice C57BL/6N (strain 005304), C3H/HeJ (strain 000659), FVB/NJ (strain 001800), BALB/cJ (strain 000651) and NSG mice (stock 005557) were purchased from the Jackson Laboratory. CD-1 (stock 022) mice were purchased from Charles River. Mice (6–20-week-old) of each strain/background were used for teratoma assays. Mice were housed in a pathogen-free facility…
Pan-Cancer Analysis and Validation of Opioid-Related Receptors Reveals
Introduction The potential role of opioids used in oncology patients has been controversial. Epidemiological and retrospective studies have demonstrated that lower opioid doses and regional anesthesia (epidural, intrathecal, or paravertebral) for breast,1 colon,2 or melanoma3 are linked to lower rates of cancer recurrence, while general anesthesia with high opioid doses…
Functional filter for whole-genome sequencing data identifies HHT and stress-associated non-coding SMAD4 polyadenylation site variants >5 kb from coding DNA
Summary Despite whole-genome sequencing (WGS), many cases of single-gene disorders remain unsolved, impeding diagnosis and preventative care for people whose disease-causing variants escape detection. Since early WGS data analytic steps prioritize protein-coding sequences, to simultaneously prioritize variants in non-coding regions rich in transcribed and critical regulatory sequences, we developed GROFFFY,…
Analysis of nucleoporin 107 overexpression
Introduction Lung cancer is one of the most common types of cancer worldwide and the leading cause of cancer death.1 The main category of lung cancer is non-small cell lung cancer, accounting for about 85%, and lung adenocarcinoma, as a kind of non-small cell lung cancer, is the most frequently…
Megakaryocytes possess a STING pathway that is transferred to platelets to potentiate activation
Introduction Host defence against infection relies on two important systems: the immune and the coagulation systems. Platelets are anucleate cells produced by megakaryocytes and are responsible for blood clotting and haemostasis (Lefrancais et al, 2017). They are also very abundant and play unexpected roles in immune responses (Maouia et al,…
AMD Delivers More Options for AI Developers by Ext…
We recently launched AMD ROCm™ 5.7 for the AMD Radeon™ RX 7900 XTX and Radeon™ PRO W7900 GPUs for Machine Learning (ML) development workflows with PyTorch. We have now extended support to include the Radeon™ RX 7900 XT GPU, introducing even more options for AI developers and researchers. The…
Magnetic Beads Market Journey of Discovery Ethnography’s Influence on Consumer Behavior | Thermo Fisher Scientific, Advanced BioChemicals | Taiwan News
The “Magnetic Beads Market” is poised for significant growth from 2023 to 2032, with the market size projected to increase from USD Million in 2023 to USD Million by 2032, exhibiting a substantial Compound Annual Growth Rate (CAGR) during the forecast period. This report offers a comprehensive analysis of the market, including key trends, opportunities, recent…
Elevated stress response marks deeply quiescent reserve cells of gastric chief cells
Generation of inducible H2b-GFP knock-in mice Generation of inducible H2b-GFP knock-in mice was performed by using CRISPR/Cas943. In brief, a mixture containing a sgRosa26-1 crRNA43 (8.7 ng/μl, Fasmac, Japan), a tracrRNA (14.3 ng/μl, Fasmac, Japan), a single strand oligo donor nucleotide (ssODN) composed of 5′ arm, adenovirus splicing acceptor, SV40 pA, TRE3G…
Cataloging bacterial diversity within tumor samples
It is said in Spanish, “si no existe, créalo” or “if it does not exist, create it.” This is exactly what sometimes occurs at the Fred Hutch. When we do not have the tools to test a hypothesis, we must be creative! A great example is a collaboration between Dr. Susan Bullman,…
A single pseudouridine on rRNA regulates ribosome structure and function in the mammalian parasite Trypanosoma brucei
Cell growth and transfections Procyclic form (PCF) T. brucei, strain 29-1354, which carries integrated genes for the T7 polymerase and the tetracycline repressor, was grown in SDM-79 medium supplemented with 10% fetal calf serum, in the presence of 50 μg/ml hygromycin. Cells were grown in the presence of 15 μg/ml G418 for…
Insects | Free Full-Text | Novel Insights into the circRNA-Modulated Developmental Mechanism of Western Honey Bee Larval Guts
1. Introduction As a representative social insect with crucial ecological, economic and scientific value, the western honey bee (Apis mellifera) is widely reared and applied in the apicultural industry in considerable countries around the world [1]. In addition, A. mellifera has been applied as a research model for development, social…
LncRNA INHEG promotes glioma stem cell maintenance and tumorigenicity through regulating rRNA 2’-O-methylation
Ethics statement All mice procedures in this study were performed under an animal protocol approved by the Institutional Animal Care and Use Committee guidelines of Westlake University. The procedures and protocols for glioma patients were approved by the institutional review board of Beijing Tiantan Hospital. Informed consent was obtained from…
Iron derived from NCOA4-mediated ferritinophagy causes cellular senescence via the cGAS-STING pathway
Materials and reagents Tert-butyl hydroperoxide (TBH) were purchased from Sigma-Aldrich (St. Louis, USA). Ferric ammonium citrate (FAC) and D-galactose (D-gal) was obtained from Selleck (Shanghai, China) and Aladdin (Shanghai, China), respectively. Deferoxamine (DFO), Mito-TEMPO (Mito-T), 3-Methyladenine (3-MA), Chloroquine (CQ), Bafilomycin A1 (Baf-A1), and H-151 were purchased from MedChemExpress (NJ, USA)….
Knockdown of GNL3L alleviates the progression of COPD
Introduction Chronic obstructive pulmonary disease (COPD) is a common chronic bronchitis disease characterized by persistent airflow limitation, which can be prevented and treated. COPD is the third leading cause of death in the world reported in 2020.1 With the progression of the disease, COPD will lead to respiratory failure, pulmonary…
Advancing personalized medicine in brain cancer: exploring the role of mRNA vaccines | Journal of Translational Medicine
Personalized medicine aims to revolutionize healthcare by providing tailored treatments based on an individual’s unique characteristics. Genetic information of the host and target plays a crucial role in determining disease susceptibility and treatment response [1, 2]. By utilizing genomic analysis, biomarker identification, risk assessment, tailored treatment strategies, and continuous monitoring,…
GDF11 slows excitatory neuronal senescence and brain ageing by repressing p21
Experimental model and subject details Mice Male ICR mice (Laboratory Animal Center of Zhejiang Academy of Medical Sciences) at age of 3 months (M), 9 M and 36 M, male C57BL/B6 wild‐type (WT) mice (Shanghai Slac Laboratory) at age of 3 M and 10 M, male GDF11-flox mice (GDF11f/f, mice carrying the “floxed” GDF11…
IDG-SW3 Cell Culture in a Three-Dimensional Extracellular Matrix
Here, we present a protocol for culturing IDG-SW3 cells in a three-dimensional (3D) extracellular matrix. We detailed a protocol to establish a 3D system using an extracellular metrics along with collagen one for analyzing formation and gene expression through osteogenesis. Extracellular metrics can increase the transparency of the collagen one…
Problem Set 8 Fa23 – Problem Set 8 Bioinformatics Name ______________________________ (total 20 pts)
Problem Set 8 Bioinformatics Name ______________________________ (total 20 pts) PART 1 – BLAST BLAST (Basic Local Alignment Search Tool) is a bioinformatics program, which “finds regions of similarity between biological sequences.” It can help you find a homologous gene in another species or it can compare two sequences for similarity….
COL10A1 promotes tumorigenesis by modulating CD276 in pancreatic adenocarcinoma | BMC Gastroenterology
Bioinformatics analysis The GEO database (www.ncbi.nlm.nih.gov/geo/) provided detailed gene expression information for the GSE62165 microarray. Differentially expressed genes were identified using the online tool Morpheus (software.broadinstitute.org/morpheus/) (fold change = normal pancreatic tissue gene expression/PDAC tissue gene expression, P value < 0.05 and |log2(fold change)|>1). The downstream analysis was based on the genes with the…
Novel Assay May Help Detect and Treat Patients With AML
By The ASCO Post StaffPosted: 11/15/2023 10:20:00 AM Last Updated: 11/15/2023 11:37:35 AM A novel assay may be effective at detecting a unique molecular marker in patients with acute myeloid leukemia (AML), according to a recent study published by Young et al in The Journal of Molecular Diagnostics. The new…
Single-cell CRISPR screens in vivo map T cell fate regulomes in cancer
Mice The research conducted in this study complied with all of the relevant ethical regulations. The animal protocols were approved by and performed in accordance with the Institutional Animal Care and Use Committee of St. Jude Children’s Research Hospital. C57BL/6, OT-I50, pmel51 and Rosa26-Cas9 knock-in52 mice were purchased from The…
RhoA suppresses pseudorabies virus replication in vitro | Virology Journal
Materials The Cell Counting Kit-8 (CCK-8) was ordered from Yeasen BioTechnologies co, Ltd. (Shanghai, China). Anti-GAPDH was purchased from Proteintech Group, Inc. (Chicago, USA). Anti RhoA was purchased from Novus Biologicals (Colorado, USA). Antiserum against PRV glycoprotein gB was generated by immunization of mice with purified recombinant gB. Goat anti-Mouse…
Electroporation Transformation of Barley | SpringerLink
Ahloowalia BS (1987) Plant regeneration from embryo-callus culture in barley. Euphytica 36: 659–665 CrossRef Google Scholar Ahokas H (1989) Transfection of germinating barley seed electrophoretically with exogenous DNA. Theor Appl Genet 77: 469–472 CrossRef CAS Google Scholar Barro F, Cannell ME, Lazzeri PA, Barcelo P (1998) The influence of auxins…
mRNA Extraction and Purification Market to Record an Exponential CAGR by 2030
InsightAce Analytic Pvt. Ltd. has announced the publication of a market research report titled “Global mRNA Extraction and Purification Market– By Product (Kits/Reagents, Instruments) End-user (Academics and Research Institutes, Pharmaceutical & Biotechnology Companies, Contract Research Organizations, Other End Users) Trends, Industry Competition Analysis, Revenue and Forecast To 2030.” According to…
Lexogen Unveils LUTHOR High-Definition Single Cell 3′ mRNA-Seq Kit, Revolutionizing Single-Cell RNA Sequencing
VIENNA, Nov. 14, 2023 /PRNewswire/ — Lexogen, a pioneer in the field of genomics and transcriptomics, is proud to introduce the groundbreaking LUTHOR High-Definition Single Cell 3′ mRNA-Seq Kit, a game-changing innovation that sets new standards in single-cell RNA sequencing. Lexogen Current Logo LUTHOR HD is a cutting-edge protocol that…
PPP1R12A is a recycling endosomal phosphatase that facilitates YAP activation
Antibodies Antibodies used in the present study were as follows: rabbit anti-phospho-YAP (S127) (#13008, dilution 1:500), rabbit anti-phospho-LATS1 (S909) (#9157, dilution 1:500), rabbit anti-YAP (#14074, dilution 1:100 for immunofluorescence), and rabbit anti-PPP1R12A (#8574, dilution 1:1000 for western blot, 1:200 for immunofluorescence) from Cell Signaling Technology; rabbit anti-LATS1 (A300-477A, dilution 1:2000)…
Rapid detection of avian influenza virus based on CRISPR-Cas12a | Virology Journal
Materials Escherichia coli strains expressing the LbCas12a protein, plasmids containing the AIV M and NP genes, and H1–H16 subtypes of AIV, newcastle disease virus (NDV), infectious bursal disease virus (IBDV), and infectious bronchitis virus (IBV) were conserved in the State Key Laboratory of Harbin Veterinary Research Institute (HVRI), Chinese Academy…
ABCB1 and immune genes in breast cancer
Introduction Chemoresistance is a major challenge for breast cancer treatment.1 The mechanisms of chemoresistance are complex because of crosstalk between receptor tyrosine kinases and downstream pathways, deregulation of cell-cycle and apoptosis regulators, and modulation of tumor-infiltrating immune cells.2 The ATP-binding cassette (ABC) superfamily is one of the largest families of…
New assay could revolutionize detection and treatment of acute myeloid leukemia
Design of droplet digital PCR (ddPCR) assay. A: Schematic of ddPCR assay. Primers spanned the fusion break points (KMT2A-AF4 depicted). Nested fluorescently labeled probes recognized unique sequences in KMT2A (FAM) and the fusion partner AFF1-AF4 (HEX). B: Example ddPCR result depicting double-positive droplets containing cDNA with an oncogenic KMT2A fusion…
A Cre-dependent massively parallel reporter assay allows for cell-type specific assessment of the functional effects of non-coding elements in vivo
Animal models All procedures involving animals were approved by the Institutional Animal Care and Use Committee (IACUC) at Washington University in St. Louis, MO. Veterinary care and housing was provided by the veterinarians and veterinary technicians of Washington University School of Medicine under Dougherty lab’s approved IACUC protocol. All protocols…
Myristoylated, alanine-rich C-kinase substrate (MARCKS) regulates toll-like receptor 4 signaling in macrophages
Cell line and LPS stimulation conditions Immortalized mouse macrophages (IMM), including the IMMs from TLR4 -/- mouse (generated by Bruce Beutler’s laboratory47) and available from Jackson Laboratory) were a generous gift from Dr. Eicke Latz48,49. The cells were cultured in complete DMEM (Gibco, Grand Island, NY, USA) complemented with 10%…
RNAseq from P4 murine whole kidneys with Polycystic Kidney Disease
Snap frozen Postnatal day4 murine kidney tissues were crushed using micropestles in RLT Buffer and RNA was extracted from these tissues using QiaShredders followed by Qiagen RNAeasy Mini Kits according to manufacturer’s protocol. RNA concentration and integrity were determined by Aligent bioanalyzer. cDNA library preparation was carried out using NEB…
DNA microarray technique for infectious disease diagnostics.
Introduction Infectious diseases are illnesses caused by pathogenic microbes such as bacteria, viruses, parasites, or fungus, which can be transmitted directly or indirectly from one person to another.1 Throughout human history, infectious illnesses have been a major cause of morbidity and mortality. One-third of all death worldwide is caused by…
Why am I getting different results with kallisto?
Why am I getting different results with kallisto? 1 Hello, I created a reference for my species of interest using the cDNA file from ensembl and then aligned my data to it using kallisto. Then, i was asked to add the ncRNA to the reference and a egfp sequence. I…
PIGx ChIP-seq pipeline error
Hi Lisa, You also need to modify the gtf annotation file using: sed ‘/^#/d’ annotation_file.gtf > annotation_file_no_header.gtf Best, Alex > On 12. Oct 2022, at 15:07, Bora Uyar <borauy…@gmail.com> wrote: > > You would need to check how your fasta headers look and how the chromosomes are represented in…
Circular extrachromosomal DNA promotes tumor heterogeneity in high-risk medulloblastoma
Statistical methods Statistical tests, test statistics and P values are indicated where appropriate in the main text. Categorical associations were established using the chi-squared test of independence if n > 5 for all categories and Fisherʼs exact test otherwise. For both tests, the Python package scipy.stats v1.5.3 implementation was used64. Multiple hypothesis corrections…
CRISPR/Cas9-based disease modelling and functional correction of Interleukin 7 Receptor alpha Severe Combined Immunodeficiency in T-lymphocytes and hematopoietic stem cells
Abstract Interleukin 7 Receptor Alpha Severe Combined Immunodeficiency (IL7R-SCID) is a life-threatening disorder caused by homozygous mutations in the IL7RA gene. Defective IL7R expression in humans hampers T cell precursors proliferation and differentiation during lymphopoiesis resulting in absence of T cells in newborns, who succumb to severe infections and death…
FAT10 is phosphorylated by IKK{beta} to inhibit the antiviral type-I interferon response
Introduction The innate immune system represents the host´s first-line defense against viral infections (Koyama et al, 2008). In this context, IFN-I are produced by all nucleated cells and represent the principal cytokines that counteract viral replication (Ivashkiv & Donlin, 2014). In fact, several receptors of the infected cell can recognize…