Reproducible image-based profiling with Pycytominer

Technological advances in high-throughput microscopy have facilitated the acquisition of cell images at a rapid pace, and data pipelines can now extract and process thousands of image-based features from microscopy images. These features represent valuable single-cell phenotypes that contain information about cell state and biological processes. The use of these features for biological discovery is known as image-based or morphological profiling. However, these raw features need processing before use and image-based profiling lacks scalable and reproducible open-source software. Inconsistent processing across studies makes it difficult to compare datasets and processing steps, further delaying the development of optimal pipelines, methods, and analyses. To address these issues, we present Pycytominer, an open-source software package with a vibrant community that establishes an image-based profiling standard. Pycytominer has a simple, user-friendly Application Programming Interface (API) that implements image-based profiling functions for processing high-dimensional morphological features extracted from microscopy images of cells. Establishing Pycytominer as a standard image-based profiling toolkit ensures consistent data processing pipelines with data provenance, therefore minimizing potential inconsistencies and enabling researchers to confidently derive accurate conclusions and discover novel insights from their data, thus driving progress in our field.Comment: 13 pages, 4 figure

Oncological outcome after free jejunal flap reconstruction for carcinoma of the hypopharynx

It has been a common practice among the oncologist to reduce the dosage of adjuvant radiotherapy for patients after free jejunal flap reconstruction. The current aims to study potential risk of radiation to the visceral flap and the subsequent oncological outcome. Between 1996 and 2010, consecutive patients with carcinoma of the hypopharynx requiring laryngectomy, circumferential pharyngectomy and post-operative irradiation were recruited. Ninety-six patients were recruited. TNM tumor staging at presentation was: stage II (40.6%), stage III (34.4%) and stage IV (25.0%). Median follow-up period after surgery was 68 months. After tumor ablation, reconstruction was performed using free jejunal flap (60.4%), pectoralis major myocutaneous (PM) flap (31.3%) and free anterolateral thigh (ALT) flap (8.3%). All patients underwent adjuvant radiotherapy within 6.4 weeks after surgery. The mean total dose of radiation given to those receiving cutaneous and jejunal flap reconstruction was 62.2 Gy and 54.8 Gy, respectively. There was no secondary ischaemia or necrosis of the flaps after radiotherapy. The 5-year actuarial loco-regional tumor control for the cutaneous flap and jejunal flap group was: stage II (61 vs. 69%, p = 0.9), stage III (36 vs. 46%, p = 0.2) and stage IV (32 vs. 14%, p = 0.04), respectively. Reduction of radiation dosage in free jejunal group adversely affects the oncological control in stage IV hypopharyngeal carcinoma. In such circumstances, tubed cutaneous flaps are the preferred reconstructive option, so that full-dose radiotherapy can be given

Multi-wavelength study of X-ray luminous clusters at z ~ 0.3 I. Star formation activity of cluster galaxies

The current paradigm of cosmic formation and evolution of galaxy clusters foresees growth mostly through merging. Galaxies in the infall region or in the core of a cluster undergo transformations owing to different environmental stresses. For two X-ray luminous clusters at redshift z ~ 0.3 with opposite X-ray morphologies, RXCJ0014.3-3022 and RXCJ2308.3-0211, we assess differences in galaxy populations as a function of cluster topography. Cluster large-scale structure and substructure are determined from the combined photometry in the B, V, and R bands, and from multi-object optical spectroscopy at low resolution. A spectral index analysis is performed, based on the [OII] and Hdelta features, and the D4000 break, available for more than 100 member galaxies per cluster. Combination of spectral indices and FUV-optical colours provides a picture of the star formation history in galaxies. In spite of the potential presence of a small fraction of galaxies with obscured star formation activity, the average star-formation history of cluster members is found to depend on cluster-centric distance and on substructure. There is a sharp increase in star formation activity along two well-defined filamentary structures of the merging cluster RXCJ0014.3-3022, out to its virial radius and beyond, produced by luminous (L ~ L*) and sub-L* galaxies. Conversely, the regular cool-core cluster RXCJ2308.3-0211 mostly hosts galaxies which either populate the red sequence or are becoming passive. These results suggest the existence of a correspondence between assembly state and overall age of the stellar populations of galaxies inside the virialized region and in the surrounding large scale structure of massive clusters at z ~ 0.3. (Abridged)Comment: 18 pages, 17 figures, accepted for publication in Astronomy & Astrophysic

Agglutination-Inhibition Assay for the Detection of Recombinant Proteins Tagged with Peptide Epitopes

We have demonstrated that the expression of recombinant proteins labeled with an immunoreactive epitope can be rapidly assessed and quantitated using a modified haemagglutination inhibition assay in enzyme-linked immunosorbent assay (ELISA) trays. The agglutination of erythrocytes from a droplet of whole blood provided a simple visual assay. The additional reagents required for the assay were a recombinant anti-human erythrocyte Fab fragment fused to a peptide epitope and a bivalent antibody with specificity to the same epitope. In this report, we found that a convenient and sensitive epitope was the octapeptide FLAG® in conjunction with the M2 anti-FLAG antibody, which had affinity to FLAG incorporated either at the C-terminus or N-terminus of the recombinant protein. The agglutination-inhibition (AI) assay was configured to detect as little as 1 mg/L of soluble recombinant protein in a 30-min assay. Since the AI assay was substantially more rapid and convenient than dot-blot or Western blot analyses, our laboratory now uses this method routinely for the assay of FLAG-labeled recombinant products following protein expression and subsequent small- and large-scale purification procedures

Gadolinium-DTPA amphiphile nanoassemblies: Agents for magnetic resonance imaging and neutron capture therapy

Engineering biocompatible and physiologically stable nanoscaled therapeutics and imaging agents with the ability to target tumor tissue is a key challenge for the advancement of cancer therapeutics and diagnostic imaging. Here, we present chelating amphiphiles with the capacity to form nanoassembled colloidal particles containing high payloads of gadolinium (Gd) ions. We present the in situ synthesis and complexation of Gd with colloidal nanoassemblies (NAs) based on diethylenetriamine pentaacetic acid (DTPA) amphiphiles. This method allows for facile simultaneous incorporation of several metal ions for applications in multimodal imaging and therapeutics. The diverse internally nanostructured NAs made from sole precursor amphiphiles and their Gd-complexes were investigated by synchrotron small angle X-ray scattering (SAXS) and cryo-TEM. Depending on the molecular structure of the amphiphiles, the structures of NAs range from micelles to liposomes, to colloidal particles of inverse hexagonal (hexosomes) and inverse bicontinuous cubic phases (cubosomes), to multilayered nanospheres. The in vitro contrast activity of these NAs exhibited high relaxivity values as T1-weighted magnetic resonance imaging (MRI) contrast enhancement agents. Further, an α-Flag antibody fragment (Fab′) was bioconjugated to the surface of the Gd-complexed NAs. The binding ability of these targeted NAs to a FLAG-tagged protein was confirmed by SDS-PAGE. The in vitro cytotoxicity against two cell lines showed that except for the negatively charged micellar Gd-DTPA amphiphile, liposomal and higher order internally nanostructured NAs had low cell toxicity. The efficient cellular uptake of Gd-NAs by melanoma cancer cells was also investigated. This journal i

Sugar analog synthesis by in vitro biocatalytic cascade:A comparison of alternative enzyme complements for dihydroxyacetone phosphate production as a precursor to rare chiral sugar synthesis

Carbon-carbon bond formation is one of the most challenging reactions in synthetic organic chemistry, and aldol reactions catalysed by dihydroxyacetone phosphate-dependent aldolases provide a powerful biocatalytic tool for combining C-C bond formation with the generation of two new stereo-centres, with access to all four possible stereoisomers of a compound. Dihydroxyacetone phosphate (DHAP) is unstable so the provision of DHAP for DHAP-dependent aldolases in biocatalytic processes remains complicated. Our research has investigated the efficiency of several different enzymatic cascades for the conversion of glycerol to DHAP, including characterising new candidate enzymes for some of the reaction steps. The most efficient cascade for DHAP production, comprising a one-pot four-enzyme reaction with glycerol kinase, acetate kinase, glycerophosphate oxidase and catalase, was coupled with a DHAP-dependent fructose-1,6-biphosphate aldolase enzyme to demonstrate the production of several rare chiral sugars. The limitation of batch biocatalysis for these reactions and the potential for improvement using kinetic modelling and flow biocatalysis systems is discussed.</p

Engineering of an anti-epidermal growth factor receptor antibody to single chain format and labeling by sortase A-mediated protein ligation

Sortase-mediated protein ligation is a biological covalent conjugation system developed from the enzymatic cell wall display mechanism found in Staphylococcus aureus. This three-component system requires: (i) purified Sortase A (SrtA) enzyme; (ii) a substrate containing the LPXTG peptide recognition sequence; and (iii) an oligo-glycine acceptor molecule. We describe cloning of the single-chain antibody sc528, which binds to the extracellular domain of the epidermal growth factor receptor (EGFR), from the parental monoclonal antibody and incorporation of a LPETGG tag sequence. Utilizing recombinant SrtA, we demonstrate successful incorporation of biotin from GGG-biotin onto sc528. EGFR is an important cancer target and is over-expressed in human tumor tissues and cancer lines, such as the A431 epithelial carcinoma cells. SrtA-biotinylated sc528 specifically bound EGFR expressed on A431 cells, but not negative control lines. Similarly, when sc528 was labeled with fluorescein we observed antigen-specific labeling. The ability to introduce functionality into recombinant antibodies in a controlled, site-specific manner has applications in experimental, diagnostic, and potentially clinical settings. For example, we demonstrate addition of all three reaction components in situ within a biosensor flow cell, resulting in oriented covalent capture and presentation of sc528, and determination of precise affinities for the antibody-receptor interaction

DHAP production <i>via</i> two step enzymatic cascade.

<p>DHAP production <i>via</i> two step enzymatic cascade.</p