Analysis of metabolomic profiling data from gas chromatography−mass spectrometry (GC/MS) measurements usually relies upon reference libraries metabolite mass spectra to structurally identify and track metabolites. In general, techniques enumerate unidentified metabolites are nonsystematic require manual curation. We present a method software implementation, freely available at http://spectconnect.mit.edu, that can systematically detect components conserved across samples without the need for...

Calibration using the same sample being measured enables quantitative in-the-field diagnostics for complex biological samples.

The first discovery of metabolic changes in cancer occurred almost a century ago. While the genetic underpinnings have dominated its study since then, altered metabolism has recently been acknowledged as key hallmark and metabolism-focused research received renewed attention. emerging field metabolomics - which attempts to profile all metabolites within cell or biological system is now being used analyze on system-wide scale, painting broad picture pathways their interactions with each...

In this paper, we present a fully integrated multi-modality CMOS cellular sensor array with four sensing modalities to characterize different cell physiological responses, including extracellular voltage recording, impedance mapping, optical detection shadow imaging and bioluminescence sensing, thermal monitoring. The consists of nine parallel pixel groups corresponding signal conditioning blocks. Each group comprises one temperature 16 tri-modality pixels, while each can be independently...

Deficiencies in vitamins and minerals (micronutrients) are a critical global health concern, part due to logistical difficulties assessing population micronutrient status. Whole-cell biosensors offer unique opportunity address this issue, with the potential move sample analysis from centralized, resource-intensive clinics minimal-resource, on-site measurement. Here, we present proof-of-concept whole-cell biosensor Escherichia coli for detecting zinc, which deficiencies significant public...

Ruminants play a great role in sustainable livestock since they transform pastures, silage, and crop residues into high-quality human food (i.e. milk beef). Animals with better ability to convert animal protein, measured as trait called feed efficiency (FE), also produce less manure greenhouse gas per kilogram of produced meat. Thus, the identification high cattle is important for nutritional management. Our aim was evaluate potential serum metabolites identify FE beef before enter feedlot.A...

Abstract Biologists pioneering the new field of comparative functional genomics attempt to infer mechanisms gene regulation by looking for similarities and differences activity over time across multiple species. They use three kinds data: data such as measurements, pathway that represent a series reactions within cellular process, phylogenetic relationship describe relatedness No existing visualization tool can visually encode biologically interesting relationships between pathways, genes,...

The development of simple, inexpensive, deployable clinical diagnostics could have a global impact on public health by making measurements patient status more widely accessible to patients regardless of...

Conventional laboratory protein detection techniques are not suitable for point-of-care (POC) use because they require expensive equipment and laborious protocols, existing POC assays suffer from long development timescales. Here, we describe a modular cell-free biosensing platform generalizable that call TLISA (T7 RNA polymerase-linked immunosensing assay), designed extreme flexibility equipment-free use. uses split T7 polymerase fused to affinity domains against protein. The target antigen...

Motif discovery in sequential data is a problem of great interest and with many applications. However, previous methods have been unable to combine exhaustive search complex motif representations are each typically only applicable certain class problems.Here we present generic algorithm (Gemoda) for data. Gemoda can be applied any dataset character, including both categorical real-valued As show, deterministically discovers motifs that maximal composition length. well, the allows choice...

Abstract Simultaneous detection of multiple analytes from a single sample (multiplexing), particularly when done at the point need, can guide complex decision-making without increasing required volume or cost per test. Despite recent advances, multiplexed analyte sensing still typically faces critical limitation measuring only one type molecule (e.g., small molecules nucleic acids) assay platform. Here, we address this bottleneck with customizable platform that integrates cell-free...

Introduction Recently, multicellular spheroids were isolated from a well-established epithelial ovarian cancer cell line, OVCAR-3, and propagated in vitro. These spheroid-derived cells displayed numerous hallmarks of stem cells, which are chemo- radioresistant thought to be significant cause recurrence resultant mortality. Gene set enrichment analysis expression data the OVCAR-3 putative identified several metabolic pathways enriched differentially expressed genes. Before this, there had...

Biotechnology has transformed the production of various chemicals and pharmaceuticals due to its efficient selective processes, but it is inherently limited by use live cells as "biocatalysts." Cell-free expression (CFE) systems, which a protein lysate isolated from whole cells, have potential overcome these challenges broaden scope biomanufacturing. Implementation CFE systems at scale will require determining clear markers activity developing supplementation approaches that compensate for...

Bacterial biosensors can enable programmable, selective chemical production, but difficulties incorporating metabolic pathways into complex sensor circuits have limited their development and applications. Here we overcome these challenges present the of fast-responding, tunable cells that produce different pigmented metabolites based on extracellular concentrations zinc (a critical micronutrient). We create a library dual-input synthetic promoters decouple cell growth from zinc-specific...

Cell-free systems provide a versatile platform for the development of low-cost, easy-to-use sensors diverse analytes. However, sensor affinity dictates response sensitivity, and improving binding can be challenging. Here, we describe efforts to address this problem while developing biosensor vitamin B12, critical micronutrient. We first use B12-responsive transcription factor enable B12-dependent output in cell-free reaction, but resulting responds B12 far above clinically relevant...

Electroporation is a basic yet powerful method for delivering small molecules (RNA, DNA, drugs) across cell membranes by application of an electrical field. It used many diverse applications, from genetically engineering cells to drug- and DNA-based vaccine delivery. Despite this broad utility, the high cost electroporators can keep approach out reach budget-conscious laboratories. To address need, we develop simple, inexpensive, handheld electroporator inspired derived common household...