Mapping the hallmarks of lung adenocarcinoma with massively parallel sequencing.

Lung adenocarcinoma, the most common subtype of non-small cell lung cancer, is responsible for more than 500,000 deaths per year worldwide. Here, we report exome and genome sequences of 183 lung adenocarcinoma tumor/normal DNA pairs. These analyses revealed a mean exonic somatic mutation rate of 12.0 events/megabase and identified the majority of genes previously reported as significantly mutated in lung adenocarcinoma. In addition, we identified statistically recurrent somatic mutations in the splicing factor gene U2AF1 and truncating mutations affecting RBM10 and ARID1A. Analysis of nucleotide context-specific mutation signatures grouped the sample set into distinct clusters that correlated with smoking history and alterations of reported lung adenocarcinoma genes. Whole-genome sequence analysis revealed frequent structural rearrangements, including in-frame exonic alterations within EGFR and SIK2 kinases. The candidate genes identified in this study are attractive targets for biological characterization and therapeutic targeting of lung adenocarcinoma.

Protein Corona Formation and Aggregation of Amyloid ß 1-40-Coated Gold Nanocolloids.

Amyloid fibrillogenesis is a pathogenic protein aggregation process that occurs through a highly ordered process of protein-protein interactions. To better understand the protein-protein interactions involved in amyloid fibril formation, we formed nanogold colloid aggregates by stepwise additions of ∼2 nmol of amyloid ß 1-40 peptide (Aß1-40) at pH ∼3.7 and ∼25 °C. The processes of protein corona formation and building of gold colloid [diameters (d) of 20 and 80 nm] aggregates were confirmed by a red-shift of the surface plasmon resonance (SPR) band, λpeak, as the number of Aß1-40 peptides [N(Aß1-40)] increased. The normalized red-shift of λpeak, Δλ, was correlated with the degree of protein aggregation, and this process was approximated as the adsorption isotherm explained by the Langmuir-Freundlich model. As the coverage fraction (θ) was analyzed as a function of ϕ, which is the N(Aß1-40) per total surface area of nanogold colloids available for adsorption, the parameters for explaining the Langmuir-Freundlich model were in good agreement for both 20 and 80 nm gold, indicating that ϕ could define the stage of the aggregation process. Surface-enhanced Raman scattering (SERS) imaging was conducted at designated values of ϕ and suggested that a protein-gold surface interaction during the initial adsorption stage may be dependent on the nanosize. The 20 nm gold case seems to prefer a relatively smaller contacting section, such as a -C-N or C═C bond, but a plane of the benzene ring may play a significant role for 80 nm gold. Regardless of the size of the particles, the ß-sheet and random coil conformations were considered to be used to form gold colloid aggregates. The methodology developed in this study allows for new insights into protein-protein interactions at distinct stages of aggregation.

A framework for deriving analytic steady states of biochemical reaction networks.

The long-term behaviors of biochemical systems are often described by their steady states. Deriving these states directly for complex networks arising from real-world applications, however, is often challenging. Recent work has consequently focused on network-based approaches. Specifically, biochemical reaction networks are transformed into weakly reversible and deficiency zero generalized networks, which allows the derivation of their analytic steady states. Identifying this transformation, however, can be challenging for large and complex networks. In this paper, we address this difficulty by breaking the complex network into smaller independent subnetworks and then transforming the subnetworks to derive the analytic steady states of each subnetwork. We show that stitching these solutions together leads to the analytic steady states of the original network. To facilitate this process, we develop a user-friendly and publicly available package, COMPILES (COMPutIng anaLytic stEady States). With COMPILES, we can easily test the presence of bistability of a CRISPRi toggle switch model, which was previously investigated via tremendous number of numerical simulations and within a limited range of parameters. Furthermore, COMPILES can be used to identify absolute concentration robustness (ACR), the property of a system that maintains the concentration of particular species at a steady state regardless of any initial concentrations. Specifically, our approach completely identifies all the species with and without ACR in a complex insulin model. Our method provides an effective approach to analyzing and understanding complex biochemical systems.

A model-based strategy for the COVID-19 vaccine roll-out in the Philippines.

COVID-19 has affected millions of people worldwide, causing illness and death, and disrupting daily life while imposing a significant social and economic burden. Vaccination is an important control measure that significantly reduces mortality if properly and efficiently distributed. In this work, an age-structured model of COVID-19 transmission, incorporating an unreported infectious compartment, is developed. Three age groups are considered: young (0-19 years), adult (20-64 years), and elderly (65+ years). The transmission rate and reporting rate are determined for each group by utilizing the number of COVID-19 cases in the National Capital Region in the Philippines. Optimal control theory is employed to identify the best vaccine allocation to different age groups. Further, three different vaccination periods are considered to reflect phases of vaccination priority groups: the first, second, and third account for the inoculation of the elderly, adult and elderly, and all three age groups, respectively. This study could guide in making informed decisions in mitigating a population-structured disease transmission under limited resources.

Use of a Continuous Glucose Monitoring System in High-Risk Hospitalized Noncritically Ill Patients With Diabetes After Cardiac Surgery and During Their Transition of Care From the Intensive Care Unit During COVID-19: A Pilot Study.

OBJECTIVE: Continuous glucose monitoring (CGM) has demonstrated benefits in managing inpatient diabetes. We initiated this single-arm pilot feasibility study during the COVID-19 pandemic in 11 patients with diabetes to determine the feasibility and accuracy of real-time CGM in patients who underwent cardiac surgery and whose care was being transitioned from the intensive care unit. METHODS: A Clarke error grid analysis was used to compare CGM and point-of-care measurements. The mean absolute relative difference (MARD) of the paired measurements was calculated to assess the accuracy of CGM for glucose measurements during the first 24 hours on CGM, the remaining time on CGM, and for different chronic kidney disease (CKD) strata. RESULTS: Overall MARD between point-of-care and CGM measurements was 14.80%. MARD for patients without CKD IV and V with an estimated glomerular filtration rate (eGFR) of ≥20 mL/min/1.73 m2 was 12.13%. Overall, 97% of the CGM values were within the no-risk zone of the Clarke error grid analysis. For the first 24 hours, a sensitivity analysis of the overall MARD for all patients and those with an eGFR of ≥20 mL/min/1.73 m2 was 15.42% ± 14.44% and 12.80% ± 7.85%, respectively. Beyond the first 24 hours, overall MARD for all patients and those with an eGFR of ≥20 mL/min/1.73 m2 was 14.54% ± 13.21% and 11.86% ± 7.64%, respectively. CONCLUSION: CGM has shown great promise in optimizing inpatient diabetes management in the noncritical care setting and after the transition of care from the intensive care unit with high clinical reliability and accuracy. More studies are needed to further assess CGM in patients with advanced CKD.

Independent Decompositions of Chemical Reaction Networks.

A chemical reaction network (CRN) is composed of reactions that can be seen as interactions among entities called species, which exist within the system. Endowed with kinetics, CRN has a corresponding set of ordinary differential equations (ODEs). In chemical reaction network theory, we are interested with connections between the structure of the CRN and qualitative properties of the corresponding ODEs. One of the results in decomposition theory of CRNs is that the intersection of the sets of positive steady states of the subsystems is equal to the set of positive steady states of the whole system, if the decomposition is independent. Hence, computational approach using independent decompositions can be used as an efficient tool in studying large systems. In this work, we provide a necessary and sufficient condition for the existence of a nontrivial independent decomposition of a CRN, which leads to a novel step-by-step method to obtain such decomposition, if it exists. We also illustrate these results using real-life examples. In particular, we show that a CRN of a popular model of anaerobic yeast fermentation pathway has a nontrivial independent decomposition, while a particular biological system, which is a metabolic network with one positive feedforward and a negative feedback has none. Finally, we analyze properties of positive steady states of reaction networks of specific influenza virus models.

Mutational heterogeneity in cancer and the search for new cancer-associated genes.

Major international projects are underway that are aimed at creating a comprehensive catalogue of all the genes responsible for the initiation and progression of cancer. These studies involve the sequencing of matched tumour-normal samples followed by mathematical analysis to identify those genes in which mutations occur more frequently than expected by random chance. Here we describe a fundamental problem with cancer genome studies: as the sample size increases, the list of putatively significant genes produced by current analytical methods burgeons into the hundreds. The list includes many implausible genes (such as those encoding olfactory receptors and the muscle protein titin), suggesting extensive false-positive findings that overshadow true driver events. We show that this problem stems largely from mutational heterogeneity and provide a novel analytical methodology, MutSigCV, for resolving the problem. We apply MutSigCV to exome sequences from 3,083 tumour-normal pairs and discover extraordinary variation in mutation frequency and spectrum within cancer types, which sheds light on mutational processes and disease aetiology, and in mutation frequency across the genome, which is strongly correlated with DNA replication timing and also with transcriptional activity. By incorporating mutational heterogeneity into the analyses, MutSigCV is able to eliminate most of the apparent artefactual findings and enable the identification of genes truly associated with cancer.

Accurate measurement of transgene copy number in crop plants using droplet digital PCR.

Genetic transformation is a powerful means for the improvement of crop plants, but requires labor- and resource-intensive methods. An efficient method for identifying single-copy transgene insertion events from a population of independent transgenic lines is desirable. Currently, transgene copy number is estimated by either Southern blot hybridization analyses or quantitative polymerase chain reaction (qPCR) experiments. Southern hybridization is a convincing and reliable method, but it also is expensive, time-consuming and often requires a large amount of genomic DNA and radioactively labeled probes. Alternatively, qPCR requires less DNA and is potentially simpler to perform, but its results can lack the accuracy and precision needed to confidently distinguish between one- and two-copy events in transgenic plants with large genomes. To address this need, we developed a droplet digital PCR-based method for transgene copy number measurement in an array of crops: rice, citrus, potato, maize, tomato and wheat. The method utilizes specific primers to amplify target transgenes, and endogenous reference genes in a single duplexed reaction containing thousands of droplets. Endpoint amplicon production in the droplets is detected and quantified using sequence-specific fluorescently labeled probes. The results demonstrate that this approach can generate confident copy number measurements in independent transgenic lines in these crop species. This method and the compendium of probes and primers will be a useful resource for the plant research community, enabling the simple and accurate determination of transgene copy number in these six important crop species.

Paramagnetic rim lesions and the central vein sign: Characterizing multiple sclerosis imaging markers.

BACKGROUND AND PURPOSE: Paramagnetic rims and the central vein sign (CVS) are proposed imaging markers of multiple sclerosis (MS) lesions. Using 7 tesla magnetic resonance imaging, we aimed to: (1) characterize the appearance of paramagnetic rim lesions (PRLs); (2) assess whether PRLs and the CVS are associated with higher levels of MS pathology; and (3) compare the characteristics between subjects with and without PRLs in early MS. METHODS: Prospective study of 32 treatment-naïve subjects around the time of diagnosis who were assessed for the presence of PRLs and the CVS. Comparisons of lesion volume and macromolecular pool size ratio (PSR) index, a proxy of myelin integrity, between PRLs and non-PRLs, and CVS-positive and CVS-negative lesions were carried out. Differences in clinical/demographic characteristics between patients with PRLs and those without were tested. RESULTS: Fifteen subjects had ≥1 PRL for a total of 36 PRLs, of which two-thirds had a full rim. PRLs predicted a larger lesion size and decreased PSR signal. Lesion volume and presence of cervical spine lesions were significantly different between subjects with PRLs and those without, although neither remained significant after adjusting for multiple comparisons. One hundred and eighty-one lesions with CVS were identified with no differences between CVS-positive and CVS-negative lesions in volume (p = .27) and PSR values (p = .62). CONCLUSIONS: PRLs, but not CVS-positive lesions, are larger and have lower myelin integrity. Our findings indicate that PRLs are associated with higher levels of lesion-specific pathology prior to the start of disease-modifying therapy.

Modifications of microvascular EC surface modulate phototoxicity of a porphycene anti-ICAM-1 immunoconjugate; therapeutic implications.

Inflammation and shear stress can upregulate expression of cellular adhesion molecules in endothelial cells (EC). The modified EC surface becomes a mediating interface between the circulating blood elements and the endothelium, and grants opportunity for immunotherapy. In photodynamic therapy (PDT), immunotargeting might overcome the lack of selectivity of currently used sensitizers. In this study, we hypothesized that differential ICAM-1 expression modulates the effects of a drug targeted to surface ICAM-1. A novel porphycene-anti-ICAM-1 conjugate was synthesized and applied to treat endothelial cells from macro and microvasculature. Results show that the conjugate induces phototoxicity in inflamed, but not in healthy, microvascular EC. Conversely, macrovascular EC exhibited phototoxicity regardless of their state. These findings have two major implications; the relevance of ICAM-1 as a modulator of drug effects in microvasculature, and the potential of the porphycene bioconjugate as a promising novel PDT agent.

The reference genome and abiotic stress responses of the model perennial grass Brachypodium sylvaticum.

Perennial grasses are important forage crops and emerging biomass crops and have the potential to be more sustainable grain crops. However, most perennial grass crops are difficult experimental subjects due to their large size, difficult genetics, and/or their recalcitrance to transformation. Thus, a tractable model perennial grass could be used to rapidly make discoveries that can be translated to perennial grass crops. Brachypodium sylvaticum has the potential to serve as such a model because of its small size, rapid generation time, simple genetics, and transformability. Here, we provide a high-quality genome assembly and annotation for B. sylvaticum, an essential resource for a modern model system. In addition, we conducted transcriptomic studies under 4 abiotic stresses (water, heat, salt, and freezing). Our results indicate that crowns are more responsive to freezing than leaves which may help them overwinter. We observed extensive transcriptional responses with varying temporal dynamics to all abiotic stresses, including classic heat-responsive genes. These results can be used to form testable hypotheses about how perennial grasses respond to these stresses. Taken together, these results will allow B. sylvaticum to serve as a truly tractable perennial model system.

Morphology and permeability transitions in plant mitochondria: Different aspects of the same event?

Plant mitochondria are sensitive organelles affected by changing environmental stressors. Upon heat shock or the presence of reactive oxygen species, plant mitochondria undergo in vivo morphological derangements associated with the extensively characterized opening of the mitochondrial permeability transition pore. Nevertheless, the classic mitochondrial permeability transition is known to be triggered by calcium overload causing mitochondrial swelling and dysfunction. Here we review evidence concerning calcium handling, permeability transition and mitochondrial impairments in plants, supporting the notion that the mitochondrial morphology transition is an in vivo indicator of the permeability transition.

Phenotypic Examination of Camelina sativa (L.) Crantz Accessions from the USDA-ARS National Genetics Resource Program.

Camelina sativa (L.) Crntz. is a hardy self-pollinated oilseed plant that belongs to the Brassicaceae family; widely grown throughout the northern hemisphere until the 1940s for production of vegetable oil but was later displaced by higher-yielding rapeseed and sunflower crops. However, interest in camelina as an alternative oil source has been renewed due to its high oil content that is rich in polyunsaturated fatty acids, antioxidants as well as its ability to grow on marginal lands with minimal requirements. For this reason, our group decided to screen the existing (2011) National Genetic Resources Program (NGRP) center collection of camelina for its genetic diversity and provide a phenotypic evaluation of the cultivars available. Properties evaluated include seed and oil traits, developmental and mature morphologies, as well as chromosome content. Selectable marker genes were also evaluated for potential use in biotech manipulation. Data is provided in a raw uncompiled format to allow other researchers to analyze the unbiased information for their own studies. Our evaluation has determined that the NGRP collection has a wide range of genetic potential for both breeding and biotechnological manipulation purposes. Accessions were identified within the NGRP collection that appear to have desirable seed harvest weight (5.06 g/plant) and oil content (44.1%). Other cultivars were identified as having fatty acid characteristics that may be suitable for meal and/or food use, such as low (<2%) erucic acid content, which is often considered for healthy consumption and ranged from a high of 4.79% to a low of 1.83%. Descriptive statistics are provided for a breadth of traits from 41 accessions, as well as raw data, and key seed traits are further explored. Data presented is available for public use.

A mathematical model of the interaction of abscisic acid, ethylene and methyl jasmonate on stomatal closure in plants.

Stomatal closure is affected by various stimuli such as light, atmospheric carbon dioxide concentration, humidity and phytohormones. Our research focuses on phytohormones, specifically: abscisic acid (ABA), ethylene (ET) and methyl jasmonate (MeJA) that are responsible for the regulation of several plant processes, especially in guard cell signalling. While several studies show that these three phytohormones cause stomatal closure in plants, only two studies are notable for establishing a mathematical model of guard cell signalling involving phytohormones. Those two studies employed Boolean modelling and mechanistic ordinary differential equations modelling. In this study, we propose a new mathematical model of guard cell transduction network for stomatal closure using continuous logical modelling framework. Results showed how the different components of the network function. Furthermore, the model verified the role of antioxidants in the closure mechanism, and the diminished closure level of stomata with combined ABA-ET stimulus. The analysis was extended to ABA-ET-MeJA crosstalk.

Screening for Victims of Sex Trafficking in the Emergency Department: A Pilot Program.

INTRODUCTION: Estimates suggest that hundreds of thousands of sex trafficking victims live in the United States. Several screening tools for healthcare professionals to identify sex trafficking victims have been proposed, but the effectiveness of these tools in the emergency department (ED) remains unclear. Our primary objective in this study was to evaluate the feasibility of a screening survey to identify adult victims of sex trafficking in the ED. We also compared the sensitivity of emergency physician concern and a screening survey for identifying sex trafficking victims in the ED and determined the most effective question(s) for identifying adult victims of sex trafficking. METHODS: We enrolled a convenience sample of medically stable female ED patients, age 18-40 years. Patients completed a 14-question survey. Physician concern for sex trafficking was documented prior to informing the physician of the survey results. A "yes" answer to any question or physician concern was considered a positive screen, and the patient was offered social work consultation. We defined a "true positive" as a patient admission for or social work documentation of sex trafficking. Demographic and clinical information were collected from the electronic medical record. RESULTS: We enrolled 143 patients, and of those 39 (27%, 95% confidence interval [CI] [20%-35%]) screened positive, including 10 (25%, 95% CI [13%-41%]) ultimately identified as victims of sex trafficking. Sensitivity of the screening survey (100%, 95% CI [74%-100%]) was better than physician concern (40%, 95% CI [12%-74%]) for identifying victims of sex trafficking, difference 60%, 95% CI [30%-90%]. Physician specificity (91%, 95% CI [85%-95%]), however, was slightly better than the screening survey (78%, 95% CI [70%-85%]), difference 13%, 95% CI [4%-21%]. All 10 (100%, 95%CI [74%-100%]) "true positive" cases answered "yes" to the screening question regarding abuse. CONCLUSION: Identifying adult victims of sex trafficking in the ED is feasible. A screening survey appears to have greater sensitivity than physician concern, and a single screening question may be sufficient to identify all adult victims of sex trafficking in the ED.

Use of Agrobacterium rhizogenes Strain 18r12v and Paromomycin Selection for Transformation of Brachypodium distachyon and Brachypodium sylvaticum.

The genetic transformation of monocot grasses is a resource intensive process, the quality and efficiency of which is dependent in part upon the method of DNA introduction, as well as the ability to effectively separate transformed from wildtype tissue. Agrobacterium-mediated transformation of Brachypodium has relied mainly on Agrobacterium tumefaciens strain AGL1. Currently the antibiotic hygromycin B has been the selective agent of choice for robust identification of transgenic calli in Brachypodium distachyon and Brachypodium sylvaticum but few other chemicals have been shown to work as well for selection of transgenic Brachypodium cells in tissue culture. This study demonstrates that Agrobacterium rhizogenes strain 18r12v and paromomycin selection can be successfully used for the efficient generation of transgenic B. distachyon and B. sylvaticum. Additionally we observed that the transformation rates were similar to or higher than those obtained with A. tumefaciens strain AGL1 and hygromycin selection. The A. rhizogenes strain 18r12v harboring the pARS1 binary vector and paromomycin selection is an effective means of generating transgenic Brachypodium plants. This novel approach will facilitate the transgenic complementation of T-DNA knockout mutants of B. distachyon which were created using hygromycin selection, as well as aid the implementation of more complex genome manipulation strategies which require multiple rounds of transformation.

Pan-cancer patterns of somatic copy number alteration.

Determining how somatic copy number alterations (SCNAs) promote cancer is an important goal. We characterized SCNA patterns in 4,934 cancers from The Cancer Genome Atlas Pan-Cancer data set. Whole-genome doubling, observed in 37% of cancers, was associated with higher rates of every other type of SCNA, TP53 mutations, CCNE1 amplifications and alterations of the PPP2R complex. SCNAs that were internal to chromosomes tended to be shorter than telomere-bounded SCNAs, suggesting different mechanisms underlying their generation. Significantly recurrent focal SCNAs were observed in 140 regions, including 102 without known oncogene or tumor suppressor gene targets and 50 with significantly mutated genes. Amplified regions without known oncogenes were enriched for genes involved in epigenetic regulation. When levels of genomic disruption were accounted for, 7% of region pairs were anticorrelated, and these regions tended to encompass genes whose proteins physically interact, suggesting related functions. These results provide insights into mechanisms of generation and functional consequences of cancer-related SCNAs.