Functional annotation of human long noncoding RNAs via molecular phenotyping

Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-todate lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.Peer reviewe

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Advanced High-Frequency Measurement Techniques for Electrical and Biological Characterization in CMOS

Precision measurements play crucial roles in science, biology, and engineering. Inparticular, current trends in high-frequency circuit and system designs put extraordinarydemands on accurate device characterization and modeling. On the other hand, the needfor better point-of-care requires substantial innovation in developing miniaturized sensorsand medical devices that ease the biological analysis without sacrificing the accuracy.This research presents two advanced measurement techniques for electrical andbiological characterization applications.In the first part, a novel single-element on-wafer VNA calibration algorithm ispresented dedicated for device characterization at mm-Waves. Conventional calibrationapproaches such as thru-reflect-line (TRL) require at least three precisely-machined andwell-characterized standards. The necessity of probe re-positioning leads to significantmeasurement errors due to mechanical uncertainty as the measurement frequencyapproaches sub-THz. By exploiting on-chip impedance modulation, such an electroniccalibration (E-Cal) algorithm can work with single element without any prior knowledgeof the impedance behavior. This CMOS-based approach opens a new direction in thefield of VNA calibration.In the second part, the implementation of a dielectric spectroscopy biosensor aimingfor single-cell analysis is presented. Most present day clinical flow cytometers usefluorescence-activated cell sorting (FACS), which requires bulky optical detection systemas well as complex sample-labeling process, limiting the assay time and the wide-spreadadoption in the point-of-care (POC) setting. To address these issues, this researchpresents the design and the implementation of a sensor-on-CMOS spectrometer thatmeasures the microwave signature of single cell as a potentially label-free analytic tool.The sensor covers four frequency bands across 6.5 – 30 GHz, offering sub-aF noisesensitivity at 100-kHz bandwidth. Such performance is enabled with injection-lockedoscillator sensors in interferometry architecture. With microfluidic integration,experiments on flow cytometry and molecular sensing are demonstrated