Time-lapse microscopy is a powerful tool for studying the cell biology of bacterial cells. The development of pipelines that facilitate the automated analysis of these datasets is a long-standing goal of the field. In this paper, we describe , an updated version of our pipeline, developed as an open-source, modular, and holistic suite of algorithms whose input is raw microscopy images and whose output is a wide range of quantitative cellular analyses, including dynamical cell cytometry data and cellular visualizations.
View Article and Find Full Text PDFProtein expression levels optimize cell fitness: Too low an expression level of essential proteins will slow growth by compromising essential processes; whereas overexpression slows growth by increasing the metabolic load. This trade-off naïvely predicts that cells maximize their fitness by sufficiency, expressing just enough of each essential protein for function. We test this prediction in the naturally-competent bacterium by characterizing the proliferation dynamics of essential-gene knockouts at a single-cell scale (by imaging) as well as at a genome-wide scale (by TFNseq).
View Article and Find Full Text PDFProtein expression levels optimize cell fitness: Too low an expression level of essential proteins will slow growth by compromising essential processes; whereas overexpression slows growth by increasing the metabolic load. This trade-off naïvely predicts that cells maximize their fitness by sufficiency, expressing just enough of each essential protein for function. We test this prediction in the naturally-competent bacterium by characterizing the proliferation dynamics of essential-gene knockouts at a single-cell scale (by imaging) as well as at a genome-wide scale (by TFNseq).
View Article and Find Full Text PDFNeil J Watt and Keith Cutler argue that Defra's aim of achieving officially bovine tuberculosis (bTB)-free status for England by 2038 is unlikely to be met without a drastic change to testing and policy.
View Article and Find Full Text PDFBovine tuberculosis is usually diagnosed using tuberculin skin tests or at post-mortem. Recently, we have developed a serological test for bovine tuberculosis in cattle which shows a high degree of accuracy using serum samples. Here, we have assessed the performance of the test using individual bovine milk samples.
View Article and Find Full Text PDFStreptomyces are a genus of ubiquitous soil bacteria from which the majority of clinically utilized antibiotics derive. The production of these antibacterial molecules reflects the relentless competition Streptomyces engage in with other bacteria, including other Streptomyces species. Here we show that in addition to small-molecule antibiotics, Streptomyces produce and secrete antibacterial protein complexes that feature a large, degenerate repeat-containing polymorphic toxin protein.
View Article and Find Full Text PDFApproximately 1 in 6 children in the United States, and 1 in 5 children in our local county (Hamilton County, Ohio), are food insecure. Here, we describe a novel community-academic partnership to address food inequity through distributed leadership and shared power with local neighborhood leaders. Using neighborhood-level data and community voice, 3 Cincinnati neighborhoods with high rates of poverty and food insecurity were selected as the primary intervention targets.
View Article and Find Full Text PDFPurpose: To review the long-term outcomes of complex abdominal wall reconstruction using anterior and posterior component separation (CS) techniques in our center.
Methods: This was a descriptive analytical study. Analysis of data from a prospectively collected database of patients who had undergone Component Separation (CS) repair of incisional hernias was performed.
Bovine tuberculosis is usually diagnosed using tuberculin skin and interferon gamma tests. However, it is clear these tests miss infected animals due to poor sensitivity. The Enferplex Bovine TB antibody test has been validated by the World Organisation for Animal Health as fit for purpose in diagnosing bovine TB.
View Article and Find Full Text PDFBovine tuberculosis is a contagious bacterial disease of worldwide economic, zoonotic and welfare importance caused mainly by Mycobacterium bovis infection. Current regulatory diagnostic methods lack sensitivity and require improvement. We have developed a multiplex serological test for bovine tuberculosis and here we provide an estimate of the diagnostic accuracy of the test in cattle.
View Article and Find Full Text PDFIntroduction: Pediatric firearm injuries are the leading cause of death among American children. While assault is the most commonly cited cause, few studies have investigated circumstances surrounding such injuries. Violence intervention programs (VIPs) have been utilized to combat firearm violence, though a similar lack of knowledge exists regarding possible associations between firearm injury circumstances and youth VIP enrollment.
View Article and Find Full Text PDFAdvances in microscopy hold great promise for allowing quantitative and precise measurement of morphological and molecular phenomena at the single-cell level in bacteria; however, the potential of this approach is ultimately limited by the availability of methods to faithfully segment cells independent of their morphological or optical characteristics. Here, we present Omnipose, a deep neural network image-segmentation algorithm. Unique network outputs such as the gradient of the distance field allow Omnipose to accurately segment cells on which current algorithms, including its predecessor, Cellpose, produce errors.
View Article and Find Full Text PDFThe synthesis of new proteins and the degradation of old proteins in vivo can be quantified in serial samples using metabolic isotope labeling to measure turnover. Because serial biopsies in humans are impractical, we set out to develop a method to calculate the turnover rates of proteins from single human biopsies. This method involved a new metabolic labeling approach and adjustments to the calculations used in previous work to calculate protein turnover.
View Article and Find Full Text PDFConsumer and community engagement (CCE) in the implementation of genomics into health services and associated research is needed to ensure that changes benefit the affected patients. Queensland Genomics was a program to implement genomics into a public health service. We describe its Community Advisory Group's (CAG) structure and function and provide recommendations based on the CAG members' perspectives.
View Article and Find Full Text PDFDNA-protein interactions are central to fundamental cellular processes, yet widely implemented technologies for measuring these interactions on a genome scale in bacteria are laborious and capture only a snapshot of binding events. We devised a facile method for mapping DNA-protein interaction sites in vivo using the double-stranded DNA-specific cytosine deaminase toxin DddA. In 3D-seq (DddA-sequencing), strains containing DddA fused to a DNA-binding protein of interest accumulate characteristic mutations in DNA sequence adjacent to sites occupied by the DNA-bound fusion protein.
View Article and Find Full Text PDFHealth Interpreters enable effective communication between health practitioners and patients with limited knowledge of the predominant language. This study developed and evaluated a training session introducing Health Interpreters to genetics. The online training was delivered multiple times as a single 2-h session comprising lectures and activities.
View Article and Find Full Text PDFThe establishment of genomics in health care systems has been occurring for the past decade. It is recognised that implementing genomics within a health service is challenging without a system-wide approach. Globally, as clinical genomics implementation programs have matured there is a growing body of information around program design and outcomes.
View Article and Find Full Text PDFSignificance: Diffuse optical spectroscopic imaging (DOSI) is a versatile technology sensitive to changes in tissue composition and hemodynamics and has been used for a wide variety of clinical applications. Specific applications have prompted the development of versions of the DOSI technology to fit specific clinical needs. This work describes the development and characterization of a multi-modal DOSI (MM-DOSI) system that can acquire metabolic, compositional, and pulsatile information at multiple penetration depths in a single hardware platform.
View Article and Find Full Text PDF