Long nanopore reads are advantageous in de novo genome assembly. However, nanopore reads usually have broad error distribution and high-error-rate subsequences. Existing error correction tools cannot ...correct nanopore reads efficiently and effectively. Most methods trim high-error-rate subsequences during error correction, which reduces both the length of the reads and contiguity of the final assembly. Here, we develop an error correction, and de novo assembly tool designed to overcome complex errors in nanopore reads. We propose an adaptive read selection and two-step progressive method to quickly correct nanopore reads to high accuracy. We introduce a two-stage assembler to utilize the full length of nanopore reads. Our tool achieves superior performance in both error correction and de novo assembling nanopore reads. It requires only 8122 hours to assemble a 35X coverage human genome and achieves a 2.47-fold improvement in NG50. Furthermore, our assembly of the human WERI cell line shows an NG50 of 22 Mbp. The high-quality assembly of nanopore reads can significantly reduce false positives in structure variation detection.
SN‐38, the active metabolite of irinotecan, is released upon liver hydrolysis to mediate potent antitumor activity. Systemic exposure to SN‐38, however, also leads to serious side effects. To reduce ...systemic toxicity by controlling where and when SN‐38 is generated, a new prodrug was specifically designed to be metabolically stable and undergo rapid palladium‐mediated activation. Blocking the phenolic OH of SN‐38 with a 2,6‐bis(propargyloxy)benzyl group led to significant reduction of cytotoxic activity (up to 44‐fold). Anticancer properties were swiftly restored in the presence of heterogeneous palladium (Pd) catalysts to kill colorectal cancer and glioma cells, proving the efficacy of this novel masking strategy for aromatic hydroxyls. Combination with a Pd‐activated 5FU prodrug augmented the antiproliferative potency of the treatment, while displaying no activity in the absence of the Pd source, which illustrates the benefit of achieving controlled release of multiple approved therapeutics—sequentially or simultaneously—by the same bioorthogonal catalyst to increase anticancer activity.
Palladium‐functionalized microdevices were used to uncage newly developed prodrug that releases SN‐38 (irinotecan′s active metabolite) in combination with previously known anticancer prodrug of 5FU.
Recent advances in bioorthogonal catalysis are increasing the capacity of researchers to manipulate the fate of molecules in complex biological systems. A bioorthogonal uncaging strategy is ...presented, which is triggered by heterogeneous gold catalysis and facilitates the activation of a structurally diverse range of therapeutics in cancer cell culture. Furthermore, this solid‐supported catalytic system enabled locally controlled release of a fluorescent dye into the brain of a zebrafish for the first time, offering a novel way to modulate the activity of bioorthogonal reagents in the most fragile and complex organs.
Hidden in the glorious wildness like unmined gold! A bioorthogonal uncaging strategy triggered by heterogeneous gold catalysis mediates the activation of probes and therapeutics both in vitro and in vivo. Scale bar: 100 μm.
The incorporation of transition metal catalysts to the bioorthogonal toolbox has opened the possibility of producing supra-stoichiometric amounts of xenobiotics in living systems in a non-enzymatic ...fashion. For medical use, such metals could be embedded in implantable devices (
heterogeneous catalyst) to "synthesize" drugs in desired locations (
in a tumour) with high specificity and for extended periods of time, overcoming the useful life limitations of current local therapy modalities directed to specific organ sites (
brachytherapy, controlled release systems). To translate this approach into a bona fide therapeutic option, it is essential to develop clinically-accessible implantation procedures and to understand and validate the activation process in relevant preclinical models. Herein we report the development of a novel Pd-activatable precursor of the red-fluorescent drug doxorubicin and Pd devices of optimized size and activity. Screening in state-of-the-art cancer models provided fundamental insights into the insertion protocols, safety and stability of the devices and into the prodrug distribution profile before and after activation.
5-Fluorouracil (5-FU) is an antineoplastic antimetabolite that is widely administered to cancer patients by bolus injection, especially to those suffering from colorectal and pancreatic cancer. ...Because of its suboptimal route of administration and dose-limiting toxicities, diverse 5-FU prodrugs have been developed to confer oral bioavailability and increase the safety profile of 5-FU chemotherapy regimens. Our contribution to this goal is presented herein with the development of a novel palladium-activated prodrug designed to evade the metabolic machinery responsible for 5-FU anabolic activation and catabolic processing. The new prodrug is completely innocuous to cells and highly resistant to metabolization by primary hepatocytes and liver S9 fractions (the main metabolic route for 5-FU degradation), whereas it is rapidly converted into 5-FU in the presence of a palladium (Pd) source. In vivo pharmokinetic analysis shows the prodrug is rapidly and completely absorbed after oral administration and exhibits a longer half-life than 5-FU. In vivo efficacy studies in a xenograft colon cancer model served to prove, for the first time, that orally administered prodrugs can be locally converted to active drugs by intratumorally inserted Pd implants.
There are many transmembrane receptor-like proteins whose ligands have not been identified. A strategy for finding ligands when little is known about their tissue source is to screen each ...extracellular protein individually expressed in an array format by using a sensitive functional readout. Taking this approach, we have screened a large collection (3,191 proteins) of extracellular proteins for their ability to activate signaling of an orphan receptor, leukocyte tyrosine kinase (LTK). Only two related secreted factors, FAM150A and FAM150B (family with sequence similarity 150 member A and member B), stimulated LTK phosphorylation. FAM150A binds LTK extracellular domain with high affinity ( K D = 28 pM). FAM150A stimulates LTK phosphorylation in a ligand-dependent manner. This strategy provides an efficient approach for identifying functional ligands for other orphan receptors.
Significance Secreted factors and their cell-surface receptors play important roles in the communication between cells in normal and pathological conditions. There are many transmembrane receptor-like proteins whose ligands have not been identified (also known as orphan receptors). Knowledge of the ligand should help in understanding the biological role of the receptor. We used a strategy of screening the extracellular proteome, one protein at a time, to identify ligands for such receptors. We discovered the ligands for the orphan receptor leukocyte tyrosine kinase. To our knowledge, this is the first case in which secreted factor ligands were identified for an orphan receptor with this technique. This approach is especially valuable when little is known about the ligand.
Herein, we report a straightforward method for the scalable preparation of Pd nanoparticles (Pd-NPs) with reduced inherent cytotoxicity and high photothermal conversion capacity. These Pd-NPs are ...rapidly taken up by cells and able to kill labeled cancer cells upon short exposure to near-infrared (NIR) light. Following cell treatment with Pd-NPs, ablated areas were patterned with high precision by laser scanning microscopy, allowing one to perform cell migration assays with unprecedented accuracy. Using coherent Raman microscopy, cells containing Pd-NPs were simultaneously ablated and imaged. This novel methodology was combined with intravital imaging to mediate microablation of cancerous tissue in tumor xenografts in mice.
Systemic side effects limit the efficacy of chemotherapy regimens. To reduce toxicity, a metabolically stable prodrug of SN‐38 (irinotecan's active metabolite) has been designed to be exclusively ...activated by Pd‐functionalized microdevices that can be implanted into tumors. It is also shown the first concomitant uncaging of two drugs used in clinical combinations by the same bioorthogonal method. More information can be found in the Full Paper by P. M. Brennan, A. Unciti‐Broceta, et al. on page 16783 ff.
Thiols are ubiquitous in living systems where they bind strongly to gold surfaces and render interactions with other functional groups basically non‐existent. In their Communication on page 12548 ...ff., J. Santamaría and A. Unciti‐Broceta et al. describe heterogeneous gold catalysts that enable bioorthogonal uncaging (by O/N‐depropargylation) of clinically approved anticancer drugs in cancer cell culture, and the first intracranial activation of a bioorthogonal probe in a zebrafish.
In the decades following the Second World War, and particularly within the context of the newly-formed welfare state, British social work was building a professional identity, albeit an often ...precarious one. Social workers in Britain recognised that an important part of this process was fostering proactive international relationships with colleagues in other countries. This existed alongside more reactive work with the immigrant populations who arrived in the post-war period. This article analyses how both forms of transnationalism had an impact on social workers' professional identities, and how such encounters offer an insight into the everyday negotiation of transnational phenomenon.
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