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Tag: HeLa
Altered quorum sensing and physiology of Staphylococcus aureus during spaceflight detected by multi-omics data analysis
CDC. (ed CDC) (U.S. Department of Health and Human Services, CDC; 2019, Atlanta, GA, 2019). Krismer, B., Weidenmaier, C., Zipperer, A. & Peschel, A. The commensal lifestyle of Staphylococcus aureus and its interactions with the nasal microbiota. Nat. Rev. Microbiol. 15, 675–687 (2017). Article CAS PubMed Google Scholar Somerville, G….
Human RAD52 stimulates the RAD51-mediated homology search
Introduction Homologous recombination (HR) is an evolutionarily conserved process that plays a pivotal role in genome stability, diversity, and plasticity. HR is indeed a key repair pathway able to faithfully repair DNA damages including double-strand breaks (DSBs) and DNA gaps by copying the error-free information from the template DNA normally…
IJMS | Free Full-Text | The Link of mRNA and rRNA Transcription by PUF60/FIR through TFIIH/P62 as a Novel Therapeutic Target for Cancer
This study demonstrated the novel coactivation mechanism of mRNA and rRNA underlying the role of FIR and its splicing variant, FIRΔexon2. Because FIR is immunoprecipitated with P89 and P62 of TFIIH [7], FIR potentially affects RNAPII-mediated transcription via TFIIH. As expected, FIR affected the mRNA expression of various cancer-related genes…
Why are HEK293 cells used for transfection?
What is one example of ongoing gene therapy can be used in keratoplasty?5 answersGene therapy in ophthalmology has shown potential for use in keratoplasty. The cornea is an ideal target for gene therapy due to its accessibility, low volume, and special immunological status. Studies have focused on improving gene transfer…
A Step Forward In Vaccine Technology: Exploring The Effects Of N1-methylpseudouridine In MRNA Translation
In a recent study published in Nature, a group of researchers explored how the incorporation of N1-methylpseudouridine (1-methylΨ) into messenger ribonucleic acids (mRNAs) affects ribosomal frameshifting and the overall fidelity of mRNA translation. Study: N1-methylpseudouridylation of mRNA causes +1 ribosomal frameshifting. Image Credit: MattL_Images/Shutterstock.com Background Therapeutic in vitro-transcribed (IVT) mRNAs,…
Whole Genome Amplification (WGA) Industry on Track to Surpass US$ 5.5 Billion Mark by 2033-FMI Report
Whole genome amplification industry value is anticipated to surpass US$ 5.5 Billion by the end of 2033, according to Future Market Insights (FMI) in its market analysis, as the demand for WGA in forensics and the study of genetic disorders is on the rise. Whole genome amplification sales are anticipated…
Noncoding mutations cause super-enhancer retargeting resulting in protein synthesis dysregulation during B cell lymphoma progression
B cells undergo a series of programmed genomic alterations that enable the immunoglobulin light and heavy chain loci to generate high-affinity antibodies against invading pathogens. First, B cells undergo variability, diversity and joining (VDJ) recombination in the bone marrow with subsequent somatic hypermutation (SHM) and class switch recombination (CSR) occurring…
Creating a Variant containing FASTA for proteomics search from VCF and genomic FASTA
Creating a Variant containing FASTA for proteomics search from VCF and genomic FASTA 0 Dear Biostar Community I’m currently trying to generate a protein FASTA containing all known variants from HeLa (from Cosmic CellLinesProject) for variant detection in proteomics measurements. For this, I’ve downloaded the variants file (VCF) and the…
Molecular detection and whole genome sequencing of Pectobacterium and Dickeya, the casual agents of soft rot disease in lettuce
Azadmanesh S, Marefat A (2013) and Kayhan Azadmanesh. Detection of Pectobacteria causal agents of potato soft rot in north-western provinces of Iran. J Plant Pathol Microbiol 4(1) Babadoost M (1990) Bacterial soft rot of vegetables, fruits and ornamentals. Rep Plant Dis 943:7 Google Scholar Ben Fekih I, Zhang C, Li…
Detection of cellular traction forces via the force-triggered Cas12a-mediated catalytic cleavage of a fluorogenic reporter strand
Orr, A. W., Helmke, B. P., Blackman, B. R. & Schwartz, M. A. Mechanisms of mechanotransduction. Dev. Cell 10, 11–20 (2006). Article CAS PubMed Google Scholar Zhang, Y. et al. Platelet integrins exhibit anisotropic mechanosensing and harness piconewton forces to mediate platelet aggregation. Proc. Natl Acad. Sci. USA 115, 325–330…
Whole genome sequencing in high-grade cervical intraepitheli… : Medicine
1. Introduction Cervical cancer (CC) is the third most common cancer in women worldwide and has a high mortality rate among women. In 2008, CC was responsible for 275,000 deaths, thereby being the fourth leading cause of cancer death in females worldwide.[1,2] In China, CC is the second most…
Whole Genome Amplification (WGA) Market on Track to Exceed US$ 5.5 Billion by 2033-FMI Projection
Whole genome amplification market value is anticipated to surpass US$ 5.5 Billion by the end of 2033, according to Future Market Insights (FMI) in its market analysis, as the demand for WGA in forensics and the study of genetic disorders is on the rise. Whole genome amplification sales are anticipated to…
Preparation and in vitro Activity of Anti-EpCAM Immunotoxin
Preparation and in vitro Activity of Anti-EpCAM Immunotoxin LIU Yu-ping1,DENG Chang-ping2,MA Xing-yuan2,LIU Qiu-li1,BAO Wen1,ZHENG Wen-yun1,**() 1 Shanghai Key Laboratory…
How black woman’s DNA helped cancer treatments and Covid vaccines | UK News
Henrietta Lacks died from an aggressive form of cervical cancer in 1951 (Picture: AP/BBC Picture Archives) The DNA of a black woman which helped create the Covid vaccine and is considered ‘the mother of modern medicine’ is ‘finally getting the recognition deserved’. Henrietta Lacks, from Virginia, US, was diagnosed with…
Transgenic expression in zebrafish embryos with an intact chorion by electroporation and microinjection
Biotechnol Rep (Amst). 2023 Dec; 40: e00814. Nusrat Tazin aDepartment of Electrical and Computer Engineering, University of Utah, Salt Lake City, UT, USA Christopher Jordon Lambert bDepartment of Mechanical Engineering, University of Utah, Salt Lake City, Utah, USA Raheel Samuel bDepartment of Mechanical Engineering, University of Utah, Salt Lake City,…
Visualization and Quantification of Endogenous Intra-Organelle Protein Interactions at ER-Mitochondria Contact Sites by Proximity Ligation Assays
The need for new approaches to study membrane contact sites (MCSs) has grown due to increasing interest in studying these cellular structures and their components. Here, we present a protocol that integrates previously available microscopy technologies to identify and quantify intra-organelle and inter-organelle protein complexes that reside at MCSs. Our…
Identification of CCZ1 as an essential lysosomal trafficking regulator in Marburg and Ebola virus infections
Cells and viruses Haploid mSCs AN3–12 are a feeder independent clonal derivative of HMSc2 isolated from mice oocyte and maintained at IMBA52. The AN3–12 library and knocked out cells used for the haploid screening was obtained from IMBA (Austria)14,52. AN3–12 cells were validated by STR analysis. Haploid mES cells were…
HOXC-AS3 as an Oncological Biomarker and Therapeutic Target
1Department of Gastrointestinal Surgery, The Second Affiliated Hospital of Nanchang University, Nanchang, Jiangxi, 330008, People’s Republic of China; 2Department of General Surgery, Jiujiang Hospital of Traditional Chinese Medicine, Jiujiang, Jiangxi, 332007, People’s Republic of China; 3Queen Mary School, Nanchang University, Nanchang, Jiangxi, 330038, People’s Republic of China Correspondence: Hongliang Luo,…
Passive diffusion accounts for the majority of intracellular nanovesicle transport
Introduction Trafficking of proteins, lipids, and other molecules between cellular compartments is carried out by vesicular carriers. Material destined for transfer is packaged into a small trafficking vesicle at the donor compartment; the vesicle must then travel to its destination, before fusing with the target compartment to deliver the material…
Clinical Microfluidic Chip Platform for the Isolation of Versatile Circulating Tumor Cells
The clinical microfluidic chip is an important biomedical analysis technique that simplifies clinical patient blood sample preprocessing and immunofluorescently stains circulating tumor cells (CTCs) in situ on the chip, allowing the rapid detection and identification of a single CTC. This protocol described a method for red tumor cell enumeration, and…
Untold Tales of Scientific Breakthroughs
Overview Introduction to scientific breakthroughs Scientific breakthroughs have revolutionized the way we understand the world and have paved the way for incredible advancements in various fields. These breakthroughs are the result of years of dedicated research, experimentation, and collaboration among scientists from different disciplines. They have not only expanded our…
Genome Engineering Oxford (GEO) Facility
We also are actively involved in developing new gene editing methods and provide opportunities for collaborations on more extensive or challenging uses of CRISPR techniques such as development of new construct designs, application to whole organisms, development and use of pooled genome-wide CRISPR libraries. Services/Equipment available Engineered mammalian and bacterial…
5.docx – Show Cell breakdown in the lungs is a compromising improvement starting from bronchial epithelial cells and is the important driver of unrest
Show Cell breakdown in the lungs is a compromising improvement starting from bronchial epithelial cells and is the important driver of unrest related passing in China1. Over 80% of them are non-little cell breakdown in the lungs (NSCLC) taking into account morphological characteristics. Development, drug treatment and radiotherapy are taken…
1. After measuring the O.D.260 of the genomic DNA and
Transcribed image text: 1. After measuring the O.D.260 of the genomic DNA and RNA samples that you isolated from HeLa and HEK293 cells in lab, you obtain the following values: a. Assuming you did not dilute your sample before taking these measurements, what are the concentrations of DNA and RNA…
The histone acetyl transferases CBP and p300 regulate stress response pathways in synovial fibroblasts at transcriptional and functional levels
Hypoxia, the formation of reactive oxygen species (ROS), and subsequent oxidative stress in synovial tissues are key events in the pathogenesis of RA1. We provide here evidence that CBP and p300 are pivotal regulators of the adaptive response of SF that integrate the cell`s transcriptional and functional regulation of stress…
Rab41-mediated ESCRT machinery repairs membrane rupture by a bacterial toxin in xenophagy
Rab8A and Rab41 are required for xenophagy of GAS For comprehensive screening of Rab GTPases involved in xenophagy against GAS infection, we first knocked down the expression of Rab GTPases in HeLa cells. We examined bacterial survival in cells at 6 h post-infection (hpi) compared with that at 2 hpi because…
Cervical cancer could be diagnosed earlier with new DNA biosensor
Cervical cancer is the fourth most common cancer among women globally. Each year in the United States, about 11,500 new cases of cervical cancer are diagnosed with approximately 4,000 women die of this cancer. In addition, women living with HIV are 6 times more likely to develop cervical cancer compared to women…
Cost-effective DNA methylation profiling by FML-seq
The FML-seq method The protocol for FML-seq comprises only three steps (Fig 1A). First, genomic DNA (gDNA) is digested by a methylation-dependent restriction endonuclease that cuts at a certain distance from the 5-methylcytosine or 5-hydroxymethylcytosine in its motif and leaves a short overhang (10). Second, a master mix is added…
P 005 All data in this figure are presented as mean SD n 3 Downloaded from
PAGE13OF 15Nucleic Acids Research, 2023, Vol. 51, No. 4e24 miR-21-5p, respectively. In both cases, the circRNA cir- cuit showed better performance of duration than the linear RNA circuit with m1(1.5- to 137-fold duration) after ap- proximately 96 h of RNA transfection (Figure6C and D), indicating that our circRNA circuits improved…
Innovative strategies of reprograming immune system cells
Introduction Cancer is well characterized by genomic instability resulting in structural alterations that build up with tumor progression.1,2 A subpopulation of undifferentiated cancer cells, known as cancer stem cells (CSCs) are found within the tumor bulk. These cells are responsible for cancer initiation, recurrence and show therapeutic resistance and these…
ncRNA | Free Full-Text | The Intergenic Type lncRNA (LINC RNA) Faces in Cancer with In Silico Scope and a Directed Lens to LINC00511: A Step toward ncRNA Precision
CRC Upregulated 153-5p HIF-1 activates LINC00511, targeting HIF-1’s 3-UTR and +ve feedback loop [78] Oncogene Human CRC tissues vs. paired adjacent non-tumor and CRC cell lines HT29, LOVO, SW620, SW480 vs. normal colon epithelial FHC cell line and athymic BALB/c nude mice for implantation – HNF4 promotes LINC00511 transcription, interaction…
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…
Henrietta Lacks’ family gets justice on the stolen cells controversy
For what would have been Henrietta Lacks’ 103rd birthday last month, her family settled a lawsuit with Thermo Fisher – a multinational biotech company that had used her cells without seeking consent for several years – who regarded the win as a “fitting day” for justice. While the settlement took…
Wright’s staining for accurate diagnosis of leukemia
Introduction Leukemia, a generic term, encompasses several life threatening malignant disorders that present with incremental amounts of leucocytes in blood and bone marrow. Leukemia cells have the innate ability for migration and invasion.1 Dedifferentiated and malignant leucocytes not only retain the benign leucocytes capacity for cell motility and survival in…
CCDC50, an essential driver involved in tumorigenesis, is a potential severity marker of diffuse large B cell lymphoma
Data collection and bioinformatic analysis GSE10846, GSE19246, GSE32918, GSE50721, GSE64820, and GSE94669, were downloaded from the Gene Expression Omnibus database (www.ncbi.nlm.nih.gov/geo/). DLBCL datasets from the GEPIA (Gene Expression Profiling Interactive Analysis) (gepia.cancer-pku.cn) and the TCGA (The Cancer Genome Atlas) (xenabrowser.net/datapages/) were also used in this study. A total of 284…
The Best Phase 3 Movies In The MCU
Phase Three. The end of the first Marvel saga and where some of its most acclaimed movies lie. Even more characters were introduced, while others received an ending to their stories, with deaths, retirement, mantles being passed, and some still keeping their hero status for future endeavors. THEGAMER VIDEO OF…
CRISPR imaging reveals chromatin fluctuation at the centromere region related to cellular senescence
Plasmid construction For CRISPR imaging, an sgRNA expression vector, pLH-spsgRNA 2 plasmid (Addgene, Watertown, MA, USA), was amplified, and the oligonucleotides targeting α-satellite DNA repeats (sgRNA1-5)33,49 and 5S rDNA34 were inserted into the BbsI site as previously described16. The sgRNA sequences were as follows: sgRNA1: 5′-CTTTTTGTGGAATTTGCAAG-3′ sgRNA2: 5′-GACTTGAAACACTCTTTTTG-3′ sgRNA3: 5′-TGGAGATTTCAGCCGCTTTG-3′…
Suppression of tumor formation in vivo by expression of the JE gene in malignant cells.
Suppression of tumor formation in vivo by expression of the JE gene in malignant cells. Publication , Journal Article Rollins, BJ; Sunday, ME Published in: Mol Cell Biol The early growth response gene JE encodes a monocyte chemoattractant, MCP-1. The JE/MCP-1 protein attracts and stimulates human monocytes and induces monocyte-mediated inhibition…
Q&A: How the Henrietta Lacks settlement challenges biotech’s view on ethics
Pharmaceutical Technology spoke with bioethicist Robert Klitzman on the recent Henrietta Lacks lawsuits. Image Credit: Shutterstock / HappySloth Earlier this month, the family of Henrietta Lacks reached a settlement with the biotech company Thermo Fisher Scientific over the company’s use of Lacks’s “immortal cells”. Lacks was an African American woman…
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…
Translation dysregulation in neurodegenerative diseases: a focus on ALS | Molecular Neurodegeneration
Tandan R, Bradley WG. Amyotrophic lateral sclerosis: part 1. Clinical features, pathology, and ethical issues in management. Annals of Neurology: Official Journal of the American Neurological Association and the Child Neurology Society. 1985;18:271–80. Article CAS Google Scholar Mehta P et al. Prevalence of amyotrophic lateral sclerosis (ALS), United States, 2016….
An electrogenetic interface to program mammalian gene expression by direct current
Key plasmids used in this study Construction details for all vectors are provided in Supplementary Table 1. Key plasmids included (1) a constitutive KEAP1 expression vector (pJH1004, PhCMV-KEAP1-pA) and the corresponding vector containing inverted terminal repeats (ITRs) of Sleeping Beauty (SB) transposase (pJH1054, ITR-PhCMV-KEAP1-P2A-BlastR-pA-ITR) for stable cell line generation; (2)…
ncRNA | Free Full-Text | Crosstalk between Long Non-Coding RNA and Spliceosomal microRNA as a Novel Biomarker for Cancer
3.1.1. HAGLR (HOXD Antisense Growth-Associated Long Non-Coding RNA) HAGLR, known also as HOXD-AS1, is located between the HOXD1 and HOXD3 genes on chromosome 2q31.1 (Figure 1A) and has been reported to play a critical role in the development and progression of different human cancers, including bladder, cervical, colorectal, gastric, ovarian,…
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…
S1 Data –
The biogenesis of ribosomes requires tightly controlled transcription and processing of pre-rRNA which comprises ribosomal RNAs forming the core of large and small ribosomal subunits. Early steps of the pre-rRNA processing and assembly of the ribosomal subunits require a large set of proteins that perform folding and nucleolytic cleavage of…
SURF6 co-localizes with ITS2 part of pre-rRNA in the nucleoli of HeLa cells.
The confocal images of the nuclei stained with anti-SURF6 antibody (A, D, G, J; green) or FISH hybridized with the probes specific to ITS1 (B), ITS2 (E), 18S rRNA (H), 28S rRNA (K) (red). Panels (C, F, I, L)–merged images of SURF6 and FISH confocal sections. Arrows point to the…
Transcription and FACT facilitate the restoration of replication-coupled chromatin assembly defects
Struhl, K. & Segal, E. Determinants of nucleosome positioning. Nat. Struct. Mol. Biol. 20, 267–273 (2013). Article CAS PubMed PubMed Central Google Scholar Chereji, R. V. & Clark, D. J. Major determinants of nucleosome positioning. Biophys. J. 114, 2279–2289 (2018). Article ADS CAS PubMed PubMed Central Google Scholar Morgan, M….
MIT Researchers Capture mRNA Translation With New In Situ Sequencing-Based Spatial Assay
NEW YORK – A new method can capture mRNA that is being translated by ribosomes throughout tissues, with potential to help elucidate much of RNA biology from transcription to degradation. Last week, researchers from MIT and the Broad Institute led by Xiao Wang published a study in Science describing ribosome-bound…
G4access identifies G-quadruplexes and their associations with open chromatin and imprinting control regions
Jiang, C. & Pugh, B. F. Nucleosome positioning and gene regulation: advances through genomics. Nat. Rev. Genet. 10, 161–172 (2009). Article CAS PubMed PubMed Central Google Scholar Fenouil, R. et al. CpG islands and GC content dictate nucleosome depletion in a transcription-independent manner at mammalian promoters. Genome Res. 22, 2399–2408…
The performance of whole genome bisulfite sequencing on DNBSEQ-Tx platform examined by different library preparation strategies
Background: Whole-genome bisulfite sequencing (WGBS) technology can provide comprehensive DNA methylation at a single-base resolution on a genome-wide scale, and is considered to be the gold standard for the detection of 5-methylcytosine (5 mC). However, the International Human Epigenome Consortium propose a full DNA methylome should have at least 30…
Claim that COVID-19 mRNA vaccines contain DNA contaminants based on study of vials of “unknown provenance”; no evidence COVID-19 mRNA vaccines can alter DNA in people
CLAIM DNA in COVID mRNA shots “may have the ability to alter the human genome”; “SV40 has been linked to cancer in humans”; “Regulatory Agencies Knew There Was a Contamination Problem” DETAILS Misleading: While SV40 is known to cause cancer in certain animals like hamsters, epidemiological studies didn’t find an…
ZNF330/NOA36 interacts with HSPA1 and HSPA8 and modulates cell cycle and proliferation in response to heat shock in HEK293 cells | Biology Direct
Cell lines, culture conditions, heat shock treatment and transfections HeLa, HEK293 and 2D12 (a NOA36-knockout HEK293-cell line generated in this work) cells were cultured in Dulbecco’s modified Eagle’s medium supplemented with 10% fetal bovine serum and 100 U/mL penicillin and 100 µg/mL streptomycin at 37 °C in a CO2 incubator. For heat…
Growth Medium 1S – Nordic Biosite
Additional Information This liquid Growth Medium is a complete medium optimized to culture select BPS Bioscience cell lines. Optimized for Use With: CRISPRa (SAM) HeLa Cell Line (BPS Bioscience, #78193), CRISPRa (SAM) HepG2 Cell Line (BPS Bioscience, #78194) Article No BPS-78221 Country Availability SE, FI, DK, NO, IS, EE, LV,…
Cancers | Free Full-Text | mRNA-Lipid Nanoparticle (LNP) Delivery of Humanized EpCAM-CD3 Bispecific Antibody Significantly Blocks Colorectal Cancer Tumor Growth
Author Contributions Conceptualization, L.W., W.B. and V.G.; methodology, Y.H., J.S. (John Sienkiewicz), J.S. (Jinying Sun), H.Z., H.H., S.X., R.B. and L.H.; software, Y.H., J.S. (John Sienkiewicz) and J.S. (Jinying Sun); validation, H.Z. and J.S. (John Sienkiewicz); formal analysis, V.G.; investigation, V.G. and L.W.; resources, L.W.; data curation, Y.H., J.S. (John…
CRISPR-Cas13 guide RNA predictor for transcript depletion
Cite As: Krohannon A, Srivastava M, Rauch S, Srivastava R, Dickinson BC, Janga SC. CASowary: CRISPR-Cas13 guide RNA predictor for transcript depletion. BMC Genomics. 2022;23(1):172. Published 2022 Mar 2. doi:10.1186/s12864-022-08366-2 Abstract: Background: Recent discovery of the gene editing system – CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats) associated proteins (Cas),…
Discovery of two new isoforms of the human DUT gene
Overview of the isoform-specific determination of dUTPase gene expression Our aim was to determine the mRNA expression level of the dUTPase isoforms specifically. First, we investigated the Ensemble, the UniProt, and the NCBI Reference Sequences (RefSeq) databases and also took into account the Consensus CDS (CCDS) project. In the Ensemble…
Streamlined quantitative analysis of histone modification abundance at nucleosome-scale resolution with siQ-ChIP version 2.0
In this section, we derive a simplified expression for the proportionality constant \(\alpha\) that enables quantitative ChIP-seq and we introduce some consequences for track building. This new expression is more intuitive to understand, easier to evaluate, and more accurate to sequencing outcomes than the previous expression. While values derived from…
Full article: The Importance of Being RNA-est: considering RNA-mediated ribosome plasticity
The Ribosome: historical monolith – evolutionary chameleon The ribosome is generally considered a highly conserved ribonucleoprotein complex translating messenger RNA (mRNA) into proteins, a function that makes it essential across all species and domains of life. Composed of ribosomal RNAs (rRNAs) and proteins (r-proteins), and assembled from a small and…
Phase-separated nucleocapsid protein of SARS-CoV-2 suppresses cGAS-DNA recognition by disrupting cGAS-G3BP1 complex
SARS-CoV-2 infection induces mtDNA release and recognition by cGAS Recent studies revealed that SARS-CoV-2 stimulation could cause the accumulation of intracellular and intercellular DNA due to cell fusion, cell death and even tissue damage.17,19,27 To detect SARS-CoV-2-triggered release of DNA during infection, we first detected the cytosolic dsDNA pattern by…
Efficient evolution of human antibodies from general protein language models
Acquiring amino acid substitutions via language model consensus We select amino acid substitutions recommended by a consensus of language models. We take as input a single wild-type sequence x = (x1,…,xN)∈ \(\mathcal{X}\)N, where \(\mathcal{X}\) is the set of amino acids, and N is the sequence length. We also require a set of…
Human CEACAM1 is targeted by a Streptococcus pyogenes adhesin implicated in puerperal sepsis pathogenesis
Ethics Human blood was obtained from healthy donors, approved by the Regional Ethics Committee and Imperial College Healthcare NHS Trust Tissue Bank (Regional Ethics Committee approval no. 17/WA/0161, Imperial College Healthcare Tissue Bank Human Tissue Authority license no. 12275, and Imperial College Research Ethics Committee no. 19IC5166). All samples were…
Judicial Watch: Records Show Funding for EcoHealth/Wuhan Institute Research to Create Coronavirus ‘Mutants’
April 19, 2023 | Judicial Watch (Washington, DC) – Judicial Watch announced today it received 552 pages of records from the U.S. Department of Health and Human Services (HHS) which include the initial grant application and annual reports to the National Institutes of Health (NIH) from EcoHealth Alliance, describing the…
Nanocages developed to deliver small interfering RNAs
Small interfering RNAs (siRNAs) are novel therapeutics that can be used to treat a wide range of diseases. This has led to a growing demand for selective, efficient, and safe ways of delivering siRNA in cells. Now, in a cooperation between the universities of Amsterdam and Leiden in the Netherlands,…
A human metallothionein pseudogene containing AG/CT repetitive elements
Crabtree GR, Kant JA (1982) Organization of the rat γ-fibrinogen gene: alternative mRNA splice patterns produce the γα and γβ (γ′) chains of fibrinogen. Cell 31:159–166 Article PubMed Google Scholar Durnam DM, Palmiter RD (1981) Transcriptional regulation of the mouse metallothionein-I gene by heavy metals. Proc Natl Acad Sci USA…
In vitro kinase assay reveals ADP-heptose-dependent ALPK1 autophosphorylation and altered kinase activity of disease-associated ALPK1 mutants
Cell culture and reagents HEK293 and HeLa cells (American Type Culture Collection) were cultured in Dulbecco’s modified Eagle’s medium (DMEM) supplemented with 10% fetal calf serum, 2 mM GlutaMAX‐1, 100 μg/mL streptomycin and 100 U/mL penicillin (complete growth medium) at 37 °C under 5% CO2. HeLa cells stably expressing GFP-TIFA were previously described8. Cells…
A ferritin-based COVID-19 nanoparticle vaccine that elicits robust, durable, broad-spectrum neutralizing antisera in non-human primates
IgG plasmids Antibody sequences and Fc-tagged ACE2 were cloned into the CMV/R plasmid backbone for expression under a CMV promoter. The antibodies with variable HC/LC were cloned between the CMV promoter and the bGH poly(A) signal sequence of the CMV/R plasmid to facilitate improved protein expression. The variable region was…
Possible frequent multiple mitochondrial DNA copies in a single nucleoid in HeLa cells
Cells Human cervix epitheloid carcinoma HeLa cells (ECACC 93021013; RRID:CVCL_0030) were cultured at 37 °C in Dulbecco′s Modified Eagle′s Medium (DMEM) with 3 mM glutamine, 10% (v/v) fetal calf serum (FCS), 10 mM HEPES, 100 IU/ml penicillin, 100 μg/ml streptomycin, and 5 mM glucose in humidified air with 5% CO2. Human osteosarcoma 143B cells were purchased…
KEGG ORTHOLOGY: K25971
KEGG ORTHOLOGY: K25971 ORTHOLOGY: K25971 Help Entry K25971 KO Symbol A25 Name Orthopoxvirus A-type inclusion protein A25 Pathway Brite KEGG Orthology (KO) [BR:ko00001] 09120 Genetic Information Processing 09125 Information processing in viruses 03268 Virion – Orthopoxvirus K25971 A25; Orthopoxvirus A-type inclusion protein A25 09180 Brite Hierarchies 09185 Viral protein families 03200 Viral proteins K25971 A25; Orthopoxvirus A-type inclusion protein A25Viral…
Uncovering biology by single-cell proteomics
To meet the challenge of sample depletion during preparation, there have been a number of recent advances in what is now a rapidly moving field of study of SCP, with important contributions from several investigators. Earlier work combined capillary electrophoresis (CE) with high-resolution mass spectrometry (HRMS) to analyze proteomes of…
Deep genomic characterization highlights complexities and prognostic markers of pediatric acute myeloid leukemia
FG spectrum in pediatric AML patients A combinatorial approach, including conventional and next-generation sequencing (NGS)-based assays, was employed to profile the FG landscape (see Methods). FG analysis was feasible for 138 patients (94% of the entire cohort, Supplementary Data 1) from whom suitable testing materials were available. The most common FGs…
Conserved Stem II of the Box C/D Motif Is Essential for Nucleolar Localization and Is Required, Along with the 15.5K Protein, for the Hierarchical Assembly of the Box C/D snoRNP: Molecular and Cellular Biology: Vol 22, No 23
The 5′ stem-loop of the U4 snRNA and the box C/D motif of the box C/D snoRNAs can both be folded into a similar stem-internal loop-stem structure that binds the 15.5K protein. The homologous proteins NOP56 and NOP58 and 61K (hPrp31) associate with the box C/D snoRNPs and the U4/U6…
CD30-Positive Extracellular Vesicles Enable the Targeting involving CD30-Negative DLBCL Cellular material from the CD30 Antibody-Drug Conjugate Brentuximab Vedotin.
The effect of hygrothermal conditions on the linear as well as nonlinear free flexural vibration of anisotropic shear deformable laminated rounded backside can be looked at. The rounded layer is made from fiber-reinforced composites (FRCs) with all the support staying allocated both evenly (UD) or perhaps functionally scored (FG) of…
Understanding how cohesin makes DNA loops in the human genome and its role in Cornelia de Lange syndrome
NIPBL KD affects cohesin-STAG1 and cohesin-STAG2 in opposite ways. a Asynchronously growing HeLa cells mock transfected (control) or transfected with siRNA against NIPBL (NIPBL KD) were analyzed by flow cytometry 72 h later. Contour plots of the indicated proteins in control (gray plots) and NIPBL KD cells (colored plots) were overlapped…
Evolutionary conservation of the fidelity of transcription
Multiple proteins are required to maintain the fidelity of transcription in yeast Using genetically engineered yeast strains21,36,37 and massively parallel sequencing technology34,35, we and others previously demonstrated that the non-essential subunits Rpb9 and TFIIS enhance the fidelity of transcription of RNAPII in living cells16,21,26,34,35,36,37,38,39. In addition, we showed that the…
ncRNA | Free Full-Text | Long Noncoding RNA H19: A Novel Oncogene in Liver Cancer
Received: 9 February 2023 / Revised: 4 March 2023 / Accepted: 6 March 2023 / Published: 9 March 2023 Round 1 Reviewer 1 Report In this paper, they reviewed the role of a long non-coding RNA, H19, in liver cancer. H19 is a lncRNA, which has been extensively studied. Multiple…
SARS-CoV-2 infection activates the cyclic guanosine monophosphate-adenosine monophosphate synthase-stimulator of interferon genes pathway in the lung: a review
Keywords SARS-CoV-2, COVID-19, cyclic guanosine monophosphate-adenosine monophosphate synthase-stimulator of interferon genes pathway, lung damage, interferon, cytokines Introduction Severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) caused the coronavirus disease 2019 (COVID-19) pandemic with origin in Wuhan, China [1]. With confirmed 522 million infections and death of 6.27 million until May…
Anti-Smad4 antibody KO Tested (ab110175)
Overview Product name Description Rabbit polyclonal to Smad4 Host species Rabbit Tested applications Species reactivity Reacts with: HumanPredicted to work with: Mouse, Rat, Sheep, Horse, Cow, Dog, Pig, Chimpanzee,…
Recombinant Anti-XRCC1 antibody [EPR4389(2)] (ab134056)
Overview Product name Description Rabbit monoclonal [EPR4389(2)] to XRCC1 Host species Rabbit Tested applications Suitable for: WB, IHC-P, ICC/IFmore detailsUnsuitable for: Flow Cyt or IP Species reactivity Reacts with: …
Almost no peak output after peakcalling of mtDNA with MACS2
Almost no peak output after peakcalling of mtDNA with MACS2 0 I am new to the CHIP-seq analysis. I am basically trying to call peaks using MACS 2 with the proccessed data of mitochondrial DNA only in bedgraph format given in the accession number GSE48176 under the link www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE48176. I…
An In-House-Built and Light-Emitting-Diode-Based Photodynamic Therapy Device for Enhancing Verteporfin Cytotoxicity in a 2D Cell Culture Model
Here, we describe a novel, simple, and low-cost device to successfully perform in vitro photodynamic therapy (PDT) assays using two-dimensional HeLa cell culture and verteporfin as a photosensitizer. Photodynamic therapy, PDT, offers several advantage to cancer treatment, and its efficacy depends on a light source to activate a photosensitizer. Although…
Isolating Mitochondria, Mitoplasts, and mtDNA from Cultured Mammalian Cells
Rath S, Sharma R, Gupta R, Ast T, Chan C, Durham TJ, Goodman RP, Grabarek Z, Haas ME, Hung WHW et al (2021) MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations. Nucleic Acids Res 49:D1541–D1547 CrossRef CAS PubMed Google Scholar Smith AC, Robinson AJ (2016) MitoMiner…
Barrier-to-autointegration factor 1 promotes gammaherpesvirus reactivation from latency
Biosafety statement All experiments with cell lines and viral infections were carried out in a Biosafety Level 2 facility under the approval of the Biosafety Office in the Department of Environment, Health and Safety and the Institutional Biosafety Committee at the University of North Carolina at Chapel Hill. The laboratory…
CircRNA Circ_0000118 Regulates Malignancy of Cervical Cancer Cells by Regulating miR-211-5p/miR-377-3p/AKT2 Axis
Samples and Cell Lines A total of 78 pairs of tumor samples and the adjacent non-carcinoma control samples were collected by surgery from CC patients in our study. The peripheral blood was also sampled from each individual and the serum was prepared and preserved under − 80 °C till further analysis. The Medical…
Immunofluorescence-based assay to assess LRRK2 recruitment by Rab29
Feb 01, 2023 DOI: dx.doi.org/10.17504/protocols.io.bp2l69r8klqe/v1 Protocol Citation: Francesca Tonelli 2023. Immunofluorescence-based assay to assess LRRK2 recruitment by Rab29. protocols.io dx.doi.org/10.17504/protocols.io.bp2l69r8klqe/v1 License: This is an open access protocol distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited…
Rapid clonal identification of biallelic CRISPR/Cas9 knock-ins using SNEAK PEEC
Here we provide a tool that directly selects biallelically edited knock-ins using cell-surface displays, thereby eliminating the need for extensive clonal verification. By doing so SNEAK PEEC greatly reduces the considerable effort currently expended to obtain biallelically edited clones. The ability to generate a clonal population with multiple edits is…
SARS-CoV-2 hijacks cellular kinase CDK2 to promote viral RNA synthesis
CDKs support SARS-CoV-2 RdRp-mediated gene expression To identify cellular proteins that modulate the SARS-CoV-2 RNA synthesis, we first performed immunoprecipitation coupled with mass spectrometry (MS) to determine cellular proteins that associate with SARS-CoV-2 RdRp. Briefly, Flag-tagged nsp7, Flag-tagged nsp8, and Flag-tagged nsp12 plasmids were co-transfected into HEK293T cells, and the…
Affinity microfluidics enables high-throughput protein degradation analysis in cell-free extracts
We designed pDOC to support multiple strategies for analyzing protein degradation in vitro, specifically cell-free systems. The device is based on a MITOMI integrated microfluidic chip, originally developed to quantify protein-ligand interactions at equilibrium24,33. The MITOMI module was modified to contain an array of 16 × 64, 32 × 32…
Cellular glycan modification by B3GAT1 broadly restricts influenza virus infection
Ethics statement All procedures involving laboratory mice were approved by the Duke University IACUC under the protocol numbers A189-18-08 and A142-21-07. Mice were housed with up to five mice per cage and the ambient room conditions ranged from 70–74 °F and 30–70% humidity with a 12-hour dark/light cycle. Animals were assessed…
Transcription-independent regulation of STING activation and innate immune responses by IRF8 in monocytes
Reagents, antibodies, viruses and cells LMW-Poly(I:C), LPS, 2′3′-cGAMP and DMXAA (InvivoGen); hydroxyurea, camptothecin and mitomycin C (MCE); GM-CSF, Flt3L (peproTech); lipofectamine 2000 (Invitrogen); polybrene (Millipore); RNAiso Plus (Takara); HT-DNA (Sigma); SYBR (BIO-RAD); dual-specific luciferase assay kit (Promega); ELISA kit for murine Ifn-β (PBL); ELISA kits for murine IP-10 (Biolegend) were…
Comparative Study of PID Control and Model Predictive Control for a Microfluidic Electroporation System – HKUST SPD
Bibliographic Details Author Ghadami, Mohammad Shagoshtasbi, Hooman Mahjoob, Mohammad Jahromi Lee, Yi-Kuen Issue Date 2013 Source The 8th Annual IEEE International Conference on Nano/Micro Engineered and Molecular Systems (NEMS 2013), Institute of Electrical and Electronics Engineers (IEEE), 2013, p. 895-898 Abstract This paper describes a comparative study of two feedback…
Postdoctoral fellow in Bioinformatics with focus on antibiotic resistance
Göteborgs universitet möter samhällets utmaningar med mångsidig kunskap. 56 000 studenter och 6 600 medarbetare gör universitetet till en stor och inspirerande arbetsplats. Stark forskning och attraktiva utbildningar lockar forskare och studenter från hela världen. Med ny kunskap och nya perspektiv bidrar Göteborgs universitet till en bättre framtid. We seek…
A Highly Robust Silicon Nano-pillar Chip for Electroporation Chip for Delivering Molecules to HeLa Cells – HKUST SPD
Bibliographic Details Author Zhao, Xu Liu, Haixiang Wang, Xiaoyi Zhao, Cong Izhar Tang, Benzhong Lee, Yi-kuen Issue Date 2020 Source 15th IEEE International Conference on Nano/Micro Engineered and Molecular System, NEMS 2020 / IEEE. New York, NY, USA : IEEE, 2020, p. 230-233, Article no.: 9265581 Abstract Electroporation (EP) is…
Biogenesis, biology and characterization of circular RNAs
Biogenesis, biology and characterization of circular RNAs Kristensen LS et al. The biogenesis, biology and characterization of circular RNAs. Nat Rev Genet. (2019) Summary text Biogenesis and properties of circRNAs Biogenesis of cirRNA Characteristics of circRNAs Discover and analyze circRNAs circRNA genome-wide analysis CircRNA site-specific analysis circRNA visualization Biological functions…
N6-methyladenosine modification of CENPK mRNA by ZC3H13 promotes cervical cancer stemness and chemoresistance | Military Medical Research
Bioinformatics analyses revealed the involvement of m6A modification in cervical cancer progression To better understand whether and how m6A regulators contribute to cervical cancer progression, we first identified 9 m6A writers (WTAP, ZC3H13, METTL3, METTL14, METTL16, VIRMA, RBM15B, RBM15, and CBLL1), 15 m6A readers (FMR1, hnRNPA2B1, hnRNPC, YTHDF1/2/3, YTHDC1/2, LRPPRC,…
A genome-scale screen for synthetic drivers of T cell proliferation
Abramson, J. S. et al. Transcend NHL 001: immunotherapy with the CD19-directed CAR T-cell product JCAR017 results in high complete response rates in relapsed or refractory B-cell non-Hodgkin lymphoma. Blood 128, 4192–4192 (2016). Google Scholar Shifrut, E. et al. Genome-wide CRISPR screens in primary human T cells reveal key regulators…
Using a micro electroporation chip to determine the optimal physical parameters in the uptake of biomolecules in HeLa cells
doi.org/10.1016/j.bioelechem.2006.05.008Get rights and content Abstract In this study, a new micro electroporation (EP) cell chip with three-dimensional (3D) electrodes was fabricated by means of MEMS technology, and tested on cervical cancer (HeLa) cells. Extensive statistical data of the threshold electric field and pulse duration were determined to construct an EP…
The long non-coding RNA LNC_000397 negatively regulates PRRSV replication through induction of interferon-stimulated genes | Virology Journal
Badaoui B, Rutigliano T, Anselmo A, Vanhee M, Nauwynck H, Giuffra E, Botti S. RNA-sequence analysis of primary alveolar macrophages after in vitro infection with porcine reproductive and respiratory syndrome virus strains of differing virulence. PLOS ONE. 2014;9:91918. Article Google Scholar Bateman A, Birney E, Cerruti L, Durbin R, Etwiller…
Glutamine synthetase licenses APC/C-mediated mitotic progression to drive cell growth
Altman, B. J., Stine, Z. E. & Dang, C. V. From Krebs to clinic: glutamine metabolism to cancer therapy. Nat. Rev. Cancer 16, 619–634 (2016). CAS Article Google Scholar Hensley, C. T., Wasti, A. T. & DeBerardinis, R. J. Glutamine and cancer: cell biology, physiology, and clinical opportunities. J. Clin….
RStudio AI Weblog: Picture segmentation with U-Internet
Certain, it’s good when I’ve an image of some object, and a neural community can inform me what sort of object that’s. Extra realistically, there is perhaps a number of salient objects in that image, and it tells me what they’re, and the place they’re. The latter process (referred to…
NoClassDefFoundError: htsjdk/samtools/util/IntervalTree
NoClassDefFoundError: htsjdk/samtools/util/IntervalTree 0 When I run circm6A (github.com/canceromics/circm6a) example code: cd ../.. java -Xmx16g -jar circm6a.jar -ip test_data/HeLa_eluate_rep_1.chr22.bam -input test_data/HeLa_input_rep_1.chr22.bam -r test_data/gencode_chr22.gtf -g test_data/hg38_chr22.fa -o test_data/example_Hela The following error occurred: Start at 2021-12-12 16:33:26 Exception in thread “main” java.lang.NoClassDefFoundError: htsjdk/samtools/util/IntervalTree at main.Method.loadGenes(Method.java:200) at main.Method.run(Method.java:66) at main.Main.main(Main.java:9) Caused by: java.lang.ClassNotFoundException: htsjdk.samtools.util.IntervalTree…