Tag: GAPDH

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…

Continue Reading Endogenous Coriobacteriaceae enriched by a high-fat diet promotes colorectal tumorigenesis through the CPT1A-ERK axis

Proteomic analysis of SARS-CoV-2 particles unveils a key role of G3BP proteins in viral assembly

Capturing proteins associated with SARS-CoV-2 virions To identify host cell proteins potentially present in extracellular SARS-CoV-2 virions, viral particles were produced from two lung epithelial cell models, A549 cells overexpressing ACE2 receptor (A549-ACE2) and Calu-3 cells that naturally express ACE2 receptor and TMPRSS2. Following infection with the D614G SARS-CoV-2 strain32,…

Continue Reading Proteomic analysis of SARS-CoV-2 particles unveils a key role of G3BP proteins in viral assembly

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…

Continue Reading 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

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…

Continue Reading Apoptosis-resistant megakaryocytes produce large and hyperreactive platelets in response to radiation injury | Military Medical Research

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…

Continue Reading LncRNA/circRNA-mRNA networks in CARAS | JIR

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…

Continue Reading Potent latency reversal by Tat RNA-containing nanoparticle enables multi-omic analysis of the HIV-1 reservoir

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…

Continue Reading Evidence of an intracellular creatine-sensing mechanism that modulates creatine biosynthesis via AGAT expression in human HAP1 cells

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…

Continue Reading Gadolinium Oxide Nanoparticles reinforce immune response

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…

Continue Reading Comprehensive Review of Small Interfering RNAs (siRNAs)

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…

Continue Reading Phenotypic profiling of solute carriers characterizes serine transport in cancer

CRISPRi gene modulation and all-optical electrophysiology in post-differentiated human iPSC-cardiomyocytes

A feasibility CRISPRi study was performed in post-differentiated iPSC-CMs targeting key genes important in cardiac electrophysiology. Comprehensive analysis using all-optical electrophysiology and a pipeline enabling correlative analysis of functional and molecular data in the same samples helped quantify the CRISPRi gene modulation in this in vitro model. Time-dependent control of…

Continue Reading CRISPRi gene modulation and all-optical electrophysiology in post-differentiated human iPSC-cardiomyocytes

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…

Continue Reading The role of APOBEC3B in lung tumor evolution and targeted cancer therapy resistance

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…

Continue Reading ESRP1 controls biogenesis and function of a large abundant multiexon circRNA | Nucleic Acids Research

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…

Continue Reading 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

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…

Continue Reading Biophysical properties of NaV1.5 channels from atrial-like and ventricular-like cardiomyocytes derived from human induced pluripotent stem cells

High-throughput screening of genetic and cellular drivers of syncytium formation induced by the spike protein of SARS-CoV-2

Plasmid construction All the constructs used in this study were generated with standard cloning strategies, including PCR, overlapping PCR, oligo annealing, digestion and ligation. Primers were purchased from Genewiz. The plasmid sequence was verified by Sanger sequencing. The pCAG-spike(D614G)-GFP11-mCherry plasmid was modified from Addgene plasmid 158761. Briefly, GFP11 and mCherry…

Continue Reading High-throughput screening of genetic and cellular drivers of syncytium formation induced by the spike protein of SARS-CoV-2

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…

Continue Reading Pan-Cancer Analysis and Validation of Opioid-Related Receptors Reveals

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…

Continue Reading Knockdown of GNL3L alleviates the progression of COPD

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…

Continue Reading COL10A1 promotes tumorigenesis by modulating CD276 in pancreatic adenocarcinoma | BMC Gastroenterology

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…

Continue Reading RhoA suppresses pseudorabies virus replication in vitro | Virology Journal

Molecular-based classification of endometrial carcinoma in Northern Thailand: impact on prognosis and potential for implementation in resource-limited settings | BMC Women’s Health

Study population The study cohort included women diagnosed with endometrial carcinoma at Chiang Mai University Hospital during January 2015 to December 2017. Inclusion criteria were patients with informed consent, available hysterectomy specimens for evaluation, and available clinical information and pathological results. We excluded individual without histologic materials and formalin-fixed paraffin-embedded…

Continue Reading Molecular-based classification of endometrial carcinoma in Northern Thailand: impact on prognosis and potential for implementation in resource-limited settings | BMC Women’s Health

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)…

Continue Reading PPP1R12A is a recycling endosomal phosphatase that facilitates YAP activation

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…

Continue Reading ABCB1 and immune genes in breast cancer

Identification of DNA damage response-related genes as biomarkers for castration-resistant prostate cancer

mRNA expressions of DDR-related genes are upregulated in CRPC compared to those in Pca To identify a cluster of upregulated genes in CRPC, we previously conducted directional RNA-seq analysis using clinical samples obtained from localized Pca and CRPC patients21. We used RNA samples obtained from prostate cancer patients by radical…

Continue Reading Identification of DNA damage response-related genes as biomarkers for castration-resistant prostate cancer

IJMS | Free Full-Text | CRISPR/Cas9 Directed Reprogramming of iPSC for Accelerated Motor Neuron Differentiation Leads to Dysregulation of Neuronal Fate Patterning and Function

1. Introduction As the world population ages, neurodegenerative diseases are increasing. The outcome of these diagnoses varies but can lead to fatality 50% of the time within 15–20 months [1]. Treatments for neurodegeneration, in particular motor neuron (MN) diseases, are restricted due to the limitations of motor neuron repair and…

Continue Reading IJMS | Free Full-Text | CRISPR/Cas9 Directed Reprogramming of iPSC for Accelerated Motor Neuron Differentiation Leads to Dysregulation of Neuronal Fate Patterning and Function

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…

Continue Reading FAT10 is phosphorylated by IKK{beta} to inhibit the antiviral type-I interferon response

Nascent ribosomal RNA act as surfactant that suppresses growth of fibrillar centers in nucleolus

Transcription and RNA processing The occupancy \({n}_{{{{{{\rm{ps}}}}}}}\) of the TSS of the active rDNA by Pol I follows the kinetic equation $$\frac{d}{{dt}}{n}_{{{{{{\rm{ps}}}}}}}={k}_{{{{{{\rm{on}}}}}}}\rho \left(1-{n}_{{{{{{\rm{ps}}}}}}}\right)-{k}_{{{{{{\rm{off}}}}}}}{n}_{{{{{{\rm{ps}}}}}}}-{k}_{{{{{{\rm{e}}}}}}}{n}_{{{{{{\rm{ps}}}}}}}.$$ (5) Equation (5) suggests that the occupancy \({n}_{{{{{{\rm{ps}}}}}}}\) changes due to the binding of Pol I from the FC (the first term), the unbinding of Pol I…

Continue Reading Nascent ribosomal RNA act as surfactant that suppresses growth of fibrillar centers in nucleolus

Expression profiles of circRNAs and biomarkers for COPD

Introduction Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory lung disease featured by airflow obstruction with high prevalence, morbidity, and mortality. It is reported that COPD is the third leading cause of death globally at present, and the incidence of COPD in adults over 40 years is more than…

Continue Reading Expression profiles of circRNAs and biomarkers for COPD

The DNA-binding induced (de)AMPylation activity of a Coxiella burnetii Fic enzyme targets Histone H3

Statistics and reproducibility Anti-AMP IP for LC-MS/MS analysis was performed in three independent biological replicates (n = 3). TSA assay data represents technical triplicates. Time-resolved (de)AMPylation analyzed by LC-MS was performed as biological triplicates. CD measurements were performed in technical triplicates. Anisotropy data is shown as technical triplicates. Anisotropy measurements were repeated…

Continue Reading The DNA-binding induced (de)AMPylation activity of a Coxiella burnetii Fic enzyme targets Histone H3

DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle

Overview of this study In this study, we measured the DNA methylome from mouse liver and skeletal muscle, integrated the data with the transcriptome and proteome of these mouse tissues22,23, and examined how tissue-dominant protein and gene expression were associated with DNA hypomethylation (Fig. 1). In this study, we measured DNA…

Continue Reading DNA hypomethylation characterizes genes encoding tissue-dominant functional proteins in liver and skeletal muscle

Both chimpanzee adenovirus-vectored and DNA vaccines induced long-term immunity against Nipah virus infection

Ethics statement The animal experiments were approved by the Animal Ethics Committee of the Wuhan Institute of Virology, Chinese Academy of Sciences (approval number: WIVA21202104). All animal experiments involving NiV were executed in the animal biosafety level 4 (ABSL-4) facility at the National Biosafety Laboratory (Wuhan), Chinese Academy of Sciences….

Continue Reading Both chimpanzee adenovirus-vectored and DNA vaccines induced long-term immunity against Nipah virus infection

Single-cell transcriptomics reveals the brain evolution of web-building spiders

Animals for single-cell sequencing Adult samples of the aerial web-building spider (Hylyphantes graminicola) were collected from Anci district, Langfang, Hebei, China (39° 31.90’ N, 116° 38.15’ E) between September and October 2020. Collected spiders used for brain dissection were housed individually in a glass tube (Φ12 mm × 80 mm) at temperature- and humidity-controlled condition (24–26 °C and 50–60%…

Continue Reading Single-cell transcriptomics reveals the brain evolution of web-building spiders

Genomic disturbance of vitellogenin 2 (vtg2) leads to vitellin membrane deficiencies and significant mortalities at early stages of embryonic development in zebrafish (Danio rerio)

A large deletion mutation of 2811 bp of gDNA was introduced into zebrafish vtg2 via CRISPR/Cas9 genome editing. A schematic representation of the general strategy for CRISPR target design and application is given in Fig. 1A–C. The introduced deletion involved 1692 bp of the vtg2 transcript, encoding 564 aa of its respective protein, and…

Continue Reading Genomic disturbance of vitellogenin 2 (vtg2) leads to vitellin membrane deficiencies and significant mortalities at early stages of embryonic development in zebrafish (Danio rerio)

Reduction of retinal ganglion cell death in mouse models of familial dysautonomia using AAV-mediated gene therapy and splicing modulators

Animals All mice were housed in the AALAC-accredited Animal Resource Center at Montana State University. All animal use protocols were approved by the Montana State University Institutional Animal Care and Use Committee (IACUC) (protocol No. 2020-15-IA; Bozeman, MT). The study fulfilled the ARRIVE guidelines, and all experiments complied with relevant…

Continue Reading Reduction of retinal ganglion cell death in mouse models of familial dysautonomia using AAV-mediated gene therapy and splicing modulators

Proteomics uncovers molecular features for relapse risk stratification in patients with diffuse large B-cell lymphoma

Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoid cancer, constituting approximately one third of all cases [1]. Although immunochemotherapy cures ~60–75% of patients, a significant proportion of patients still experience relapse [2, 3]. Relapsed DLBCL patients have poor outcomes, with a median overall survival of only 6.3 months…

Continue Reading Proteomics uncovers molecular features for relapse risk stratification in patients with diffuse large B-cell lymphoma

Bioinformatic Analysis of circRNAs in Human ASO

Introduction Arteriosclerosis obliterans (ASO) is a chronic disorder with atherosclerosis involving lower extremity arteries leading to arterial stenosis or occlusion. The incidence continues to increase with age, affecting about 202 million people worldwide to varying degree.1–3 Despite the proposed theories of lipid infiltration, arterial intimal injury, and chronic inflammation, the…

Continue Reading Bioinformatic Analysis of circRNAs in Human ASO

Chromatin compartmentalization regulates the response to DNA damage

Cell culture and treatments DIvA (AsiSI-ER-U2OS)19, AID-DIvA (AID-AsiSI-ER-U2OS)23 and 53BP1-GFP DIvA20 cells were developed in U2OS (ATCC HTB-96) cells and were previously described. Authentication of the U2OS cell line was performed by the provider ATCC, which uses morphology and short tandem repeat profiling to confirm the identity of human cell…

Continue Reading Chromatin compartmentalization regulates the response to DNA damage

Inactive S. aureus Cas9 downregulates alpha-synuclein and reduces mtDNA damage and oxidative stress levels in human stem cell model of Parkinson’s disease

Cloning of CRISPR/sgRNA lentiviral constructs with fluorescent selection markers A tetracycline-inducible promoter (TRE3G) was used to control the expression of S. aureus dCas9 in a lentiviral vector. To facilitate selection of cells by FACS, pHR:TRE3G-SadCas9-2xKRAB-p2a-tdTomato (Addgene ID #209298) was subcloned from a pHR:TRE3G-SadCas9-2xKRAB-p2a-zeo (A gift from Professor Stanley Qi), where zeocin…

Continue Reading Inactive S. aureus Cas9 downregulates alpha-synuclein and reduces mtDNA damage and oxidative stress levels in human stem cell model of Parkinson’s disease

Crohn’s Disease treatment after failure of anti-TNF therapy

Introduction Crohn’s Disease (CD) is a typical group of inflammatory bowel disease, a chronic intestinal disease with an unclear cause that fluctuates between clinical remission and relapse. The disease may affect the entirety of the gastrointestinal tract, frequently manifesting as segmental, asymmetric, and transmural lesions. 21–47% of patients present with…

Continue Reading Crohn’s Disease treatment after failure of anti-TNF therapy

EOGT enables residual Notch signaling in mouse intestinal cells lacking POFUT1

Single cell RNAseq bioinformatics Bioinformatic trajectory analysis of scRNAseq data obtained from Epcam+CD45− C57Bl6/J adult intestinal crypt cells and deposited as GSE188339 was performed as described35. Primers and antibodies Primer sequences are given in Supplementary Table 1 and antibodies are given in Supplementary Table 2. Generation of Chinese hamster ovary…

Continue Reading EOGT enables residual Notch signaling in mouse intestinal cells lacking POFUT1

DNA damage induced by CDK4 and CDK6 blockade triggers anti-tumor immune responses through cGAS-STING pathway

Patients’ tumor tissues and clinical data This study recruited 125 breast cancer patients for immunohistochemical (IHC) analysis and 10 breast cancer patients for RNA-seq analysis from the Affiliated Tumor Hospital of Nantong University. Tumor tissues collected from surgical patients were fixed with formalin and embedded with paraffin and then examined….

Continue Reading DNA damage induced by CDK4 and CDK6 blockade triggers anti-tumor immune responses through cGAS-STING pathway

Direct regulation of the cardiac ryanodine receptor (RyR2) by O-GlcNAcylation | Cardiovascular Diabetology

Human right atrial appendages (RAA) Human RAA were obtained from consenting patients (ethics: LRS/12/01/001/AM17), with or without Type 2 Diabetic Mellitus (T2DM), undergoing on-pump coronary artery bypass graft surgery. Patient characteristics are shown in Table 1. Patients with pre-operative arrhythmia were excluded from the study. Table 1 Patient characteristics Patients were…

Continue Reading Direct regulation of the cardiac ryanodine receptor (RyR2) by O-GlcNAcylation | Cardiovascular Diabetology

LINC01343 targets miR-526b-5p to facilitate the development of hepatocellular carcinoma by upregulating ROBO1

Tissue samples All the enrolled patients provided written informed consent. Patients who had undergone chemotherapy or radiotherapy before surgery were excluded from the study. Surgical procedures were performed to obtain 40 pairs of HCC tumor and adjacent non-tumor tissue specimens from patients admitted to the First Affiliated Hospital of Chengdu…

Continue Reading LINC01343 targets miR-526b-5p to facilitate the development of hepatocellular carcinoma by upregulating ROBO1

Immunoglobulin superfamily member 3 is required for the vagal neural crest cell migration and enteric neuronal network organization

Immunohistochemistry The tissue sections were processed using the TSA kit (Perkin Elmer) according to the manufacturer’s instructions. The deparaffinization of fixed tissues were performed by immersing the slides in tissue clear and rehydrated with graded ethanol (100–70%) and water. The heat-induced antigen retrieval was performed using citrate buffer (1.8 mM…

Continue Reading Immunoglobulin superfamily member 3 is required for the vagal neural crest cell migration and enteric neuronal network organization

Differentially expressed circRNAs in peripheral blood samples as potential biomarkers and therapeutic targets for acute angle-closure glaucoma

Study approval and patient consent The study protocol was approved by the Ethics Committee of Qinghai Provincial People’s Hospital (approval number: 2023-141) and conducted in accordance with the ethical principles for medical research involving human subjects described in the Declaration of Helsinki in addition to relevant Chinese laws and institutional…

Continue Reading Differentially expressed circRNAs in peripheral blood samples as potential biomarkers and therapeutic targets for acute angle-closure glaucoma

Molecular characterization and functional implications on mouse peripheral blood mononuclear cells of annexin proteins from Echinococcus granulosus sensu lato | Parasites & Vectors

Parasites and animals PSCs were collected from hydatid cysts isolated from the liver of sheep infected with E. granulosus s.l. from a slaughterhouse in Sichuan province, China. The PSCs and cyst walls were separated and treated as described in previous reports [22]. The viability and molecular genotyping of PSCs were…

Continue Reading Molecular characterization and functional implications on mouse peripheral blood mononuclear cells of annexin proteins from Echinococcus granulosus sensu lato | Parasites & Vectors

The Therapeutic Effects of MUC1-C shRNA@Fe3O4 Magnetic Nanoparticles i

Introduction Breast cancer (BC) is a malignant tumor originating from the epithelial tissue of the breast and is the most common malignancy in women.1 It is estimated that by 2040, there will be 3,000,000 new cases of BC and 100,000 deaths worldwide. Triple-negative breast cancer (TNBC), which accounts for 15–20%…

Continue Reading The Therapeutic Effects of MUC1-C shRNA@Fe3O4 Magnetic Nanoparticles i

Filter, Plot, and Explore with Seurat in RStudio

First thing’s first, we need to load the packages we will be using. In order to use any functions of a package, we must first call the library of that package. In your console (likely in the lower left corner of your RStudio window), run the following lines of code…

Continue Reading Filter, Plot, and Explore with Seurat in RStudio

Assembloid CRISPR screens reveal impact of disease genes in human neurodevelopment

Culture of hiPS cells The hiPS cell lines used in this study were validated as previously described51. The SEC61B-mEGFP hiPS cell line (AICS-0059 cl.36) was developed at the Allen Institute for Cell Science (www.allencell.org/cell-catalog.html) and is distributed through Coriell43. The CAG::Cas9 cell line was genetically engineered in the laboratory (the…

Continue Reading Assembloid CRISPR screens reveal impact of disease genes in human neurodevelopment

KCNQ potassium channels modulate Wnt activity in gastro-oesophageal adenocarcinomas

Introduction The KCNQ (potassium voltage-gated channel subfamily Q) family of ion channels encode potassium transporters (1). KCNQ proteins typically repolarise the plasma membrane of a cell after depolarisation by allowing the export of potassium ions, and are therefore involved in wide-ranging biological functions including cardiac action potentials (2), neural excitability…

Continue Reading KCNQ potassium channels modulate Wnt activity in gastro-oesophageal adenocarcinomas

Schistosoma japonicum EKLF/KLF1 is a potential immune target to tackle schistosomiasis | Parasites & Vectors

Animals and parasites Snails infected with S. japonicum (Oncomelania hupensis) were provided by the Jiangxi Provincial Institute of Parasitic Diseases, Jiangxi, China. Freshly released cercariae stimulated by light were immediately harvested. Six-week-old pathogen-free male BALB/c mice and New Zealand white rabbits (both from Vital River Laboratory Animal Technology Co., Beijing,…

Continue Reading Schistosoma japonicum EKLF/KLF1 is a potential immune target to tackle schistosomiasis | Parasites & Vectors

ATAC-seq troubleshoot – Just Noise

ATAC-seq troubleshoot – Just Noise 0 Hi everyone, I have been processing paired end 150bp ATAC-seq data, but failing to get peaks at known promoters, the data just looks like noise through out. Started with QC, where reads had poly(G) towards their ends, this is known to happen in NovaSeq…

Continue Reading ATAC-seq troubleshoot – Just Noise

Upregulation of WDR6 drives hepatic de novo lipogenesis in insulin resistance in mice

WDR6 is upregulated in response to insulin during insulin resistance We created an IR mouse model by feeding animals a HFD for 6 weeks20. Insulin injection was then performed (Fig. 1a). The phosphorylation of AKT, a key readout of the insulin signalling pathway21, showed decreased response to insulin, indicating resistance…

Continue Reading Upregulation of WDR6 drives hepatic de novo lipogenesis in insulin resistance in mice

Organisation of the orthobunyavirus tripodal spike and the structural changes induced by low pH and K+ during entry

An improved STA of the BUNV GP permits modelling of the Gc and Gn hetero-hexameric arrangement To determine the arrangement of Gn and Gc in the BUNV spike by cryo-EM, WT BUNV was concentrated and purified as previously described5,25 (Supplementary Fig. 1). Purified virions (in a pH 7.3/no K+ buffer) were…

Continue Reading Organisation of the orthobunyavirus tripodal spike and the structural changes induced by low pH and K+ during entry

Cell-free chromatin immunoprecipitation to detect molecular pathways in heart transplantation

Abstract Existing monitoring approaches in heart transplantation lack the sensitivity to provide deep molecular assessments to guide management, or require endomyocardial biopsy, an invasive and blind procedure that lacks the precision to reliably obtain biopsy samples from diseased sites. This study examined plasma cell-free DNA chromatin immunoprecipitation sequencing (cfChIP-seq) as…

Continue Reading Cell-free chromatin immunoprecipitation to detect molecular pathways in heart transplantation

MAST4 promotes primary ciliary resorption through phosphorylation of Tctex-1

Introduction The primary cilium (9 + 0 architecture) is a microtubule-based immotile sensory organelle in vertebrates (Tucker et al, 1979). Enormous progress has been made in the past several decades concerning our understanding of the structure and functions of the primary cilium (Sung & Leroux, 2013). The subdomain between the…

Continue Reading MAST4 promotes primary ciliary resorption through phosphorylation of Tctex-1

Ferroptosis-related factors in the substantia nigra are associated with Parkinson’s disease

Cell types and their proportion in the SN of PD patients Based on the cell annotation results on the Single Cell Portal uploaded by Prof. Macosko’s group, cells were extracted and classified into different types from human SN samples (Fig. 1A). After 135,344 cells were extracted from 34 PD samples and…

Continue Reading Ferroptosis-related factors in the substantia nigra are associated with Parkinson’s disease

Establishing a Stable Recombinant Protein Production Cell Line Using CRISPR-Cas9 Mediated Genome Editing of HEK293 Cells

Recombinant proteins are effective therapeutics for many diseases and thus their demand has increased over the past few decades. Today, most recombinant proteins are produced in bacteria and non-mammalian cells hosts such as Chinese Hamster Ovary (CHO) due to their high production efficiencies. Despite this, issues pertaining to the utilization…

Continue Reading Establishing a Stable Recombinant Protein Production Cell Line Using CRISPR-Cas9 Mediated Genome Editing of HEK293 Cells

RNA-sequencing and bioinformatics analysis | COPD

Introduction COPD, a common preventable and treatable disease characterized by persistent airflow limitation and respiratory symptoms, is associated with exposure to harmful environments. COPD is currently the third leading cause of death globally. The high incidence and mortality of COPD, which seriously threaten human health, represent a public health problem…

Continue Reading RNA-sequencing and bioinformatics analysis | COPD

Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa

Mice All animal husbandry and experiments were approved by the Caltech Institutional Animal Care and Use Committee (IACUC, protocol #1646). The EED mouse model was established following the previously published protocol9 with slight adaptations. On day 1 of the experiment, just-weaned, specific pathogen-free (SPF) C57BL/6 J male mice were received from…

Continue Reading Quantitative whole-tissue 3D imaging reveals bacteria in close association with mouse jejunum mucosa

SUMOylation of SMAD4 by PIAS1 in Conjunction with Vimentin Upregulation Promotes Migration Potential in Non-Small Cell Lung Cancer

1. Introduction Lung cancer is the most common cancer globally, with 2.21 million cases in 2020 and over 1.8 million deaths from lung cancer, making it the most common cause of cancer-related deaths [1]. In China, the estimated age-standardized incidence rate of lung cancer is as high as 34.8 per…

Continue Reading SUMOylation of SMAD4 by PIAS1 in Conjunction with Vimentin Upregulation Promotes Migration Potential in Non-Small Cell Lung Cancer

A G1528C Hadha knock-in mouse model recapitulates aspects of human clinical phenotypes for long-chain 3-hydroxyacyl-CoA dehydrogenase deficiency

All animal procedures were reviewed and approved by the OHSU IACUC (eIACUC #B11243). All experiments were performed in accordance with AAALAC and ARRIVE guidelines. Age, sex, and N of the mice for each experiment can be found in Supplementary Data 1. Mouse creation Mice were created through Cyagen Biosciences (Santa Clara,…

Continue Reading A G1528C Hadha knock-in mouse model recapitulates aspects of human clinical phenotypes for long-chain 3-hydroxyacyl-CoA dehydrogenase deficiency

Identification and functional validation of SRC and RAPGEF1 as new direct targets of miR-203, involved in regulation of epidermal homeostasis

Keratinocyte and fibroblast cultures Normal human skin was obtained from surgical residues of breast reduction surgery, with the patients’ written informed consent in accordance with the Helsinki Declaration and with Article L. 1243-4 of the French Code of Public Health. Patients’ written informed consents were collected and kept by the…

Continue Reading Identification and functional validation of SRC and RAPGEF1 as new direct targets of miR-203, involved in regulation of epidermal homeostasis

The H3K27ac track in the human genome browser

The H3K27ac track in the human genome browser (genome.ucsc.edu) shows experimentally measured levels of histone acetylation. Specifically, this data measures acetylation on one lysine (K27) on one histone subunit (H3) at all locations across the genome. This histone modification is typically found in promoter and enhancer regions of genes: high…

Continue Reading The H3K27ac track in the human genome browser

Non-cell-autonomous cancer progression from chromosomal instability

Cell culture IMR90, 4T1, CT26, RAW264.7 and B16F10 cell lines were purchased from the American Type Culture Collection and cultured in MEM (IMR90), DMEM (B16F10, RAW264.7) or RPMI (4T1, IMR90, CT26) supplemented with 10% FBS in the presence of penicillin (50 U ml−1) and streptomycin (50 μg ml−1). All cells were found to be…

Continue Reading Non-cell-autonomous cancer progression from chromosomal instability

CircRNA-CIRH1A Promotes the Development of Osteosarcoma by Regulating PI3K/AKT and JAK2/STAT3 Signaling Pathways

Tissue Collection The study was approved by the Medical Ethics Committee at the Fuyang Traditional Chinese Medicine Orthopedics Hospital (2019-F027). OS tumor tissues and adjacent normal tissues were collected from 40 patients diagnosed with OS at the Fuyang Traditional Chinese Medicine Orthopedics Hospital from June 2018 to Dec 2019. Patient…

Continue Reading CircRNA-CIRH1A Promotes the Development of Osteosarcoma by Regulating PI3K/AKT and JAK2/STAT3 Signaling Pathways

Cancers | Free Full-Text | High G9a Expression in DLBCL and Its Inhibition by Niclosamide to Induce Autophagy as a Therapeutic Approach

1. Introduction Diffuse large B-cell lymphoma (DLBCL) is an aggressive malignant lymphoid neoplasm, which accounts for 40% of all malignant lymphoid neoplasms and includes morphologically and molecularly heterogeneous disease subtypes [1,2]. According to gene expression profiling, different forms of DLBCL are subdivided into germinal center B-cell-like (GCB-DLBCL) and activated B-cell-like…

Continue Reading Cancers | Free Full-Text | High G9a Expression in DLBCL and Its Inhibition by Niclosamide to Induce Autophagy as a Therapeutic Approach

Ulcerative Colitis Treatment by CLP loaded with NLRP3 siRNA

Introduction Since the 20th century, tThe incidence of ulcerative colitis (UC) has been increasing over time, negatively affecting peoples’ health.1,2 UC is a multifactorial induced inflammatory bowel disease (IBD) characterized by chronic recurrent and remitting mucosal inflammation.3,4 It originates in the rectum and then extends to the proximal segments of…

Continue Reading Ulcerative Colitis Treatment by CLP loaded with NLRP3 siRNA

Platelet factors attenuate inflammation and rescue cognition in ageing

Animal models The C57BL/6 mouse line was used for all of the experiments (The Jackson Laboratory and National Institutes of Aging). Homozygous Pf4-KO mice were previously generated and characterized as described48. Pf4-KO mice were a gift from M. Anna Kowalska. Heterozygous mice were bred to generate Pf4-KO and WT littermate…

Continue Reading Platelet factors attenuate inflammation and rescue cognition in ageing

Taraxasterol suppresses the proliferation and tumor growth of androgen-independent prostate cancer cells through the FGFR2-PI3K/AKT signaling pathway

All experimental protocols were approved by Dali University. All methods were performed in accordance with relevant guidelines and regulations. Reagents and chemicals MEM medium, RPMI-1640 medium, fetal bovine serum (FBS), phosphate-buffered saline (PBS), and penicillin–streptomycin (Pen Strep) were purchased from Biological Industries (Israel). CCK-8 reagent was purchased from Proteintech (Wuhan,…

Continue Reading Taraxasterol suppresses the proliferation and tumor growth of androgen-independent prostate cancer cells through the FGFR2-PI3K/AKT signaling pathway

Evolutionary genomics of camouflage innovation in the orchid mantis

Sample collection Captive breeding individuals of H. coronatus (Mantodea, Hymenopodidae) hatched from the same ootheca that was collected from the Xishuangbanna rainforest, Yunnan Province, China in 2018. Individuals of D. lobata (Mantodea, Deroplatyidae) were collected from a captive breeding center in Beijing, China in 2018. All individuals were housed in semitransparent…

Continue Reading Evolutionary genomics of camouflage innovation in the orchid mantis

LncRNA FENDRR suppresses melanoma growth

Introduction Cutaneous melanoma is a kind of highly aggressive and metastatic cancer.1 It only occurs in 5% of all skin cancers but causes more than 75% of deaths.2,3 Melanoma can be cured by surgical removal at an early stage.4 However, when the disease progresses to an advanced stage (stage IV),…

Continue Reading LncRNA FENDRR suppresses melanoma growth

Characterizing the role of Phlda3 in the development of acute toxicity and malignant transformation of hematopoietic cells induced by total-body irradiation in mice

Mouse strains and procedures All animal procedures for this study were approved by the Institutional Animal Care and Use Committee (IACUC) at Duke University (protocol number A215-20-11 was approved on November 9, 2020). All methods were performed in accordance with the relevant guidelines and regulations. The study is reported in…

Continue Reading Characterizing the role of Phlda3 in the development of acute toxicity and malignant transformation of hematopoietic cells induced by total-body irradiation in mice

Specific detection of tau seeding activity in Alzheimer’s disease using rationally designed biosensor cells | Molecular Neurodegeneration

Zempel H, Luedtke J, Kumar Y, Biernat J, Dawson H, Mandelkow E, Mandelkow EM. Amyloid-beta oligomers induce synaptic damage via Tau-dependent microtubule severing by TTLL6 and spastin. EMBO J. 2013;32:2920–37. Article  CAS  PubMed  PubMed Central  Google Scholar  Li C, Gotz J. Somatodendritic accumulation of Tau in Alzheimer’s disease is promoted…

Continue Reading Specific detection of tau seeding activity in Alzheimer’s disease using rationally designed biosensor cells | Molecular Neurodegeneration

Identification of immuno-inflammation-related biomarkers | JIR

Introduction Acute myocardial infarction (AMI) is the sudden irreversible necrosis of heart muscle, which commonly results from atherosclerotic plaque disruption and subsequent interruption of blood flow.1 It is one of the heart diseases with the highest prevalence and incidence and brings enormous health and financial burdens.2 Despite the rapid development…

Continue Reading Identification of immuno-inflammation-related biomarkers | JIR

Transcriptional variation in Babesia gibsoni (Wuhan isolate) between in vivo and in vitro cultures in blood stage | Parasites & Vectors

Morphological observation of continuous in vitro cultured B. gibsoni (Wuhan isolate) Babesia gibsoni was successfully cultured in vitro in 20% serum. After splitting, parasitemia reached 10% ± 1.5% on day 3 (Fig. 1A). Fig. 1 Changes in parasitemia and morphology of in vitro cultured B. gibsoni (Wuhan isolate). A Changes in parasitemia of…

Continue Reading Transcriptional variation in Babesia gibsoni (Wuhan isolate) between in vivo and in vitro cultures in blood stage | Parasites & Vectors

Effects of N-acetylcysteine on CG8005 gene-mediated proliferation and apoptosis of Drosophila S2 embryonic cells

Cell lines Drosophila S2 embryonic cells were obtained from Drosophila Genomics Resource Center. Reagents and instruments The reagents and equipment information used in this study are as follows: DMEM (Gibco, USA), Fetal Bovine Serum (Bioind, Israel), LipofectamineTM2000 (Invitrogen, USA), opti-MEM (Gibco, USA), Small Interfering RNA (Suzhou Gema Gene), N-acetyl-l-cysteine (Shanghai…

Continue Reading Effects of N-acetylcysteine on CG8005 gene-mediated proliferation and apoptosis of Drosophila S2 embryonic cells

Transcriptome sequencing reveals circRNA expression profile in Parkinson’s disease-like mice after aerobic exercise

. 2022 Mar 21;46(3):227-238. doi: 10.55730/1300-0152.2611. eCollection 2022. Affiliations Expand Affiliation 1 The First Affiliated Hospital of Hainan Medical College, Hainan, China. Item in Clipboard Tianlun Fan et al. Turk J Biol. 2022. Show details Display options Display options Format AbstractPubMedPMID . 2022 Mar 21;46(3):227-238. doi: 10.55730/1300-0152.2611. eCollection 2022. Affiliation 1…

Continue Reading Transcriptome sequencing reveals circRNA expression profile in Parkinson’s disease-like mice after aerobic exercise

How can I generate a list of 100 genomic intervals from bam files?

How can I generate a list of 100 genomic intervals from bam files? 1 I want to generate a list of 100 genomic intervals that are 100kb long and in which 50 genomic intervals should overlap some genes such as (GAPDH etc) from the bam file (mapping data). I want…

Continue Reading How can I generate a list of 100 genomic intervals from bam files?

Immune Cell Infiltration and Novel Biomarkers of CAD

Introduction Coronary artery disease (CAD) is a major cause of death and disability worldwide,1 and has been proved to be triggered by the interaction of environmental and genetic risk factors. It is considered to be a systemic, progressive inflammatory disease. The atherosclerotic plaque formed in CAD accumulates chronically in the…

Continue Reading Immune Cell Infiltration and Novel Biomarkers of CAD

RARRES2 regulates lipid metabolic reprogramming to mediate the development of brain metastasis in triple negative breast cancer | Military Medical Research

Tumor samples from patients Biopsies of primary breast tumors and breast tumors that had metastasized to the brain were obtained from patients with TNBC at the National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital of the Chinese Academy of Medical Sciences and Peking Union Medical College. Single-cell RNA sequencing…

Continue Reading RARRES2 regulates lipid metabolic reprogramming to mediate the development of brain metastasis in triple negative breast cancer | Military Medical Research

Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct

Cell culture HCC2429 cells were a kind gift from the Hamon Center for Therapeutic Oncology Research at UT Southwestern Medical Center. The cells were grown in RPMI 1640 medium (Thermo Fisher Scientific, #11875119) with addition of 10% heat-inactivated Fetal Bovine Serum (Thermo Fisher Scientific, #10-438-026) and 1% penicillin—streptomycin (Thermo Fisher…

Continue Reading Molecular features driving condensate formation and gene expression by the BRD4-NUT fusion oncoprotein are overlapping but distinct

Viruses | Free Full-Text | Astragaloside IV Regulates cGAS-STING Signaling Pathway to Alleviate Immunosuppression Caused by PRRSV Infection

Received: 12 June 2023 / Revised: 1 July 2023 / Accepted: 13 July 2023 / Published: 20 July 2023 Round 1 Reviewer 1 Report This manuscript examines the effects of AS-IV treatment of PAMs infected with a strain of PRRSV-2. Specifically, aspects of immune regulation responses are investigated. Specific comments:…

Continue Reading Viruses | Free Full-Text | Astragaloside IV Regulates cGAS-STING Signaling Pathway to Alleviate Immunosuppression Caused by PRRSV Infection

Phenotypic and molecular basis of SIX1 variants linked to non-syndromic deafness and atypical branchio-otic syndrome in South Korea

Clinical phenotypes This study included eight affected patients (three males and five females) from five unrelated families, segregating with SIX1 variants (Fig. 1a). A comprehensive overview of their clinical phenotypes, encompassing both major and minor criteria, is provided in Table 1. All eight individuals (100%) experienced sensorineural hearing loss (SNHL), with…

Continue Reading Phenotypic and molecular basis of SIX1 variants linked to non-syndromic deafness and atypical branchio-otic syndrome in South Korea

Integrated analysis of copy number variation-associated lncRNAs identifies candidates contributing to the etiologies of congenital kidney anomalies

Study design We aimed to investigate the potential contribution of lncRNAs to the pathogenicity of CAKUT associated CNVs. 19 recurrent CAKUT-associated CNVs were identified based on clinical researches of congenital anomalies of the kidney and urinary tracts (CAKUT) cases3,4,12,13 (Table 1). We retrieved lncRNAs located within these genomic regions as candidate…

Continue Reading Integrated analysis of copy number variation-associated lncRNAs identifies candidates contributing to the etiologies of congenital kidney anomalies

HIV-1 promotes ubiquitination of the amyloidogenic C-terminal fragment of APP to support viral replication

Ethics Statement LifeSource Buffy Coat blood obtained from New York blood center was used for isolation of peripheral blood mononuclear cells using Ficoll-Plaque (GE). Ethical approval for the study was obtained from the Institutional Review Board of Northwestern University and all donors provided their written, informed consent. Cell cultures HEK293T…

Continue Reading HIV-1 promotes ubiquitination of the amyloidogenic C-terminal fragment of APP to support viral replication

Circular RNA RSU1 promotes retinal vascular dysfunction by regulating miR-345-3p/TAZ

Patients and samples A total of 103 diabetes mellitus (type 2) patients were recruited according to the criteria from the American Diabetes Association30. Plasma samples were collected from blood of all the patients, and the patients were classified as diabetes mellitus patients without DR (n = 53) and diabetes mellitus patients with…

Continue Reading Circular RNA RSU1 promotes retinal vascular dysfunction by regulating miR-345-3p/TAZ

A framework for individualized splice-switching oligonucleotide therapy

Patients The WGS and clinical data of 235 patients with A-T were provided by the Global A-T Family Data Platform of ATCP. Our access to the data was approved by the Data Access Committee of ATCP. Selected patients with A-T enrolled at the Manton Center for Orphan Disease Research under…

Continue Reading A framework for individualized splice-switching oligonucleotide therapy

Antisense therapy restores fragile X protein production in human cells

(A) Volcano plot of log2FC of RNA levels (FXS vs TD). Statistically significant changes (P value <0.0002) are shown as blue dots (down-regulated) and red dots (up-regulated). Gray dots refer to unchanged RNAs. (See also Dataset S2). (B) Histograms for TPM values for RNAs that are up or downregulated in…

Continue Reading Antisense therapy restores fragile X protein production in human cells

A simple and available measurement of onco-sEV dsDNA to protein ratio as a potential tumor marker | BMC Cancer

Research object In this study, 34 tumor patients treated in Nanjing Drum Tower Hospital from May 2021 to September 2021 were selected. The average age of tumor group was 59 years old, with 25 male and 9 female. There were 13 cancer types in cancer group, including gastric cancer, lung…

Continue Reading A simple and available measurement of onco-sEV dsDNA to protein ratio as a potential tumor marker | BMC Cancer

Mesenchymal stromal cells facilitate resolution of pulmonary fibrosis by miR-29c and miR-129 intercellular transfer

Cell culture hTERT immortalized adipose-derived mesenchymal stem cells (hTERT-MSC, ASC52telo (ATCC® SCRC-4000™)), hTERT-MSCs with Crispr–Cas9 miR-29с knockdown and hTERT-MSCs with Crispr–Cas9 nonsense knockdown (biobank of the Institute for Regenerative Medicine, Lomonosov MSU (human.depo.msu.ru)) were cultured in Advance Stem Cell Basal Medium with Advance Stem Cell Growth Supplement (HyClone). All experiments…

Continue Reading Mesenchymal stromal cells facilitate resolution of pulmonary fibrosis by miR-29c and miR-129 intercellular transfer

SMCHD1 and LRIF1 converge at the FSHD-associated D4Z4 repeat and LRIF1 promoter yet display different modes of action

Somatic loss of LRIF1 or SMCHD1 in control myocytes leads to insufficient DUX4 derepression We have previously shown that SMCHD1 and LRIF1L aid in transcriptional repression of the D4Z4 repeat as short-term depletion of either LRIF1L or SMCHD1 in muscle cells having a D4Z4 repeat of <20 units on a…

Continue Reading SMCHD1 and LRIF1 converge at the FSHD-associated D4Z4 repeat and LRIF1 promoter yet display different modes of action

Glutamine synthetase (GS) knockout (KO) using CRISPR/Cpf1 diversely enhances selection efficiency of CHO cells expressing therapeutic antibodies

Identification and expression of GS genes in CHO cells Database analysis (see Supplementary information 1 indicated that the endogenous GS genes in CHO-K1 include two genes on chromosome 5 (GS5) and chromosome 1 (GS1), for which in-house RNAseq data and previous publication, listed in Supplementary Table S1, showed high and low…

Continue Reading Glutamine synthetase (GS) knockout (KO) using CRISPR/Cpf1 diversely enhances selection efficiency of CHO cells expressing therapeutic antibodies

Circular RNA FEACR inhibits ferroptosis and alleviates myocardial ischemia/reperfusion injury by interacting with NAMPT | Journal of Biomedical Science

Identification and characterization of cardiac ferroptosis-associated circRNAs The death of terminally differentiated cardiomyocytes is a crucial pathogenic factor in the development of heart injury. Ferroptosis has been proven to be an important contributor to some cardiac problems, including I/R injury [3, 12, 13]. To explore the conditions under which different…

Continue Reading Circular RNA FEACR inhibits ferroptosis and alleviates myocardial ischemia/reperfusion injury by interacting with NAMPT | Journal of Biomedical Science

Engineered circular guide RNAs boost CRISPR/Cas12a- and CRISPR/Cas13d-based DNA and RNA editing | Genome Biology

Plasmid construction For U6+27 gRNA-expressing constructs, the DNA sequences including the hU6+27 promoter, a gRNA scaffold, and a gRNA insert site were synthesized and cloned into the pBluSKM vector. For Pre gRNA-expressing constructs, a second gRNA scaffold was inserted downstream of the gRNA insert site in the U6+27 gRNA-expressing constructs….

Continue Reading Engineered circular guide RNAs boost CRISPR/Cas12a- and CRISPR/Cas13d-based DNA and RNA editing | Genome Biology

The effect of inhibition of receptor tyrosine kinase AXL on DNA damage response in ovarian cancer

Cell lines and culture conditions All media and supplements were purchased from Gibco unless otherwise stated. OC cell line SKOV3, OVCA429, CH1 and NSCLC cell line H1299 and A549 were maintained using Dulbecco’s Modified Eagle Medium (DMEM) media supplemented with 10% (v/v) foetal bovine serum (FBS). OC cell lines HeyA8,…

Continue Reading The effect of inhibition of receptor tyrosine kinase AXL on DNA damage response in ovarian cancer

ICML 2023 Meeting: CFT7455 in NHL Preclinical Presentation

CFT7455: A novel IKZF1/3 degrader, demonstrates potent anti-tumor activity in peripheral and CNS models of non-Hodgkin’s lymphoma as a single agent or in combination with clinically approved agents Samantha Perino, R. Jason Kirby, Roman V. Agafonov, Prasoon Chaturvedi, Scott J. Eron, Andrew Good, June A. Hart, Minsheng…

Continue Reading ICML 2023 Meeting: CFT7455 in NHL Preclinical Presentation

IJMS | Free Full-Text | Analysis of CircRNA Expression in Peripheral Blood of Holstein Cows in Response to Heat Stress

1. Introduction With the global temperature rise, the dairy industry is confronted with a significant challenge brought about by severely damaging impacts of heat stress. Heat stress increases mortality rates and threatens the health of livestock, especially in highly productive and intolerant species. The increase in ambient temperature–humidity index (THI)…

Continue Reading IJMS | Free Full-Text | Analysis of CircRNA Expression in Peripheral Blood of Holstein Cows in Response to Heat Stress

Combination of CEACAM5, EpCAM and CK19 gene expressions in mediastinal lymph node micrometastasis is a prognostic factor for non-small cell lung cancer | Journal of Cardiothoracic Surgery

Patients From July 2013 through July 2014, 32 consecutive patients with operable NSCLC, according to NCCN guidelines stage 2B and/or lower, and with no prior neoadjuvant treatment regimens were enrolled in the study. Before the operation, every patient underwent a positron emission tomography (PET) scan and brain magnetic resonance imaging…

Continue Reading Combination of CEACAM5, EpCAM and CK19 gene expressions in mediastinal lymph node micrometastasis is a prognostic factor for non-small cell lung cancer | Journal of Cardiothoracic Surgery

Inhalable CAR-T cell-derived exosomes as paclitaxel carriers for treating lung cancer | Journal of Translational Medicine

Cells and plasmids HEK 293 T and LLC cells (ATCC) were cultured in Dulbecco’s Modified Eagle’s Medium (DMEM, Thermo Fisher Scientific) containing 10% FBS (Gibco, USA) and 1% penicillin–streptomycin (Invitrogen) at 37 °C in a 5% CO2 environment. Stbl3 and DH5α competent cells were used for plasmid transformation. The pCDH-CMV-MCS-EF1-GFP-Puro vector (cat….

Continue Reading Inhalable CAR-T cell-derived exosomes as paclitaxel carriers for treating lung cancer | Journal of Translational Medicine