wuhrlab/TMTProC
The TMTProC module is the group of Matlab scripts associated with our paper "TMTPro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level".
Johnson, Alex↗
SEARCH · Engineering Papers
Results for “multiplexing”
Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.
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Detection of Head and Neck Cancer Based on Longitudinal Changes in Serum Protein Abundance
Head and Neck Squamous Cell Carcinoma (HNSCC) is significantly represented in the military population with substantial impact on military operations. Two-thirds of new HNSCC cases are first diagnosed at advanced stage III or IV with lymph node metastases. Thus, there is an urgent need of biomarkers for early detection and risk stratification. Archived serum samples from the Department of Defense Serum Repository provide a unique resource for longitudinal studies of HNSCC in the military and the identification of early detection biomarkers. Methods: We identified 175 patients diagnosed with HNSCC with 175 matched healthy controls and retrieved a total of 978 serum samples drawn at the time of diagnosis, 2 and 4 years prior to diagnosis, and 2 years after diagnosis. Following immunoaffinity depletion, serum samples were analyzed by targeted proteomics assays for multiplexed quantification of a panel of 146 candidate protein biomarkers from the curated literature. Results: We derived a 13-protein signature that distinguishes case versus controls based on longitudinal changes in serum protein concentration. The abundances of each of the 13 proteins remain constant over time in control subjects. The area under the curve for the derived random forest classifier was 0.90. Conclusions: This 13-protein classifier is highly promising for detection of HNSCC prior to overt symptoms. Impact: Use of longitudinal samples has significant potential to identify biomarkers for detection and risk stratification.
59 BASIC BIOLOGICAL SCIENCES↗
Longitudinal Changes in Immune Activation Serum Biomarkers Prior to Diagnosis and Risk of B-cell NHL Subtypes
To examine the contribution of B-cell activation molecules to B-cell follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL), a prospective study was conducted using pre-diagnosis serial serum samples from the US Department of Defense Serum Repository. Each case (n = 142 FL, n = 211 DLBCL) was matched to two controls on age, gender, race, military branch, and blood collection dates. Immune activation molecules (IL1β, IL2, IL4, IL5, IL6, IL10, IL12, CXCL13, IL8, TNFα, IFNγ, GM-CSF, VEGF, sCD30, IgE) were quantified using ELISA or multiplex immunometric (Luminex) assay. Longitudinal data were analyzed using linear mixed modeling. As serial specimens were collected over several years before diagnosis, we evaluated the temporal dynamics of these markers. Increased serum levels of sCD30, CXCL13, and to a lesser extent IL10, were associated with both FL and DLBCL in cases compared with controls, with a median follow-up of 5.5 years from the earliest specimen collection to diagnosis date. Significant increasing sCD30 and CXCL13 trajectories for FL and DLBCL subtypes were noted starting at the earliest time points and with IL10 levels increasing significantly at time points closer to diagnosis. In conclusion, these results suggest that sCD30, CXCL13, and IL10 may contribute to the etiology of FL and DLBCL and are potential biomarkers for these non–Hodgkin lymphoma subtypes. The increasing trajectories of the B-cell activation molecules, sCD30, CXCL13, and to a lesser extent IL10, may indicate early disease-induced effects or reflect the chronic stimulation of B-cells that promotes the development of FL and DLBCL subtypes.
60 APPLIED LIFE SCIENCES↗
Colorectal Cancer Metastases in the Liver Establish Immunosuppressive Spatial Networking between Tumor-Associated SPP1 + Macrophages and Fibroblasts
Abstract Purpose: The liver is the most frequent metastatic site for colorectal cancer. Its microenvironment is modified to provide a niche that is conducive for colorectal cancer cell growth. This study focused on characterizing the cellular changes in the metastatic colorectal cancer (mCRC) liver tumor microenvironment (TME). Experimental Design: We analyzed a series of microsatellite stable (MSS) mCRCs to the liver, paired normal liver tissue, and peripheral blood mononuclear cells using single-cell RNA sequencing (scRNA-seq). We validated our findings using multiplexed spatial imaging and bulk gene expression with cell deconvolution. Results: We identified TME-specific SPP1-expressing macrophages with altered metabolism features, foam cell characteristics, and increased activity in extracellular matrix (ECM) organization. SPP1+ macrophages and fibroblasts expressed complementary ligand–receptor pairs with the potential to mutually influence their gene-expression programs. TME lacked dysfunctional CD8 T cells and contained regulatory T cells, indicative of immunosuppression. Spatial imaging validated these cell states in the TME. Moreover, TME macrophages and fibroblasts had close spatial proximity, which is a requirement for intercellular communication and networking. In an independent cohort of mCRCs in the liver, we confirmed the presence of SPP1+ macrophages and fibroblasts using gene-expression data. An increased proportion of TME fibroblasts was associated with the worst prognosis in these patients. Conclusions: We demonstrated that mCRC in the liver is characterized by transcriptional alterations of macrophages in the TME. Intercellular networking between macrophages and fibroblasts supports colorectal cancer growth in the immunosuppressed metastatic niche in the liver. These features can be used to target immune-checkpoint–resistant MSS tumors.
60 APPLIED LIFE SCIENCES↗
Transcription of hepatitis B surface antigen shifts from cccDNA to integrated HBV DNA during treatment
The cornerstone of functional cure for chronic hepatitis B (CHB) is hepatitis B surface antigen (HBsAg) loss from blood. HBsAg is encoded by covalently closed circular DNA (cccDNA) and HBV DNA integrated into the host genome (iDNA). Nucleos(t)ide analogs (NUCs), the mainstay of CHB treatment, rarely lead to HBsAg loss, which we hypothesized was due to continued iDNA transcription despite decreased cccDNA transcription. To test this, we applied a multiplex droplet digital PCR that identifies the dominant source of HBsAg mRNAs to 3,436 single cells from paired liver biopsies obtained from 10 people with CHB and HIV receiving NUCs. With increased NUC duration, cells producing HBsAg mRNAs shifted their transcription from chiefly cccDNA to chiefly iDNA. This shift was due to both a reduction in the number of cccDNA-containing cells and diminished cccDNA-derived transcription per cell; furthermore, it correlated with reduced detection of proteins deriving from cccDNA but not iDNA. Despite this shift in the primary source of HBsAg, rare cells remained with detectable cccDNA-derived transcription, suggesting a source for maintaining the replication cycle. Functional cure must address both iDNA and residual cccDNA transcription. Further research is required to understand the significance of HBsAg when chiefly derived from iDNA.
59 BASIC BIOLOGICAL SCIENCES↗
Fluorescent amplification for next generation sequencing (FA-NGS) library preparation
BACKGROUND: Next generation sequencing (NGS) has become a universal practice in modern molecular biology. As the throughput of sequencing experiments increases, the preparation of conventional multiplexed libraries becomes more labor intensive. Conventional library preparation typically requires quality control (QC) testing for individual libraries such as amplification success evaluation and quantification, none of which occur until the end of the library preparation process. RESULTS: In this study, we address the need for a more streamlined high-throughput NGS workflow by tethering real-time quantitative PCR (qPCR) to conventional workflows to save time and implement single tube and single reagent QC. We modified two distinct library preparation workflows by replacing PCR and quantification with qPCR using SYBR Green I. qPCR enabled individual library quantification for pooling in a single tube without the need for additional reagents. Additionally, a melting curve analysis was implemented as an intermediate QC test to confirm successful amplification. Sequencing analysis showed comparable percent reads for each indexed library, demonstrating that pooling calculations based on qPCR allow for an even representation of sequencing reads. To aid the modified workflow, a software toolkit was developed and used to generate pooling instructions and analyze qPCR and melting curve data. CONCLUSIONS: We successfully applied fluorescent amplification for next generation sequencing (FA-NGS) library preparation to both plasmids and bacterial genomes. As a result of using qPCR for quantification and proceeding directly to library pooling, the modified library preparation workflow has fewer overall steps. Therefore, we speculate that the FA-NGS workflow has less risk of user error. The melting curve analysis provides the necessary QC test to identify and troubleshoot library failures prior to sequencing. While this study demonstrates the value of FA-NGS for plasmid or gDNA libraries, we speculate that its versatility could lead to successful application across other library types.
59 BASIC BIOLOGICAL SCIENCES↗
Plasma proteomic biomarkers of physical frailty in heart failure: a propensity score matched discovery-based pilot study
Background: Physical frailty is highly prevalent in heart failure (HF), but we lack an understanding of the underlying pathophysiology. Proteomics evaluation of plasma samples may elucidate potential mechanisms and biomarkers of physical frailty in HF. We aimed to identify plasma proteomic biomarkers that are differentially expressed between physically frail and non physically frail adults with HF. Methods: This was a secondary analysis of a subset of data and plasma samples from a study of frailty among patients with New York Heart Association (NYHA) Functional Classification I-IV HF. Physical frailty was measured using the Frailty Phenotype Criteria. Propensity score matching was used to match pairs of physically frail (n = 20) vs. non-physically frail (n = 20) patients on clinical characteristics. Plasma samples were processed using a sensitive liquid chromatography mass spectrometry platform, utilizing a multiplexed tandem mass tag-labeled quantitative proteomics approach. Differentially expressed proteins were quantified individually using paired t tests with associated log fold change of 0.3 and Fisher’s combined p values. Results: The sample (n = 40) was 62.8±16.9 years old, 58% female, and 55% NYHA Class III/IV. Proteomics analysis revealed 7 proteins differentially expressed using full differential criteria: matrix metalloproteinase-14 was downregulated in frailty, and copine-1, low affinity immunoglobulin gamma Fc region receptor III-A and III-B, probable non-functional immunoglobulin kappa variable 2D-24, glutathione S-transferase Mu 1, and argininosuccinate lyase were upregulated in frailty. Conclusions: Proteomic biomarkers related to the immune system, stress response, and detoxification were differentially expressed between physically frail and non-physically frail adults with HF.
Biomarkers↗
Expanding the genetic toolkit: adenine and cytosine base editors for gene disruption in Aspergillus niger
Despite revolutionizing fungal genetic engineering, conventional CRISPR/Cas9-mediated knockouts rely on DNA double-strand breaks (DSBs), which can cause unwanted insertions and deletions, chromosomal abnormalities, and cytotoxicity. Base editors such as adenine base editors (ABEs), which convert A‧T to G‧C, and cytosine base editors (CBEs), which convert C‧G to T‧A, offer a safer alternative by enabling predictable, target-specific single-nucleotide changes without introducing DSBs. To overcome the limitations of traditional genome editing in filamentous fungi, we developed efficient base-editing systems in Aspergillus niger . For the first time, we constructed an ABE in A. niger , achieving up to 80% editing efficiency and inducing predictable A-to-G mutations at the intended intron sites, disrupting gene function through mRNA mis-splicing. We also developed a highly efficient CBE system, capable of introducing premature stop codons with 50–100% efficiency. To broaden the editing scope, we implemented a Cas9-NG variant recognizing a relaxed PAM sequence requiring only a single guanine (G), enabling editing at start codons and splice sites. Leveraging this expanded scope, we established gene disruption approaches by targeting start codons via ABE-mediated A-to-G conversions (ATG-to-GTG and ATG-to-ACG) and CBE-mediated C-to-T conversion (ATG-to-ATA). Additionally, our base-editing systems enable multiplex gRNA delivery and marker-free editing of multiple genes. Collectively, the scope-expanding strategies increase the number of genes targetable for disruption by base-editing in A. niger by 26.3% and enable near-complete coverage of 96% of the coding genes. Overall, this work demonstrates the potential of ABE and CBE systems as versatile, efficient, and safer alternatives to DSBs-based gene disruption in filamentous fungi.
Aspergillus↗
Approaches to genetic tool development for rapid domestication of non-model microorganisms
Abstract Non-model microorganisms often possess complex phenotypes that could be important for the future of biofuel and chemical production. They have received significant interest the last several years, but advancement is still slow due to the lack of a robust genetic toolbox in most organisms. Typically, “domestication” of a new non-model microorganism has been done on an ad hoc basis, and historically, it can take years to develop transformation and basic genetic tools. Here, we review the barriers and solutions to rapid development of genetic transformation tools in new hosts, with a major focus on Restriction-Modification systems, which are a well-known and significant barrier to efficient transformation. We further explore the tools and approaches used for efficient gene deletion, DNA insertion, and heterologous gene expression. Finally, more advanced and high-throughput tools are now being developed in diverse non-model microbes, paving the way for rapid and multiplexed genome engineering for biotechnology.
09 BIOMASS FUELS↗
Optimal production of Phanerochaete chrysosporium manganese peroxidases and Trametes sp. C30 laccase hybrid Lac131 in Aspergillus niger for lignin bioconversion
Background Incorporating the production of related ligninolytic enzymes into industrial filamentous fungus Aspergillus niger will enhance the bioconversion of lignocelluloses to various chemical products. Results In this study, transgenic expression of Phanerochaete chrysosporium manganese peroxidases (mnps) and Trametes sp. C30 laccase hybrid Lac131 (lac131) were examined and optimized in A. niger 11414 prtT∆ strain. Five mnps (mnp1, mnp2, mnp3, mnp4, and mnp5) and lac131 genes were expressed separately or in combination. The transgenic strain containing the entire mnp2 genomic coding sequence (gmnp2) exhibited the highest mnP activity among the five mnp over-expression strains in the modified minimal medium (mMM) with addition of 5 g/L bovine hemoglobin (bHg). We examined the effects of hemin and bHg on mnP production in the gmnp2 strain cultures and found that at least 1 g/L bHg was required, while hemin was not. Culture conditions for mnP production were further optimized for the gmnp2 strain and the highest mnP activities were detected in the cultures grown at 25 °C and 200 rpm with an initial pH of 4.5. Effects of soy protein, skim milk, and bovine serum albumin on mnP production were investigated; 5 g/L of soy proteins or skim milk had comparable effects to 2.5 g/L bHg, while cultures with bovine serum albumin had diminished mnP activity. Disruption of both prtT and vsm1 substantially augmented the mnP production and its activity reached 575 U/L. Trametes sp. C30 laccase hybrid lac131 was strongly expressed in either A. niger gmnp2 (1975 U/L) or 11414prtT∆ (3895 U/L) strain. Both mnP and laccase in the culture supernatants effectively decolorized selected phenolic compounds (dyes) and cleaved tagged model lignin dimers. Conclusion The mnP was successfully produced in A. niger by optimizing the culture conditions and host strain. Co-expression of all four mnp genes in the same expression host by multiplex CRISPR will lead to the mnP production reaching levels comparable to P. chrysosporium, while only requiring 36 h at 25 °C. The Lac131 activity in transgenic A. niger strain is 4- to 7-times higher than that in previous studies. Co-production of mnP and laccase in A. niger will enhance the lignin bioconversion efficiency.
Aspergillus niger↗
Exploiting universal nonlocal dispersion in optically active materials for spectro-polarimetric computational imaging
Recent years have seen significant advancements in exploring novel light-matter interactions such as hyperbolic dispersion within natural crystals. However, current studies have predominantly concentrated on local optical response of materials characterized by a dielectric tensor without spatial dispersion. Here, we investigate the nonlocal response in optically-active crystals with screw symmetries, revealing their lossless, super-dispersive properties compared to traditional optical response functions. We leverage this universal nonlocal dispersion, i.e. the dispersion of optical rotatory power, to explore a novel spectral de-multiplexing scheme compared to conventional gratings, prisms and metasurfaces. We design and demonstrate an ‘Nonlocal-Cam’ - a camera that exploits nonlocal dispersion through sampling of polarized spectral states and the application of computational spectral reconstruction algorithms. The Nonlocal-Cam captures information in both laboratory and outdoor field experiments which is unavailable to traditional intensity cameras - the spectral texture of polarization. Merging the fields of nonlocal electrodynamics and computational imaging, our work paves the way for exploiting nonlocal optics of optically active materials in a variety of applications, from biological microscopy to physics-driven machine vision and remote sensing.
Wang, Xueji [Purdue Univ., West Lafayette, IN (Uni↗
Massively parallel and universal approximation of nonlinear functions using diffractive processors
Nonlinear computation is essential for a wide range of information processing tasks, yet implementing nonlinear functions using optical systems remains a challenge due to the weak and power-intensive nature of optical nonlinearities. Overcoming this limitation without relying on nonlinear optical materials could unlock unprecedented opportunities for ultrafast and parallel optical computing systems. Here, we demonstrate that large-scale nonlinear computation can be performed using linear optics through optimized diffractive processors composed of passive phase-only surfaces. In this framework, the input variables of nonlinear functions are encoded into the phase of an optical wavefront—e.g., via a spatial light modulator (SLM)—and transformed by an optimized diffractive structure with spatially varying point-spread functions to yield output intensities that approximate a large set of unique nonlinear functions–all in parallel. We provide proof establishing that this architecture serves as a universal function approximator for an arbitrary set of bandlimited nonlinear functions, also covering wavelength-multiplexed nonlinear functions as well as multi-variate and complex-valued functions that are all-optically cascadable. Our analysis also indicates the successful approximation of typical nonlinear activation functions commonly used in neural networks, including the sigmoid, tanh, ReLU (rectified linear unit), and softplus. We numerically demonstrate the parallel computation of one million distinct nonlinear functions, accurately executed at wavelength-scale spatial density at the output of a diffractive optical processor. Furthermore, we experimentally validated this framework using in situ optical learning and approximated 35 unique nonlinear functions in a single shot using a compact setup consisting of an SLM and an image sensor. These results establish diffractive optical processors as a scalable platform for massively parallel universal nonlinear function approximation, paving the way for new capabilities in analog optical computing based on linear materials.
Rahman, Md Sadman Sakib [University of California,↗
Data from A Genetic Toolbox for Metabolic Engineering of Issatchenkia orientalis
The nonconventional yeast Issatchenkia orientalis can grow under highly acidic conditions and has been explored for production of various organic acids. However, its broader application is hampered by the lack of efficient genetic tools to enable sophisticated metabolic manipulations. We recently constructed an episomal plasmid based on the autonomously replicating sequence (ARS) from Saccharomyces cerevisiae (ScARS) in I. orientalis and developed a CRISPR/Cas9 system for multiplexed gene deletions. Here we report three additional genetic tools including: (1) identification of a 0.8 kb centromere-like (CEN-L) sequence from the I. orientalis genome by using bioinformatics and functional screening; (2) discovery and characterization of a set of constitutive promoters and terminators under different culture conditions by using RNA-Seq analysis and a fluorescent reporter; and (3) development of a rapid and efficient in vivo DNA assembly method in I. orientalis , which exhibited ~100% fidelity when assembling a 7 kb-plasmid from seven DNA fragments ranging from 0.7 kb to 1.7 kb. As proof of concept, we used these genetic tools to rapidly construct a functional xylose utilization pathway in I. orientalis .
Conversion↗
Nitrogen thermometry in an inductively coupled plasma torch using broadband nanosecond coherent anti-Stokes Raman scattering
The development of atmospheric hypersonic flight and re-entry capabilities requires the characterization of the thermo-chemical state of representative test environments. This study demonstrates the usage of multiplex nanosecond N 2 coherent anti-Stokes Raman scattering (CARS) to measure temperatures in an atmospheric, high-temperature (>6000K), air plasma plume, generated by an inductively coupled plasma torch. These are some of the highest temperatures ever accessed via gas-phase CARS, to our knowledge. Temperatures of N 2 in the equilibrium plasma plume are determined via theoretical fits to measured CARS spectra. We discuss the practical implementation of CARS at very high temperatures, including the scaling of the N 2 CARS signal strength from 300 to 6700 K, where the expected peak signal from the high-temperature plasma torch gases is two orders of magnitude less than commonly encountered in combustion environments. An intensified CCD camera enables single-laser-shot detection at temperatures as high as 6200 K, by increasing sensitivity and providing a time gate against intense background luminosity. We also discuss the impacts of unwanted two-beam CARS contributions from outside the nominal three-beam measurement volume. We present mean axial and radial temperature profiles, as well as time-series data derived from both single-laser-shot and accumulated CARS spectra. The single-laser-shot precision is 1.7%–2.6% at temperatures of 3500 to 6200 K. The presented results pave the way for the use of CARS at very high temperatures and the measurement of spatially resolved interface processes in high-enthalpy flows.
Fries, Dan (ORCID:0000000229513294)↗
PINE: Photonic Integrated Networked Energy efficient datacenters
We review the motivation, goals, and achievements of the Photonic Integrated Networked Energy efficient datacenter (PINE) project, which is part of the Advanced Research Projects Agency–Energy (ARPA-E) ENergy-efficient Light-wave Integrated Technology Enabling Networks that Enhance Dataprocessing (ENLITENED) program. Here, the PINE program leverages the unique features of photonic technologies to enable alternative mega-datacenters and high-performance computing (HPC) system architectures that deliver more substantial energy efficiency improvements than can be achieved through link energy efficiency alone. In phase 1 of the program, the PINE system architecture demonstrated an average factor of 2.2× improvement in transactions/joule across a diverse set of HPC and datacenter applications. In phase 2, PINE will demonstrate an aggressive 1.0 pJ/bit total link budget with high-bandwidth-density dense wavelength-division multiplexing (DWDM) links to enable additional 2.5× or more efficiency gains through deep resource disaggregation.
42 ENGINEERING↗
Optics-on-a-chip for ultrafast manipulation of 350-MHz hard x-ray pulses
Microelectromechanical systems (MEMS) are miniature devices integrated into a vast range of industrial and consumer applications. Optical MEMS are developed for dynamic spatiotemporal control in lightwave manipulation and communication as modulators, switches, multiplexers, spectrometer, etc. However, they have not been shown to function similarly in sub-nm wavelength regimes, namely, with hard x-rays, as high-brilliance pulsed x-rays have proven powerful for addressing challenges in time-domain science, from energy conversion to neurobiological control. While desirable temporal properties of x-ray pulses can be enhanced by optics, conventional x-ray optics are inherently massive in size, hence, never dynamic. We demonstrate highly ultrafast x-ray optics-on-a-chip based on MEMS capable of modulating hard x-ray pulses exceeding 350 MHz, 10 3 × higher than any other mechanical modulator, with a pulse purity >10 6 without compromising the spectral brilliance. Moreover, the timing characteristics of the devices can be tuned on-the-fly to deliver optimal pulse properties to create a host of dynamic x-ray instruments and applications, impossible with traditional optics of 10 9 × bulkier and more massive. The advent of the ultrafast optics-on-a-chip heralds a new paradigm of x-ray photonics, time-domain science, and accelerator diagnostics, especially at not only the future-generation light sources that offer coherent and high-frequency pulses but also lab-based facilities that normally do not offer timing structures.
42 ENGINEERING↗
Massively distributed fiber strain sensing using Brillouin lasing
Brillouin based distributed fiber sensors present a unique set of characteristics amongst fiber sensing architectures. They are able to measure absolute strain and temperature over long distances, with high spatial resolution, and very large dynamic range in off-the-shelf fiber. However, Brillouin sensors traditionally provide only modest sensitivity due to the weak dependence of the Brillouin frequency on strain and the high signal to noise ratio required to identify the resonance’s peak frequency to within a small fraction of its linewidth. Recently, we introduced a technique which substantially improves the precision of Brillouin fiber sensors by exciting a series of lasing modes in a fiber loop cavity that experience Brillouin amplification at discrete locations in the fiber. The narrow-linewidth and high intensity of the lasing modes enabled ultra-low noise Brillouin sensors with large dynamic range. However, our initial demonstration was only modestly distributed: measuring strain at 40, non-contiguous positions along a 400 m fiber. In this work, we greatly extend this methodology to enable fully distributed sensing at 1000 contiguous locations along 3.5 km of fiber—an order of magnitude increase in sensor count and range. This highly-multiplexed Brillouin fiber laser sensor provides a strain noise as low as 34 nɛ/√Hz and we analyze the limiting factors in this approach.
47 OTHER INSTRUMENTATION↗
Two-mode squeezing over deployed fiber coexisting with conventional communications
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Chapman, Joseph↗