Tag: pbs

Isolation, characterization and classification of BC-producing strain Isolation of single clones from CaCO3 halo zones in Glucose-Yeast Extract-Calcium carbonate agar and iterated subculturing in HS-Glu agar resulted in enrichment of an isolate with beige-coloured, smooth-edged and umbonate shaped colonies characteristics (Fig. S1A). The isolate is hereafter called ‘ENS15’. Under 100X magnification,…

Summary The lab of Dr. Kyle Eagen (www.eagenlab.org) at Baylor College of Medicine focuses on elucidating how DNA folds within cells and how DNA misfolding relates to human disease. Baylor College of Medicine, one of the top ranked medical schools in the country, is well known for its exceptional,…

Cells and viruses hACE2 expressing BHK-21 (BHK-21-hACE2) and Vero-E6 cells were provided by State Key Laboratory of Virology, Wuhan University. Vero-E6 cells were cultured in DMEM (Gibco, Cat.11995–040) supplemented with 10% fetal bovine serum (Gibco, Cat.10091–148) and 1% penicillin and streptomycin solution (BasalMedia, Cat.S110JV) at 37°C with 5% CO2. BHK-21-hACE2…

I am trying to run fastqc for fastq.gz files in RNA-seq Data analysis and I have written a PBS script. However, I am encountering the following error Can’t exec “java”: No such file or directory at /home/paksls/Atreya/software/FastQC/fastqc line 307 I have written the following script: #!/bin/bash #PBS -l nodes=1:ppn=6,pmem=10240MB,walltime=04:00:00 #PBS…

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…

Cells and reagents HEK293T and U87 cells were maintained in DMEM medium (Gibco) supplemented with 10% fetal bovine serum (FBS, Labtech) and 100 U ml−1 penicillin plus 100 μg ml−1 streptomycin (Pen/Strep; Gibco). THP-1-IFIT1 cells that had been modified to express Gaussia luciferase under the control of the IFIT1 promoter were described previously62. THP-1…

Animals and immunizations The study protocol and all veterinarian procedures were approved by the Bioqual IACUC per a memorandum of understanding with the Duke IACUC, and were performed based on standard operating procedures. Macaques studied were housed and maintained in an Association for Assessment and Accreditation of Laboratory Animal Care-accredited…

The present protocol describes a simple method for isolating preadipocytes from adipose tissue in broiler embryos. This method enables isolation with high yield, primary culture, and adipogenic differentiation of preadipocytes. Oil Red O staining and lipid/DNA stain measured the adipogenic ability of isolated cells induced with differentiation media. Primary preadipocytes…

Animal and ethics A total of 190 dogs, comprising both healthy dogs (n = 76) and dogs with respiratory symptoms (n = 114), were included in this study. The research assessed nasal swab (NS) and oropharyngeal swab (OS) collected between January and November 2020. The samples from the healthy group were collected from clinically…

We describe a protocol for the isolation of mesenchymal stem cells from human umbilical cord tissue and their differentiation into the skeletal muscle lineage. We describe our protocol to isolate mesenchymal stem cell from human umbilical cord tissue and a robust method to differentiate them into skeletal muscle lineage. This…

Adipose tissue-derived mesenchymal stem cells (Ad-MSCs) can be a potential source of MSCs that differentiate into insulin-producing cells (IPCs). In this protocol, we provide detailed steps for the isolation and characterization of rat epididymal Ad-MSCs, followed by a simple, short protocol for the generation of IPCs from the same rat…

A protocol outlining the formation of human blastoids that efficiently, timely, and sequentially generate blastocyst-like cells. Research on human embryos is limited by their low availability and ethical concerns, thus obtaining individual models that faithfully replicate early human development would support scientific and medical progress. The ability of this technique…

Patients and controls The patient 1 was 38 years old and consulted for infertility after he and his partner had been trying to conceive for 2 years. The patient was the first child of unrelated parents, and he had four brothers and five sisters whose fertility status could not be determined…

Introduction Pancreatic cancer (PC) is one of the most aggressive and lethal cancers (1). Previous studies have shown that aging, environmental and behavioral changes are more closely related to the dramatic increase in the incidence of PC worldwide than genetic factors (2–5). A position paper published by the European Federation…

Ethics statement and patient samples 40 pairs of OC tissues and adjacent tissue samples were collected from patients who were diagnosed with OC and received surgical resection in the Affiliated Hospital of Zunyi Medical University. None of the patients received any anti-cancer treatment before surgery, and all samples were immediately…

Brand Leading Biology Catalog Number APR27223N Product Type Polyclonal Antibodies Field of Research Cell Biology & Developmental Biology>Cell Adhesion …

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…

Mice A laboratory strain B6 was purchased from CLEA Japan Inc. (Tokyo, Japan), while nine wild strains (BFM/2, BLG2, CHD, HMI, KJR, MSM, NJL, PGN2, and SWN) were bred at NIG (Shizuoka, Japan) (Table 1). All mice were maintained at the animal facility in NIG, under specific-pathogen-free conditions and controlled…

This protocol describes the induction of Gram-negative monobacterial sepsis in a mouse model system. The model is useful in investigating the inflammatory and lethal host responses during sepsis. Sepsis is a dysregulated host immune response to microbial invasion or tissue damage, leading to organ injury at a site distant from…

Cell culture Human glioblastoma cells (U87MG and U87MG-Luc) and human embryonic kidney cells (HEK293) were obtained from the American Type Culture Collection (Manassas, Va.). Cells were cultured in Dulbecco’s Modified Eagle Medium supplemented with 10% fetal bovine serum (Gibco™ Fetal Bovine Serum South America, Thermo Scientific Fisher-US), 2 mM l-glutamine, 50 U/ml…

2022-07-17 Valued Tier3 HPC users of NHR@FAU, as briefly announced in the HPC Cafe in June, we now started with switching from Woody with Ubuntu 18.04 and Torque to Woody-NG (“Woody Next Generation”) with AlmaLinux8 as operating system and Slurm as batch system. Woody-NG uses the same operating system as…

Animal generation The Lrsam1C698R knock-in mice were generated on a C57Bl/6J background using the CRISPR/Cas9 technique. Briefly, single-cell zygotes from C57BL/6J mice were microinjected with mRNA encoding Cas9 and a guide sequence (5′-ACAGCAGCAGACGTGGCCAC-3′ at 20 ng/µl) to target the exon 26 of Lrsam1. A single stranded DNA oligo carrying the C698R mutation…

Job Functions, Duties, Responsibilities and Position Qualifications: POSITION TITLE:Senior Bioinformatics-Clinical Database Developer STANDARDIZED JOB TITLE: Database Development, Web Application Development, and Clinical Analytics EXEMPT STATUS:  Exempt POSITION SUMMARY: Sr. Database Developer works with cross-functional groups & Medical Leadership for developing a databases for a clinical assays. The candidate is expected…

HEK293 cells are a dominant platform for cell and gene therapy production because they are highly effective at producing large amounts of recombinant viral vectors. However, it is critical to remove trace host cell contamination from therapeutic products to avoid endangering patients. To meet rigorous regulatory guidelines, biopharmaceutical manufacturers need…

Background: Spinal Muscular Atrophy (SMA) is one of the most common autosomal recessive disorders in children after Duchenne muscular dystrophy affecting approximately 1 in 11,000 live births. There is no effective therapy for SMA; however, broadening our knowledge about the molecular genetics of the disease is resultant to develop potential…

Here, we present an economical and efficient method to isolate and generate high-purity bone marrow-derived dendritic cells from mice after 7 days of culture with 10 ng/mL GM-CSF/IL-4. Economical and Efficient Protocol of Isolating and Generating Bone Marrow-derived Dendritic Cells from Mouse. Procedures involving animal subjects have been approved by…

High-throughput RNA interference (RNAi) screening using a pool of lentiviral shRNAs can be a tool to detect therapeutically relevant synthetic lethal targets in malignancies. We provide a pooled shRNA screening approach to investigate the epigenetic effectors in acute myeloid leukemia (AML). The overall goal of the following video is to…

Phenolic acids are important phytochemicals that are present in whole grains. They possess bioactive properties such as antioxidant protective functions. This work aimed at reporting on a generalized method for the HPLC identification, total phenolic content estimation, and determination of the antioxidant capacity of phenolic acids in cereals and legumes….

Introduction Lung cancer is associated with high morbidity and mortality and continues to be a major public health problem worldwide (1). Lung adenocarcinoma (LUAD) is the most common histological type of lung cancer. While the 5-year survival rates of patients with lung cancer are still <15%, rates are closer to…

This protocol presents a technique for high-resolution mapping of replication sites in structurally preserved chromatin in situ that employs a combination of pre-embedding EdU-streptavidin-Nanogold labeling and ChromEMT. We present a protocol for the electron microscopic visualization of the replicative domains in the cell by the EdU labeling of the newly…

A method to reactivate quiescent neural stem cells in cultured Drosophila brain explants has been established. Using this method, the role of systemic signals can be uncoupled from tissue-intrinsic signals in the regulation of neural stem cell quiescence, entry and exit. We developed a method to reactivate quiescent neural stem…

EGF Protein, Feline, Recombinant (ECD, hFc Tag): 产品信息 纯度 > 90 % as determined by SDS-PAGE. 生物活性 Testing in progress 蛋白构建 A DNA sequence encoding the Feline EGF (NP_001009381.1) (Asn969-Arg1020) was expressed with the fused Fc region of human IgG1 at the N-terminus. 表达宿主 HEK293 Cells 分子量 The…

. 2022 Apr 30;2022:7918067. doi: 10.1155/2022/7918067. eCollection 2022. Affiliations Expand Affiliations 1 Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou 215004, Jiangsu Province, China. 2 Department of Urology, The Affiliated Hospital of Xuzhou Medical University, Xuzhou 221002, Jiangsu Province, China. Free PMC article Item in Clipboard Meng…

ACE2 Protein, Human, Recombinant (hFc Tag), Biotinylated: Product Information Purity > 95 % as determined by SDS-PAGE. Activity Testing in progress Protein Construction A DNA sequence encoding the extracellular domain (Met 1-Ser 740) of human ACE2 precursor (NP_068576.1) was expressed with the fused Fc region of human IgG1…

-e, –error=<filename pattern> Instruct Slurm to connect the batch script’s standard error directly to the file name specified in the “filename pat‐ tern”. By default both standard output and standard error are directed to the same file. For job arrays, the default file name is “slurm-%A_%a.out”, “%A” is replaced by…

Introduction Endometriosis (EMS) is a chronic gynecological disease defined as implantation and periodic growth of the endometrial glands and stroma outside the uterine cavity, causing chronic pelvic pain, severe dysmenorrhea, and infertility in 10% reproductive-age women, among which the infertility rate is approximately 30–50%.1,2 Surgical excision is commonly used for…

We introduce three methods of direct culture, direct exposure culture, and exposure culture for evaluating the in vitro cytocompatibility of biodegradable implant materials. These in vitro methods mimic different in vivo cell-implant interactions and can be applied to study various biodegradable materials. Direct and indirect culture methods for studying biodegradable…

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This website uses cookies to ensure the best experience. By continuing, you agree to our privacy policy. × Product successfully added to quote! × There are items in your quote. Brand: Reference GTX10647 Brand GeneTex Application IHC-PWB Storage Conditions Store as concentrated solution. Centrifuge briefly prior to opening vial. For…

Cell generated mechanical forces are essential to proper function in various organs throughout the body. Plus the intestines bladder, heart, and others. These organs must generate stable patterns of cell contraction and relaxation, to maintain the internal hemostatic state. Abnormal smooth muscle cell contraction can lead to the onset of…

Introduction Antibody-drug conjugates (ADCs) have been studied for decades as a promising cancer treatment. As compared to conventional chemotherapy, ADCs have a larger therapeutic window because of their ability to target antigen-expressing tumor cells.1 As ADC drug development technology continues to evolve, several ADC drugs are being introduced to the…

We present detailed protocols for the generation and characterization of 2D and 3D human induced pluripotent stem cell (hIPSC)-based models of neocortical development as well as complementary methodologies enabling qualitative and quantitative analysis of primary cilium (PC) biogenesis and function. The overall goal of the procedure we detail here is…

Introduction Escherichia coli is a common Gram-negative opportunistic pathogen that causes invasive host infections through virulence factors such as flagella, toxin secretion, and adhesins. According to the source of the infection, pathogenic E. coli can be classified as intestinal (diarrheagenic) and extraintestinal (ExPEC). Uropathogenic E. coli (UPEC) is the most…

Sepsis patients and healthy controls A total of 62 sepsis patients (male/female: 32/30; mean age, 52.3±4.9 years) who were admitted to Minhang Hospital, Fudan University between March 2018 and March 2020 were enrolled in the study. In addition, 62 healthy controls (male/female: 32/30; mean age, 52.4±4.8 years) who were at…

Here we provide a protocol for screening potential transcription factors involved in the development of dendritic cell (DC) using lentiviral transduction of shRNA to obtain stable knockdown cell lines for in vitro DC differentiation. Dendritic cells, or DCs, are key immune cells linking the innate and adaptive immune system. While…

The overall goal of this procedure is to demonstrate dissection methods for the adult leg of Drosophila. This technique removes a portion of the cuticle, exposing the underlying tissue in a way that preserves neuronal and muscle architecture. This procedure allows us to characterize the neuromuscular junction for identified motor…

Ethical compliance The research carried out in this study has been approved by the Swedish Board of Agriculture, Jordbruksverket: N343/12. Cell culture Mouse primary fibroblasts were derived from adult (>10 weeks old) CAST/EiJ × C57BL/6J or C57BL/6J × CAST/EiJ mice by skinning, mincing and culturing tail explants (for at least 10 d) in DMEM high…

Summary February 12th, 2022 This protocol shows an accurate and objective approach to visualize viral titrations using crystal violet, by comparing it with optical microscopy and immunocytochemical staining. Transcript The goal of this protocol is to produce a virus stock titration and visualize it using crystal violet staining. To do…

This paper describes ischemia-reperfusion (I/R) modeling in a 3-day chick embryo using a spinal needle customized hook to better understand I/R development and treatment. This model is simple, quick, and inexpensive. Hi, I am Dr.Syed Shadab Raza, the principal investigator for the Laboratory for Stem Cells and Restorative Neurology, located…

Extracellular vesicles (EVs) contribute to cellular biology and intercellular communications. There is a need for practical assays to visualize and quantify EVs uptake by the cells. The current protocol proposes the EV uptake assay by utilizing three-dimensional fluorescence imaging via confocal microscopy, following EV isolation by a nano-filtration-based microfluidic device….

Recycling endosomes are part of the endosomal tubular network. Here we present a method to quantify the dynamics of recycling endosomes using GFP-STX13 as an organelle marker. The microscopy-based assay to study and analyze the recycling endosomes using SNARE trafficking. These are skin melanocytes. The black-colored organelles that you see…

Significance The extracellular concentration of adenosine triphosphate (ATP) reaches several hundred micromoles in the inflamed tissues or tumor environment. A high concentration of ATP activates P2X7, a purinergic receptor, and induces the formation of a nonselective cation channel, accompanied by reversible phosphatidylserine (PtdSer) exposure, leading to cell lysis. Here, we…

INTRODUCTION Dengue is the most common mosquito-borne viral disease globally (1). This acute disease, which can be life-threatening, is caused by four different dengue viruses (DENVs) (DENV-1, DENV-2, DENV-3, and DENV-4). An estimated 390 million people are infected with these DENVs annually (2), and populations throughout the tropics face frequent…

We report a one-pot hydrothermal synthesis of manganese ferrite clusters (MFCs) that offers independent control over material dimension and composition. Magnetic separation allows rapid purification while surface functionalization using sulfonated polymers ensures the materials are non-aggregating in biologically relevant medium. The resulting products are well positioned for biomedical applications. In…

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This article describes the method for mitochondrial time-lapse imaging of astrocyte cultures equipped with MitoTimer biosensor and the resulting multiparametric analysis of mitochondrial dynamics, mobility, morphology, biogenesis, redox state, and turnover. This protocol greatly maximizes the power of microscopy as a method to track mitochondrial dynamics within individual cells over…

In this paper, we present an in vitro and in situ protocol to repair a tendon gap of up to 1.5 cm by filling it with engineered collagen graft. This was performed by developing a modified suture technique to take the mechanical load until the graft matures into the host…

Cell lines and culture Unless stated otherwise, all tumor target cell lines were sourced from the ATCC via LGC Standards. Human endogenous mesothelin (MSLN)-positive target cell lines H-226 (lung carcinoma, MSLN+, ATCC® CRL-5826™) and AsPC-1 (ATCC CRL-1682), and MSLN-negative Raji control cells (ATCC CCL-86) were cultured in RPMI-1640 Glutamax (Life Technologies,…

In this protocol, AAV2 vector is produced by co-culturing Spodoptera frugiperda (Sf9) insect cells with baculovirus (BV)-AAV2-green fluorescent protein (GFP) or therapeutic gene and BV-AAV2-rep-cap infected Sf9 cells in suspension culture. AAV particles are released from the cells using detergent, clarified, purified by affinity column chromatography, and concentrated by tangential…

How to label columns in HTSeq output 0 I’ve been working to process RNAseq data and I’ve used hisat2 to align my reads to the reference genome. When I take those output files and put them into HTSeq-count using the below code, I get a count matrix but the columns…

CD94/KLRD1 Protein, Human, Recombinant (His Tag): 产品信息 纯度 > 95 % as determined by SDS-PAGE 生物活性 Testing in progress 蛋白构建 A DNA sequence encoding the human KLRD1 (Q13241-1) (Lys32-Ile179) was expressed with a polyhistidine tag at the N-terminus. 表达宿主 HEK293 Cells 分子量 The recombinant human KLRD1 consists of…

Running Jobs on Titan Table of Contents Titan’s Job Scheduler – SLURM Documentation Translating to SLURM commands from other workload managers Basic SLURM Commands squeue sinfo scontrol sbatch scancel Titan’s Environment Module System – LMOD Listing all available modules on Titan Loading a module into your environment Listing all modules…

This protocol presents how to quantify AAV transduction efficiency in mouse retina using digital droplet PCR (dd-PCR) together with small scale AAV production, intravitreal injection, retinal imaging, and retinal genomic DNA isolation. In this video, we will show how to quantify AAV transduction in mouse retina using digital droplet PCR…

Significance Interferon (IFN)-mediated antiviral responses serve as the first line of the host innate immune defense against viral infection. Here we identify a previously uncharacterized protein designated phospholipase A2 inhibitor and LY6/PLAUR domain-containing protein (PINLYP), which is essential for embryonic development and plays an important role in type I IFN…

Introduction Renal cell carcinoma (RCC) accounts for approximately 2–3% of all malignant tumors, and its prevalence is rising. Metastatic RCC accounts for 25–30% of all RCC cases, and has an exceedingly poor prognosis.1 In 2020, among approximately 430,000 newly discovered cases of RCC, 179,000 died.2 Clear cell renal cell carcinoma…

STICR lentiviral library preparation and validation We synthesized a high-complexity lentivirus barcode library that encodes approximately 60–70 million distinct oligonucleotide RNA sequences (STICR barcodes). STICR barcodes comprised three distinct oligonucleotide fragments cloned sequentially into a multicloning site within the 3′ UTR of an enhanced green fluorescent protein (eGFP) transgene under…

How to get normalized count table from DESeq? 1 Hi, I’m using Deseq compare differential abundance. Here is my code: ds.all <- phyloseq_to_deseq2(ps0.infant.pbs, ~ sample_type) geoMeans <- apply(counts(ds.all),1,gm_mean) ds.all <- estimateSizeFactors(ds.all,geoMeans = geoMeans) dds.all <- DESeq(ds.all,fitType = “local”) Then as the results I got 8 ASVs that showed significantly different….

Computational design Protein modeling and design was performed with Rosetta version 3.5 (2015.19.57819)35,37. Python and shell scripts for generating input from Rosetta and analyzing from Rosetta are available at: github.com/raman-lab/biosensor_design The high-resolution TtgR structure co-crystalized with tetracycline was selected as the starting point for computational design (PDB: 2UXH)28. The structure…

Introduction Prostate cancer (PCa) is one of the most common genitourinary system malignant tumor in men worldwide. In Asian countries, many patients with PCa are often diagnosed at an advanced stage maybe mostly because of a large population base with relatively backward economic development and imperfect cancer screening system of…

INTRODUCTION Genomic instability often refers to the existence of a variety of DNA alterations, ranging from single nucleotide changes (such as base substitution, deletion, and insertion) to chromosomal rearrangements (e.g., gain or loss of a segment or the whole chromosome) (1). Loss of genome stability can lead to early onset…

negative PBS values 0 Are negative values for the Population Branch Statistic (from Yi et al. 2010) meaningful? I obtained per SNP pairwise WC Fst from 3 populations of different sizes from Vcftools and calculated PBS. For some SNPs, the PBS is negative for a population and I am not…

Introduction Aural infections are one of the most common diseases of the head and neck and are predominantly caused by bacterial infections of the ear canal. Several studies from different countries have reported that Pseudomonas aeruginosa is the most common pathogen isolated from ear canal secretions, followed by Staphylococcus aureus.1…

Entry EC 1.14.12.17               Enzyme                                  Name nitric oxide dioxygenase Class Oxidoreductases;Acting on paired donors, with incorporation or reduction of molecular oxygen;With NADH or NADPH as one donor, and incorporation of two atoms of oxygen into the other donorBRITE hierarchy Sysname nitric oxide,NAD(P)H:oxygen oxidoreductase Reaction(IUBMB) 2 nitric oxide + 2 O2 + NAD(P)H =…

Introduction Today, malignant tumors (cancer) still severely imperil human health and cause millions of global mortality rates.1,2 Deep-seated solid tumors are challenging to cure by most therapeutic tools, mainly blamed on the complex tumor microenvironment (TME).3,4 Adoptive cell therapy (ACT), as one of the effective immunotherapeutic means for cancer treatment,…

Hi, I am using PLINK to estimate haplotype blocks using Gabriel’s method. I am using the following command plink –file Chr$PBS_ARRAY_INDEX –noweb –all –blocks –ld-window-kb 500 And it seemed to be working just fine but when job finished no blocks were called at all. The log file does not mention…