This paper presents a proof-of-principle method, called InfoBiology, to write and encode data using arrays of genetically engineered strains of Escherichia coli with fluorescent proteins (FPs) as phenotypic markers. In InfoBiology, we encode, send, and release information using living organisms as carriers of data. Genetically engineered systems offer exquisite control of both genotype and phenotype. Living systems also offer the possibility for timed release of information as phenotypic features can take hours or days to develop. We use growth media and chemically induced gene expression as cipher keys or "biociphers" to develop encoded messages. The messages, called Steganography by Printed Arrays of Microbes (SPAM), consist of a matrix of spots generated by seven strains of E. coli, with each strain expressing a different FP. The coding scheme for these arrays relies on strings of paired, septenary digits, where each pair represents an alphanumeric character. In addition, the photophysical properties of the FPs offer another method for ciphering messages. Unique combinations of excited and emitted wavelengths generate distinct fluorescent patterns from the Steganography by Printed Arrays of Microbes (SPAM). This paper shows a new form of steganography based on information from engineered living systems. The combination of bio-and "photociphers" along with controlled timed-release exemplify the capabilities of InfoBiology, which could enable biometrics, communication through compromised channels, easy-to-read barcoding of biological products, or provide a deterrent to counterfeiting.biotechnology | infochemistry | information technology T he intrinsic high information content and information flow in biological systems has the potential to be used to translate nonbiological genetically encoded information into an easily read phenotypic signal. In this context, genetically engineered systems are of particular utility because they enable exquisite control of both genotype and phenotype (1). Here we describe the use of living organisms as the carriers of encoded messages. Phenotypic features have previously been used as cipher keys for the identification of individuals. Biometric ciphers, such as fingerprint, iris, and retinal scans, are examples of ways in which the unique phenotypic characteristics of individuals can be used to control access to facilities or data (2). Although biometrics have found their way into "real-world" applications, biometric ciphers only function as cipher keys and do not play a role in the storage, transmission, or encoding of data. Examples of information embedded in biological systems include the insertion of synthetic data-encoding DNA (nonprotein coding) for trademark and watermarking purpose (3, 4) and for long-term information storage (5-8). Although such systems seem convenient for high-density applications of data storage, decoding high-density information from nonprotein coding DNA requires sophisticated sequencing capabilities for data readout.We have previously employed chem...

The cell is the basic unit of biology and protein expression drives cellular function. Tracking protein expression in single cells enables the study of cellular pathways and behavior but requires methodologies sensitive enough to detect low numbers of protein molecules with a wide dynamic range to distinguish unique cells and quantify population distributions. This study presents an ultrasensitive and automated approach for quantifying phenotypic responses with single cell resolution using single molecule array (SiMoA) technology. We demonstrate how prostate specific antigen (PSA) expression varies over several orders of magnitude between single prostate cancer cells and how PSA expression shifts with genetic drift. Single cell SiMoA introduces a straightforward process that is capable of detecting both high and low protein expression levels. This technique could be useful for understanding fundamental biology and may eventually enable both earlier disease detection and targeted therapy.

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Background: Multiplex tissue analysis has revolutionized our understanding of the tumor microenvironment (TME) with implications for biomarker development and diagnostic testing. Multiplex labeling is used for specific clinical situations, but there remain barriers to expanded use in anatomic pathology practice.Methods: We review immunohistochemistry (IHC) and related assays used to localize molecules in tissues, with reference to United States regulatory and practice landscapes. We review multiplex methods and strategies used in clinical diagnosis and in research, particularly in immuno-oncology. Within the framework of assay design and testing phases, we examine the suitability of multiplex immunofluorescence (mIF) for clinical diagnostic workflows, considering its advantages and challenges to implementation.Results: Multiplex labeling is poised to radically transform pathologic diagnosis because it can answer questions about tissue-level biology and single-cell phenotypes that cannot be addressed with traditional IHC biomarker panels. Widespread implementation will require improved detection chemistry, illustrated by InSituPlex technology (Ultivue, Inc., Cambridge, MA) that allows coregistration of hematoxylin and eosin (H&E) and mIF images, greater standardization and interoperability of workflow and data pipelines to facilitate consistent interpretation by pathologists, and integration of multichannel images into digital pathology whole slide imaging (WSI) systems, including interpretation aided by artificial intelligence (AI). Adoption will also be facilitated by evidence that justifies incorporation into clinical practice, an ability to navigate regulatory pathways, and adequate health care budgets and reimbursement. We expand the brightfield WSI system “pixel pathway” concept to multiplex workflows, suggesting that adoption might be accelerated by data standardization centered on cell phenotypes defined by coexpression of multiple molecules.Conclusion: Multiplex labeling has the potential to complement next generation sequencing in cancer diagnosis by allowing pathologists to visualize and understand every cell in a tissue biopsy slide. Until mIF reagents, digital pathology systems including fluorescence scanners, and data pipelines are standardized, we propose that diagnostic labs will play a crucial role in driving adoption of multiplex tissue diagnostics by using retrospective data from tissue collections as a foundation for laboratory-developed test (LDT) implementation and use in prospective trials as companion diagnostics (CDx).

An immunohistochemical study was performed on three groups of young cattle (21, 60 and 300 days of age). Tonsils (palatine and pharyngeal) and mucosae (nasal and oral) were removed. Eight monoclonal antibodies (specific for CD3, CD2, CD4, CD8, WC1, cell-surface IgM, cell-surface IgG and MHC class II molecules) and an avidin/biotin complex method on frozen sections were used. The immunological cytoarchitecture of bovine tonsils is similar to that of human tonsils. Nevertheless, these lymphoid tissues are not fully developed during the first weeks of life: T and B dependent areas not well-differentiated, few germinal centres, few intra-epithelial WC1+ T lymphocytes. In contrast, at 2 months, tonsils possess all the elements of a mucosa-associated lymphoid tissue (MALT). Tonsillar or mucosal epithelium is infiltrated by a large number of CD8+, WC1+ T lymphocytes and cells which express MHC class II molecules. Between 21 and 60 days, the number of WC1+ T lymphocytes increase markedly in the tonsillar epithelium. These results accredit the hypothesis that the presence of antigens has an effect on the localization of these lymphocytes at these sites.