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Open Access Publications from the University of California

This series is home to publications and data sets from the Bourns College of Engineering at the University of California, Riverside.

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Center for Environmental Research and Technology

Genome-wide functional screens enable the prediction of high activity CRISPR-Cas9 and -Cas12a guides in Yarrowia lipolytica.

(2022)

Genome-wide functional genetic screens have been successful in discovering genotype-phenotype relationships and in engineering new phenotypes. While broadly applied in mammalian cell lines and in E. coli, use in non-conventional microorganisms has been limited, in part, due to the inability to accurately design high activity CRISPR guides in such species. Here, we develop an experimental-computational approach to sgRNA design that is specific to an organism of choice, in this case the oleaginous yeast Yarrowia lipolytica. A negative selection screen in the absence of non-homologous end-joining, the dominant DNA repair mechanism, was used to generate single guide RNA (sgRNA) activity profiles for both SpCas9 and LbCas12a. This genome-wide data served as input to a deep learning algorithm, DeepGuide, that is able to accurately predict guide activity. DeepGuide uses unsupervised learning to obtain a compressed representation of the genome, followed by supervised learning to map sgRNA sequence, genomic context, and epigenetic features with guide activity. Experimental validation, both genome-wide and with a subset of selected genes, confirms DeepGuide's ability to accurately predict high activity sgRNAs. DeepGuide provides an organism specific predictor of CRISPR guide activity that with retraining could be applied to other fungal species, prokaryotes, and other non-conventional organisms.

Cover page of Siderophores provoke extracellular superoxide production by Arthrobacter strains during carbon sources-level fluctuation.

Siderophores provoke extracellular superoxide production by Arthrobacter strains during carbon sources-level fluctuation.

(2022)

Superoxide and other reactive oxygen species (ROS) shape microbial communities and drive the transformation of metals and inorganic/organic matter. Taxonomically diverse bacteria and phytoplankton produce extracellular superoxide during laboratory cultivation. Understanding the physiological reasons for extracellular superoxide production by aerobes in the environment is a crucial question yet not fully solved. Here, we showed that iron-starving Arthrobacter sp. QXT-31 (A. QXT-31) secreted a type of siderophore [deferoxamine (DFO)], which provoked extracellular superoxide production by A. QXT-31 during carbon sources-level fluctuation. Several other siderophores also demonstrated similar effects to A. QXT-31. RNA-Seq data hinted that DFO stripped iron from iron-bearing proteins in electron transfer chain (ETC) of metabolically active A. QXT-31, resulting in electron leakage from the electron-rich (resulting from carbon sources metabolism by A. QXT-31) ETC and superoxide production. Considering that most aerobes secrete siderophore(s) and undergo carbon sources-level fluctuation, the superoxide-generation pathway is likely a common pathway by which aerobes produce extracellular superoxide in the environment, thus influencing the microbial community and cycling of elements. Our results pointed that the ubiquitous siderophore might be the potential driving force for the microbial generation of superoxide and other ROS and revealed the important role of iron physiology in microbial ROS generation.

Enhanced specificity mutations perturb allosteric signaling in CRISPR-Cas9.

(2021)

CRISPR-Cas9 (clustered regularly interspaced short palindromic repeat and associated Cas9 protein) is a molecular tool with transformative genome editing capabilities. At the molecular level, an intricate allosteric signaling is critical for DNA cleavage, but its role in the specificity enhancement of the Cas9 endonuclease is poorly understood. Here, multi-microsecond molecular dynamics is combined with solution NMR and graph theory-derived models to probe the allosteric role of key specificity-enhancing mutations. We show that mutations responsible for increasing the specificity of Cas9 alter the allosteric structure of the catalytic HNH domain, impacting the signal transmission from the DNA recognition region to the catalytic sites for cleavage. Specifically, the K855A mutation strongly disrupts the allosteric connectivity of the HNH domain, exerting the highest perturbation on the signaling transfer, while K810A and K848A result in more moderate effects on the allosteric communication. This differential perturbation of the allosteric signal correlates to the order of specificity enhancement (K855A > K848A ~ K810A) observed in biochemical studies, with the mutation achieving the highest specificity most strongly perturbing the signaling transfer. These findings suggest that alterations of the allosteric communication from DNA recognition to cleavage are critical to increasing the specificity of Cas9 and that allosteric hotspots can be targeted through mutational studies for improving the system's function.

Effect of Al2O3 Passive Layer on Stability and Doping of MoS2 Field-Effect Transistor (FET) Biosensors.

(2021)

Molybdenum disulfide (MoS2) features a band gap of 1.3 eV (indirect) to 1.9 eV (direct). This tunable band gap renders MoS2 a suitable conducting channel for field-effect transistors (FETs). In addition, the highly sensitive surface potential in MoS2 layers allows the feasibility of FET applications in biosensors, where direct immobilization and detection of biological molecules are conducted in wet conditions. In this work, we report, for the first time, the degradation of chemical vapor deposition (CVD) grown MoS2 FET-based sensors in the presence of phosphate buffer and water, which caused false positive response in detection. We conclude the degradation was originated by physical delamination of MoS2 thin films from the SiO2 substrate. The problem was alleviated by coating the sensors with a 30 nm thick aluminum oxide (Al2O3) layer using atomic layer deposition technique (ALD). This passive oxide thin film not only acted as a protecting layer against the device degradation but also induced a strong n-doping onto MoS2, which permitted a facile method of detection in MoS2 FET-based sensors using a low-power mode chemiresistive I-V measurement at zero gate voltage (Vgate = 0 V). Additionally, the oxide layer provided available sites for facile functionalization with bioreceptors. As immunoreaction plays a key role in clinical diagnosis and environmental analysis, our work presented a promising application using such enhanced Al2O3-coated MoS2 chemiresistive biosensors for detection of HIgG with high sensitivity and selectivity. The biosensor was successfully applied to detect HIgG in artificial urine, a complex matrix containing organics and salts.

6 nm super-resolution optical transmission and scattering spectroscopic imaging of carbon nanotubes using a nanometer-scale white light source.

(2021)

Optical transmission and scattering spectroscopic microscopy at the visible and adjacent wavelengths denote one of the most informative and inclusive characterization methods in material research. Unfortunately, restricted by the diffraction limit of light, it cannot resolve the nanoscale variation in light absorption and scattering, diagnostics of the local inhomogeneity in material structure and properties. Moreover, a large quantity of nanomaterials has anisotropic optical properties that are appealing yet hard to characterize through conventional optical methods. There is an increasing demand to extend the optical hyperspectral imaging into the nanometer length scale. In this work, we report a super-resolution hyperspectral imaging technique that uses a nanoscale white light source generated by superfocusing the light from a tungsten-halogen lamp to simultaneously obtain optical transmission and scattering spectroscopic images. A 6-nm spatial resolution in the visible to near-infrared wavelength regime (415-980 nm) is demonstrated on an individual single-walled carbon nanotube (SW-CNT). Both the longitudinal and transverse optical electronic transitions are measured, and the SW-CNT chiral indices can be identified. The band structure modulation in a SW-CNT through strain engineering is mapped.

Development and Utilization of Multifunctional Polymeric Scaffolds for the Regulation of Physical Cellular Microenvironments.

(2021)

Polymeric biomaterials exhibit excellent physicochemical characteristics as a scaffold for cell and tissue engineering applications. Chemical modification of the polymers has been the primary mode of functionalization to enhance biocompatibility and regulate cellular behaviors such as cell adhesion, proliferation, differentiation, and maturation. Due to the complexity of the in vivo cellular microenvironments, however, chemical functionalization alone is usually insufficient to develop functionally mature cells/tissues. Therefore, the multifunctional polymeric scaffolds that enable electrical, mechanical, and/or magnetic stimulation to the cells, have gained research interest in the past decade. Such multifunctional scaffolds are often combined with exogenous stimuli to further enhance the tissue and cell behaviors by dynamically controlling the microenvironments of the cells. Significantly improved cell proliferation and differentiation, as well as tissue functionalities, are frequently observed by applying extrinsic physical stimuli on functional polymeric scaffold systems. In this regard, the present paper discusses the current state-of-the-art functionalized polymeric scaffolds, with an emphasis on electrospun fibers, that modulate the physical cell niche to direct cellular behaviors and subsequent functional tissue development. We will also highlight the incorporation of the extrinsic stimuli to augment or activate the functionalized polymeric scaffold system to dynamically stimulate the cells.

Societal shifts due to COVID-19 reveal large-scale complexities and feedbacks between atmospheric chemistry and climate change.

(2021)

The COVID-19 global pandemic and associated government lockdowns dramatically altered human activity, providing a window into how changes in individual behavior, enacted en masse, impact atmospheric composition. The resulting reductions in anthropogenic activity represent an unprecedented event that yields a glimpse into a future where emissions to the atmosphere are reduced. Furthermore, the abrupt reduction in emissions during the lockdown periods led to clearly observable changes in atmospheric composition, which provide direct insight into feedbacks between the Earth system and human activity. While air pollutants and greenhouse gases share many common anthropogenic sources, there is a sharp difference in the response of their atmospheric concentrations to COVID-19 emissions changes, due in large part to their different lifetimes. Here, we discuss several key takeaways from modeling and observational studies. First, despite dramatic declines in mobility and associated vehicular emissions, the atmospheric growth rates of greenhouse gases were not slowed, in part due to decreased ocean uptake of CO2 and a likely increase in CH4 lifetime from reduced NO x emissions. Second, the response of O3 to decreased NO x emissions showed significant spatial and temporal variability, due to differing chemical regimes around the world. Finally, the overall response of atmospheric composition to emissions changes is heavily modulated by factors including carbon-cycle feedbacks to CH4 and CO2, background pollutant levels, the timing and location of emissions changes, and climate feedbacks on air quality, such as wildfires and the ozone climate penalty.

Cover page of Reference-agnostic representation and visualization of pan-genomes.

Reference-agnostic representation and visualization of pan-genomes.

(2021)

Background

The pan-genome of a species is the union of the genes and non-coding sequences present in all individuals (cultivar, accessions, or strains) within that species.

Results

Here we introduce PGV, a reference-agnostic representation of the pan-genome of a species based on the notion of consensus ordering. Our experimental results demonstrate that PGV enables an intuitive, effective and interactive visualization of a pan-genome by providing a genome browser that can elucidate complex structural genomic variations.

Conclusions

The PGV software can be installed via conda or downloaded from https://github.com/ucrbioinfo/PGV . The companion PGV browser at http://pgv.cs.ucr.edu can be tested using example bed tracks available from the GitHub page.

Cover page of Reducing Microfluidic Very Large-Scale Integration (mVLSI) Chip Area by Seam Carving

Reducing Microfluidic Very Large-Scale Integration (mVLSI) Chip Area by Seam Carving

(2021)

Seam carving is an algorithm that analyzes image content and can be used for size reduction in a manner that avoids direct compression or downscaling. Seam carving iteratively identifies horizontal and/or vertical paths of least visual importance and removes them from the image; each path removal reduces the length or width of the image by one row or column of pixels. This article adapts seam carving to reduce excess area of flow-based microfluidic chips that have been drawn by hand or by computer-aided heuristics without negatively impacting their functionality. The proposed approach leverages domain knowledge, wherein the image to be carved consists of I/O ports, components, and fluid channels, with known and understood fluidic behavior. Three different variants of seam carving are presented: 1) linear; 2) nonlinear; and 3) nonrectilinear; experimental results show that nonrectilinear, which is the most general of the three, yields the best results: it improves area utilization by 8.6\times and reduces fluid routing channel length by 73% across a set of benchmark microfluidic designs.