Portable BLAST-like algorithm library and its implementations for command line, Python, and R.

Basic local-alignment search tool (BLAST) is a versatile and commonly used sequence analysis tool in bioinformatics. BLAST permits fast and flexible sequence similarity searches across nucleotide and amino acid sequences, leading to diverse applications such as protein domain identification, orthology searches, and phylogenetic annotation. Most BLAST implementations are command line tools which produce output as comma-separated values files.

Re-Evaluation of Product Outcomes in the Rh-Catalyzed Ring Expansion of Aziridines with -Sulfonyl-1,2,3-Triazoles.

-heterocycles are prevalent in pharmaceuticals and natural products, but traditional methods often do not introduce significant stereochemical complexity into the ring. We previously reported a Rh-catalyzed ring expansion of aziridines and sulfonyl-1,2,3-triazoles to furnish dehydropiperazines with excellent diastereocontrol. However, later studies employing ketone-containing carbene precursors showed that [3,9]-bicyclic aziridine formation competes with production of the desired heterocyclic scaffolds.

Use of a Novel Polymer-Coated Steel as an Alternative to Traditional Can Manufacturing in the Food Industry.

Metal containers (both food and beverage cans) are made from huge steel or aluminum coils that are transformed into two- or three-piece products. During the manufacturing process, the metal is sprayed on both sides and the aerosol acts as insulation, but unfortunately produces volatile organic compounds (VOCs). The present work presents a different way to manufacture these containers using a novel prelaminated two-layer polymer steel.

Digital multiplex ligation assay for highly multiplexed screening of β-lactamase-encoding genes in bacterial isolates.

Increasing incidence of antibiotic resistance in clinical and environmental settings calls for increased scalability in their surveillance. Current screening technologies are limited by the number of samples and genes that can easily be screened. We demonstrate here digital multiplex ligation assay (dMLA) as a low-cost targeted genomic detection workflow capable of highly-parallel screening of bacterial isolates for multiple target gene regions simultaneously.

Intermolecular [3+3] ring expansion of aziridines to dehydropiperi-dines through the intermediacy of aziridinium ylides.

The importance of N-heterocycles in drugs has stimulated diverse methods for their efficient syntheses. Methods that introduce significant stereochemical complexity are attractive for identifying new bioactive amine chemical space. Here, we report a [3 + 3] ring expansion of bicyclic aziridines and rhodium-bound vinyl carbenes to form complex dehydropiperidines in a highly stereocontrolled rearrangement.

Ring Expansion of Bicyclic Methyleneaziridines via Concerted, Near-Barrierless [2,3]-Stevens Rearrangements of Aziridinium Ylides.

The synthesis of densely functionalized azetidinesin a highly stereocontrolled manner is challenging, but interest in the bioactivities of these small heterocycles has stimulated methods for their preparation. We recently reported a one-carbon ring expansion of bicyclic methylene aziridines under dirhodium catalysis capable of delivering enantioenriched azetidines. This work explores this ring expansion using computational and experimental studies.

A Stereoselective [3+1] Ring Expansion for the Synthesis of Highly Substituted Methylene Azetidines.

The reaction of rhodium-bound carbenes with strained bicyclic methylene aziridines results in a formal [3+1] ring expansion to yield highly substituted methylene azetidines with excellent regio- and stereoselectivity. The reaction appears to proceed through an ylide-type mechanism, where the unique strain and structure of the methylene aziridine promotes a ring-opening/ring-closing cascade that efficiently transfers chirality from substrate to product. The resultant products can be elaborated into new azetidine scaffolds containing vicinal tertiary-quaternary and even quaternary-quaternary stereocenters.

Anti-Endosialin Antibody-Drug Conjugate: Potential in Sarcoma and Other Malignancies.

Endosialin/TEM1/CD248 is a cell surface protein expressed at high levels by the malignant cells of about 50% of sarcomas and neuroblastomas. The antibody-drug conjugate (ADC) anti-endosialin-MC-VC-PABC-MMAE was selectively cytotoxic to endosialin-positive cells in vitro and achieved profound and durable antitumor efficacy in preclinical human tumor xenograft models of endosialin-positive disease. MC-VC-PABC-MMAE was conjugated with anti-endosialin with 3-4 MMAE molecules per ADC.

Removal of Metabolic Liabilities Enables Development of Derivatives of Procaspase-Activating Compound 1 (PAC-1) with Improved Pharmacokinetics.

Procaspase-activating compound 1 (PAC-1) is an o-hydroxy-N-acylhydrazone that induces apoptosis in cancer cells by chelation of labile inhibitory zinc from procaspase-3. PAC-1 has been assessed in a wide variety of cell culture experiments and in vivo models of cancer, with promising results, and a phase 1 clinical trial in cancer patients has been initiated (NCT02355535). For certain applications, however, the in vivo half-life of PAC-1 could be limiting.

High speed fracture fixation: assessing resulting fixation stability and fastener withdrawal strength.

A new method of bone fracture fixation has been developed in which fixation darts (small diameter nails/pins) are driven across a fracture site at high velocity with a pneumatically powered gun. When fixation darts are inserted oblique to one another, kinematic constraints prevent fragment motion and allow bone healing to progress. The primary aim of this study is to determine if fixation darts can provide reasonable fixation stability compared to bone screws, which were used as a benchmark since they represent a simple, yet well-established, surgical technique.

Targeting HER2-positive cancer with dolastatin 15 derivatives conjugated to trastuzumab, novel antibody-drug conjugates.

Purpose: Targeting tubulin binders to cancer cells using antibody-drug conjugates (ADCs) has great potential to become an effective cancer treatment with low normal tissue toxicity. The nature of the linker used to tether the tubulin binder to the antibody and the conjugation sites on the antibody and the small molecule are important factors in the ADC stability and effectiveness.

Methods: We explored the use of tubulin-targeting dolastatin 15 derivatives (Dol15) tethered covalently to a representative antibody, trastuzumab, via cleavable and non-cleavable linkers at varying antibody reactive sites (i.

SCD1 inhibition causes cancer cell death by depleting mono-unsaturated fatty acids.

Increased metabolism is a requirement for tumor cell proliferation. To understand the dependence of tumor cells on fatty acid metabolism, we evaluated various nodes of the fatty acid synthesis pathway. Using RNAi we have demonstrated that depletion of fatty-acid synthesis pathway enzymes SCD1, FASN, or ACC1 in HCT116 colon cancer cells results in cytotoxicity that is reversible by addition of exogenous fatty acids.

High speed insertion of bone fracture fixation pins: a finite element penetration model with experimental comparisons.

A new method of bone fracture fixation is considered in which small pins/darts are dynamically inserted into bone to prevent translation and rotation at the fracture site. An ABAQUS model was developed to analyze dart penetration in cortical and cancellous bone for varying dart diameter, material, and velocity, and cortical thickness. The method is advocated for bioresorbable darts, so polylactide (PLA) and magnesium are the materials examined in this study.

Parallel synthesis and biological evaluation of 837 analogues of procaspase-activating compound 1 (PAC-1).

Procaspase-Activating Compound 1 (PAC-1) is an ortho-hydroxy N-acyl hydrazone that enhances the enzymatic activity of procaspase-3 in vitro and induces apoptosis in cancer cells. An analogue of PAC-1, called S-PAC-1, was evaluated in a veterinary clinical trial in pet dogs with lymphoma and found to have considerable potential as an anticancer agent. With the goal of identifying more potent compounds in this promising class of experimental therapeutics, a combinatorial library based on PAC-1 was created, and the compounds were evaluated for their ability to induce death of cancer cells in culture.

Endosialin: a novel malignant cell therapeutic target for neuroblastoma.

Endosialin emerged recently as a potential therapeutic target for sarcoma. Since some sarcoma subtypes, such as Ewing's sarcoma, show characteristics of neuroendocrine differentiation, we wondered whether cancers with neuro-endocrine properties and/or neuroectodermal origin, such as neuroblastoma, small cell lung cancer and melanoma, may express endosialin. Endosialin protein expression was surveyed in neuroblastoma, small cell lung cancer and melanoma in human clinical specimens by immunohistochemistry (IHC) and in human cell lines by flow cytometry.

Endosialin is expressed in high grade and advanced sarcomas: evidence from clinical specimens and preclinical modeling.

We previously surveyed the expression of endosialin/ CD248/TEM-1 by immunohistochemistry in human clinical specimens of sarcomas and documented expression in tumor cells, stromal cells and vasculature. In the present study, we completed a retrospective analysis of the diagnostic reports available for these same samples in order to identify high-grade and metastatic disease. Our results show that endosialin can be detected in advanced disease.

Genz-644282, a novel non-camptothecin topoisomerase I inhibitor for cancer treatment.

Purpose: Genz-644282 [8,9-dimethoxy-5-(2-N-methylaminoethyl)-2,3-methylenedioxy-5H-dibenzo[c,h][1,6]naphthyridin-6-one] has emerged as a promising candidate for antitumor agents. This report describes the bone marrow colony-forming unit, granulocyte macrophage (CFU-GM) and tumor cell CFU activity of topoisomerase I (Top1) inhibitors, such as Genz-644282, topotecan, irinotecan/SN-38, and ARC-111, and examines their activity in several human tumor xenograft models.

Experimental Design: Colony-forming assays were conducted with mouse and human bone marrow and eight human tumor cell lines.

Bone marrow CFU-GM and human tumor xenograft efficacy of three antitumor nucleoside analogs.

Nucleoside analogs are rationally designed anticancer agents that disrupt DNA and RNA synthesis. Fludarabine and cladribine have important roles in the treatment of hematologic malignancies. Clofarabine is a next generation nucleoside analog which is under clinical investigation.

Bone marrow CFU-GM and human tumor xenograft efficacy of three tubulin binding agents.

Purpose: The dynamic instability of microtubules in cells is one of the key targets of anticancer therapeutics. Microtubule-disrupting agents such as vinca alkaloids and microtubule-stabilizing agents such as taxanes are important antitumor agents. The bone marrow toxicity and human tumor xenograft activity of three tubulin-binding compounds, vincristine, paclitaxel, and tasidotin were compared.

Bone marrow and tumor cell colony-forming units and human tumor xenograft efficacy of noncamptothecin and camptothecin topoisomerase I inhibitors.

Topoisomerase I (TopoI), an established anticancer target, is an enzyme producing a single-strand DNA break during transcription. Several noncamptothecin TopoI inhibitors have been identified. One of these, ARC-111, was compared with two clinically used camptothecins, topotecan and irinotecan/SN-38.

Reinforcement of bone cement using zirconia fibers with and without acrylic coating.

Acrylic (polymethylmethacrylate or PMMA) bone cement was modified by the addition of high-strength zirconia fibers with average lengths of 200 microm and diameters of 15 microm or 30 microm. A novel emulsion polymerization process was developed to encapsulate individual fibers in PMMA. Improvements in tensile and compressive properties as well as in fracture toughness were investigated upon incorporation of uncoated and acrylic coated zirconia fibers.

Mechanism of action of the microtubule-targeted antimitotic depsipeptide tasidotin (formerly ILX651) and its major metabolite tasidotin C-carboxylate.

Tasidotin (ILX-651), an orally active synthetic microtubule-targeted derivative of the marine depsipeptide dolastatin-15, is currently undergoing clinical evaluation for cancer treatment. Tasidotin inhibited proliferation of MCF7/GFP breast cancer cells with an IC(50) of 63 nmol/L and inhibited mitosis with an IC(50) of 72 nmol/L in the absence of detectable effects on spindle microtubule polymer mass. Tasidotin inhibited the polymerization of purified tubulin into microtubules weakly (IC(50) approximately 30 micromol/L).

The mechanism of action of docetaxel (Taxotere) in xenograft models is not limited to bcl-2 phosphorylation.

Docetaxel is a new taxoid compound with a broad spectrum of antitumor activity. Previous studies have shown that in vitro treatment of specific human tumor lines with docetaxel is associated with the phosphorylation and inactivation of the bcl-2 protein and the occurrence of apoptosis. The goal of this study was to examine whether bcl-2 expression is truly required for in vivo responsiveness to docetaxel.

Effects of pre-cooling and pre-heating procedures on cement polymerization and thermal osteonecrosis in cemented hip replacements.

Numerical studies were performed to investigate bone cement polymerization, temperature history and thermal osteonecrosis in cemented hip replacements with finite element methods. In this paper, the effects of pre-cooling and pre-heating of the prosthesis and/or the cement prior to implantation were simulated. It was found that the cement polymerization initiated near the bone-cement interface and progressed toward the prosthesis when both the cement and prosthesis were initially at room temperature.