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Kirsten Richter et al.
The Journal of biological chemistry, 295(23), 7849-7864 (2020-04-23)
Activation of the T cell receptor (TCR) results in binding of the adapter protein Nck (noncatalytic region of tyrosine kinase) to the CD3ϵ subunit of the TCR. The interaction was suggested to be important for the amplification of TCR signals
Emma R Stewart et al.
Methods in molecular biology (Clifton, N.J.), 1861, 103-112 (2018-09-16)
Immunodetection of nuclear antigens is often complicated by epitope masking, so that proteins known to function in the nucleus are sometimes not easily detected at their sites of action. Moreover, protein populations that are detected before unmasking can be very
Prasad D Trivedi et al.
Molecular therapy. Methods & clinical development, 24, 154-170 (2022-01-25)
Recent clinical successes have propelled recombinant adeno-associated virus vectors (rAAV) to the center stage for human gene therapy applications. However, the exploding demand for high titers of highly pure rAAV vectors for clinical applications and market needs remains hindered by
Rok Razpotnik et al.
International journal of molecular sciences, 22(14) (2021-07-25)
Circular RNAs (circRNAs) are increasingly recognized as having a role in cancer development. Their expression is modified in numerous cancers, including hepatocellular carcinoma (HCC); however, little is known about the mechanisms of their regulation. The aim of this study was
Karin Purshouse et al.
eLife, 11 (2022-12-09)
Extrachromosomal DNA (ecDNA) are frequently observed in human cancers and are responsible for high levels of oncogene expression. In glioblastoma (GBM), ecDNA copy number correlates with poor prognosis. It is hypothesized that their copy number, size, and chromatin accessibility facilitate
Evgeniya Trofimenko et al.
eLife, 10 (2021-10-30)
Cell-penetrating peptides (CPPs) allow intracellular delivery of bioactive cargo molecules. The mechanisms allowing CPPs to enter cells are ill-defined. Using a CRISPR/Cas9-based screening, we discovered that KCNQ5, KCNN4, and KCNK5 potassium channels positively modulate cationic CPP direct translocation into cells
David Brown et al.
Frontiers in immunology, 12, 730825-730825 (2021-11-12)
Engineered variants of recombinant adeno-associated viruses (rAAVs) are being developed rapidly to meet the need for gene-therapy delivery vehicles with particular cell-type and tissue tropisms. While high-throughput AAV engineering and selection methods have generated numerous variants, subsequent tropism and response
Bernard K van der Veer et al.
Nucleic acids research, 51(11), 5469-5498 (2023-04-07)
Gastrulation begins when the epiblast forms the primitive streak or becomes definitive ectoderm. During this lineage bifurcation, the DNA dioxygenase TET1 has bipartite functions in transcriptional activation and repression, but the mechanisms remain unclear. By converting mouse embryonic stem cells
Kornkamon Lertsuwan et al.
The Prostate, 77(7), 729-742 (2017-02-09)
Previous studies showed that human bone marrow stromal HS-5 cells secreted unidentified factor(s) inducing PCa cell death. Herein, the HS-5-derived factor (HS-5 DF) was characterized and identified. Conditioned media from confluent HS-5 cells were collected and modified for biochemical characteristic
Jianghong Zhong et al.
Communications biology, 4(1), 865-865 (2021-07-15)
A single-nucleotide polymorphism of neutrophil cytosolic factor 1 (Ncf1), leading to an impaired generation of reactive oxygen species (ROS), is a causative genetic factor for autoimmune disease. To study a possible tumor protection effect by the Ncf1 mutation in a
Marisa Müller et al.
Bio-protocol, 11(5), e3946-e3946 (2021-04-03)
RNA-protein interactions are often mediated by dedicated canonical RNA binding domains. However, interactions through non-canonical domains with unknown specificity are increasingly observed, raising the question how RNA targets are recognized. Knowledge of the intrinsic RNA binding specificity contributes to the
Paolo Fattorini et al.
International journal of molecular sciences, 21(20) (2020-10-18)
RNA isolated from fixed and paraffin-embedded tissues is widely used in biomedical research and molecular pathology for diagnosis. In the present study, we have set-up a method based on high performance liquid chromatography (HPLC) to investigate the effects of different
Ramón Cervantes-Rivera et al.
Bio-protocol, 10(18), e3757-e3757 (2021-03-05)
Gene transcription in bacteria often starts some nucleotides upstream of the start codon. Identifying the specific Transcriptional Start Site (TSS) is essential for genetic manipulation, as in many cases upstream of the start codon there are sequence elements that are
Thomas K Karikari et al.
ACS chemical neuroscience, 11(19), 3117-3129 (2020-08-25)
Tau neurofibrillary tangles are key pathological features of Alzheimer's disease and other tauopathies. Recombinant protein technology is vital for studying the structure and function of tau in physiology and aggregation in pathophysiology. However, open-source and well-characterized plasmids for efficiently expressing
Wenli Zhang et al.
Methods in molecular biology (Clifton, N.J.), 1284, 71-89 (2015-03-12)
Genomic regions associated with regulatory proteins are known to be highly sensitive to DNase I digestion and are termed DNase I hypersensitive sites (DHSs). DHSs can be identified by DNase I digestion followed by high-throughput DNA sequencing (DNase-seq). DNase-seq has
R Alexander Martino et al.
Journal of virology, 95(20), e0116421-e0116421 (2021-08-05)
One approach to improve the utility of adeno-associated virus (AAV)-based gene therapy is to engineer the AAV capsid to (i) overcome poor transport through tissue barriers and (ii) redirect the broadly tropic AAV to disease-relevant cell types. Peptide- or protein-domain
María Virumbrales-Muñoz et al.
Lab on a chip, 20(23), 4420-4432 (2020-10-27)
Clear cell renal cell carcinoma (ccRCC) is a common genitourinary cancer associated with the development of abnormal tumor angiogenesis. Although multiple anti-angiogenic therapies have been developed, responses to individual treatment are highly variable between patients. Thus, the use of one-patient
Hugo Bernard et al.
Cell reports. Medicine, 1(7), 100125-100125 (2020-11-19)
Enteroviruses are suspected to contribute to insulin-producing β cell loss and hyperglycemia-induced diabetes. However, mechanisms are not fully defined. Here, we show that coxsackievirus B type 4 (CVB4) infection in human islet-engrafted mice and in rat insulinoma cells displays loss
Yankun Wang et al.
Current protocols, 1(6), e148-e148 (2021-06-09)
DNase I hypersensitive site (DHS) mapping combined with high-throughput sequencing (DNase-seq) enables the identification of cis-regulatory DNA elements (CREs) genome wide. However, despite the wide applications of DNase-seq in plants, its application to the highly repetitive genomes of plants has
Zila Martinez-Lozada et al.
Neurochemistry international, 139, 104787-104787 (2020-07-11)
Astrocytes have diverse functions that are supported by their anatomic localization between neurons and blood vessels. One of these functions is the clearance of extracellular glutamate. Astrocytes clear glutamate using two Na+-dependent glutamate transporters, GLT-1 (also called EAAT2) and GLAST
Iana V Kim et al.
Methods in molecular biology (Clifton, N.J.), 2680, 29-54 (2023-07-10)
In planarian flatworms, piRNAs and SMEDWI (Schmidtea mediterranea PIWI) proteins are both essential for the animals' impressive regenerative ability and for their survival. A knockdown of SMEDWI proteins disrupts the specification of the planarian germline and impairs stem cell differentiation
Mariana Bresque et al.
The Journal of biological chemistry, 298(3), 101711-101711 (2022-02-13)
Acute and chronic inflammations are key homeostatic events in health and disease. Sirtuins (SIRTs), a family of NAD-dependent protein deacylases, play a pivotal role in the regulation of these inflammatory responses. Indeed, SIRTs have anti-inflammatory effects through a myriad of
Guillaume Beaudoin-Bussières et al.
Cell reports, 38(7), 110368-110368 (2022-02-07)
Emerging evidence indicates that both neutralizing and Fc-mediated effector functions of antibodies contribute to protection against SARS-CoV-2. It is unclear whether Fc-effector functions alone can protect against SARS-CoV-2. Here, we isolated CV3-13, a non-neutralizing antibody, from a convalescent individual with
Qiang Li et al.
Frontiers in oncology, 11, 619915-619915 (2021-04-13)
The long noncoding RNA (lncRNA) LINC00152, also known as CYTOR, displays aberrant expression in various cancers. However, its clinical value and functional mechanisms in breast cancer remain insufficiently understood. Our study found that LINC00152 is significantly upregulated in breast cancer
Shenli Yuan et al.
Cell discovery, 9(1), 13-13 (2023-01-31)
Although parental genomes undergo extensive epigenetic reprogramming to be equalized after fertilization, whether they play different roles in human zygotic genome activation (ZGA) remains unknown. Here, we mapped parental transcriptomes by using human parthenogenetic (PG) and androgenetic (AG) embryos during
Doaa Ibrahim et al.
Animals : an open access journal from MDPI, 11(7) (2021-07-03)
Appropriate skeletal muscle development in poultry is positively related to increasing its meat production. Synthetic peptides with growth hormone-boosting properties can intensify the effects of endogenous growth hormones. However, their effects on the mRNA and miRNA expression profiles that control
Eugene Oh
Methods in molecular biology (Clifton, N.J.), 2252, 3-26 (2021-03-26)
Modern DNA sequencing technologies have allowed for the sequencing of tens of thousands of bacterial genomes. While this explosion of information has brought about new insights into the diversity of the prokaryotic world, much less is known of the identity
Liqin Xie et al.
Cellular and molecular gastroenterology and hepatology, 14(2), 435-464 (2022-05-16)
Current management of inflammatory bowel disease leaves a clear unmet need to treat the severe epithelial damage. Modulation of Wnt signaling might present an opportunity to achieve histological remission and mucosal healing when treating IBD. Exogenous R-spondin, which amplifies Wnt
Panagiota Karagianni et al.
Cell reports, 30(5), 1319-1328 (2020-02-06)
Transcription factor binding to enhancer and promoter regions critical for homeostatic adult gene activation is established during development. To understand how cell-specific gene expression patterns are generated, we study the developmental timing of association of two prominent hepatic transcription factors
Ray A Spradlin et al.
Journal of applied physiology (Bethesda, Md. : 1985), 131(3), 881-894 (2021-07-23)
Muscle atrophy occurs as a result of prolonged periods of reduced mechanical stimulation associated with injury or disease. The growth hormone/insulin-like growth factor-1 (GH/IGF-1) axis and load sensing pathways can both aid in recovery from disuse through their shared downstream
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