An automated OpenMP mutation testing framework for performance optimization
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97 MATHEMATICS AND COMPUTING↗
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MUPPET: An automated OpenMP mutation testing framework for performance optimization
MUPPET is a tool for OpenMP programs that identifies program modifications, called mutations, aimed at improving program performance. Existing performance optimization techniques, including profiling-based and auto-tuning techniques, fail to indicate program modifications at the source level thus preventing their portability across compilers. MUPPET aims to help HPC developers reason about performance defects and missed opportunities to improve performance at the source code level.
Parasyris, Konstantinos↗
Automating test case generation for coverages required by FAA standard DO-178B
Coverage testing techniques are required by the FAA for various levels of subsystem criticality at the unit testing level. Higher levels of criticality require coverage schemes that frequently require more and more test cases, particularly when the number of conditions in a decision grows. For example, if we have a decision with n conditions of the form: if (/ci/ or /c2/ or .... or /cn/) then there are 2(n) possible combinations of condition outcomes. Given the enormous number of inputs that may be required to satisfy different coverages, and given that there are no automated tools for determining these inputs (to our knowledge), we will show how one alternative testing technique, mutation testing, can be coerced into generating inputs that satisfy a code coverage scheme X, i.e., if we modify the rules for mutant generation during mutation testing, this technique will provide test cases that satisfy X.
Voas, Jeffrey M.↗
Testing convolutional neural network based deep learning systems: a statistical metamorphic approach
Machine learning technology spans many areas and today plays a significant role in addressing a wide range of problems in critical domains,i.e., healthcare, autonomous driving, finance, manufacturing, cybersecurity,etc. Metamorphic testing (MT) is considered a simple but very powerful approach in testing such computationally complex systems for which either an oracle is not available or is available but difficult to apply. Conventional metamorphic testing techniques have certain limitations in verifying deep learning-based models (i.e., convolutional neural networks (CNNs)) that have a stochastic nature (because of randomly initializing the network weights) in their training. In this article, we attempt to address this problem by using a statistical metamorphic testing (SMT) technique that does not require software testers to worry about fixing the random seeds (to get deterministic results) to verify the metamorphic relations (MRs). We propose seven MRs combined with different statistical methods to statistically verify whether the program under test adheres to the relation(s) specified in the MR(s). We further use mutation testing techniques to show the usefulness of the proposed approach in the healthcare space and test two CNN-based deep learning models (used for pneumonia detection among patients). The empirical results show that our proposed approach uncovers 85.71% of the implementation faults in the classifiers under test (CUT). Furthermore, we also propose an MRs minimization algorithm for the CUT, thus saving computational costs and organizational testing resources.
Computer Science↗
Sensor-Enabled Alleviation of Product Inhibition in Chorismate Pyruvate-Lyase
Product inhibition is a frequent bottleneck in industrial enzymes, and testing mutations to alleviate product inhibition via traditional methods remains challenging as many variants need to be tested against multiple substrate and product concentrations. Further, traditional screening methods are conducted in vitro, and resulting enzyme variants may perform differently in vivo in the context of whole-cell metabolism and regulation. In this study, we address these two problems by establishing a high-throughput screening method to alleviate product inhibition in an industrially relevant enzyme, chorismate pyruvate-lyase (UbiC). First, we engineered a highly specific, genetically encoded biosensor for 4-hydroxybenzoate (4HB) in an industrially relevant host, Pseudomonas putida KT2440. We subsequently applied the biosensor to detect the activity of a heterologously expressed UbiC that converts chorismate into 4HB and pyruvate. By using benzoate as a product surrogate that inhibits UbiC without activating the biosensor, we were able to efficiently create and screen a diversified library for UbiC variants with reduced product inhibition. Introduction of the improved UbiC enzyme variant into an experimental production strain for the industrial precursor cis,cis-muconic acid (muconate), enabled a >2-fold yield improvement for glucose to muconate conversion when the new UbiC variant was expressed from a plasmid and a 60% yield increase when the same UbiC variant was genomically integrated into the strain. Overall, this work demonstrates that by coupling a library of enzyme variants to whole-cell catalysis and biosensing, variants with reduced product inhibition can be identified, and that this improved enzyme can result in increased titers of a downstream molecule of interest.
09 BIOMASS FUELS↗
Relationship between KRAS mutations and dual time point {sup 18}F-FDG PET/CT imaging in colorectal liver metastases
Purpose: To investigate the association between metabolic parameters of dual time point {sup 18}F-FDG PET/CT imaging and Kirsten rat sarcoma (KRAS) mutation status in colorectal liver metastases (CRLM). Methods: Forty-nine colorectal cancer patients with 87 liver metastatic lesions were included in this retrospective study. KRAS gene mutation tests were also performed for all the patients. The maximum standardized uptake value (SUV{sub max}) was measured for each hepatic metastatic lesion on both early and delayed scans, and the change of SUV{sub max} (ΔSUV{sub max}) and retention index (RI) were calculated. Uni-variate and multi-variate analyses were employed to determine the relationship between any PET/CT parameters and KRAS mutation status. Results: Thirty-seven (42.5%) liver metastatic lesions harboring KRAS mutations were identified. The SUV{sub max} of CRLM with KRAS mutation both on early and delayed scans was significantly higher than those with wild-type KRAS (10.7 ± 6.0 vs. 7.8 ± 3.3, P = 0.002; 15.5 ± 10.1 vs. 10.0 ± 4.2, P < 0.001, respectively). Compared with wild-type KRAS CRLM, ΔSUV{sub max} and RI (%) of CRLM with KRAS mutation were also significantly higher than those with wild-type KRAS (4.8 ± 4.7 vs. 2.2 ± 2.0, P < 0.001; 45.3 ± 28.2 vs. 29.6 ± 24.7, P = 0.003, respectively). Multi-variate analyses showed that the SUV{sub max} on both early and delayed scans, ΔSUV{sub max}, and RI (%) were the 4 independent factors to predict CRLM patients harboring KRAS mutations. Conclusion: The SUV{sub max} on both early and delayed scans, ΔSUV{sub max}, and RI (%) may be the 4 independent factors to predict CRLM patients harboring KRAS mutations.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Genetic effects on heavy ions in drosophila
Drosophila sex-linked recessive lethal mutation test was used to study the dose response relation and relative biological effectiveness of heavy ions. The experiments were performed using the heavy ion beams at BEVALAC of Lawrence Berkeley Laboratory. These experiments were undertaken according to the proposed milestones and included Ne-20, A-40 and Fe-65 ions with respective energies of 600 MeV, 840 MeV and 850 MeV. At these energies several doses of these radiations ranging from 20 to 1280 R were used. Space radiation exposure to astronauts is supposed to be quite low and therefore very low dose experiments i.e., 20 R, were also performed for the three ions. The mutation response was measured in all germ cell types i.e., spermatozoa, spermatids, spermatocytes and spermatogonia of treated Drosophila males. A linear dose frequency relation was observed for most of the range except at high doses where the saturation effect was observed. Also, a very significant difference was observed among the sensitivity of the four germ cell stages where spermatozoa and spermatids were more sensitive. At the higher doses of this range, most of the spermatogonia and spermatocytes were killed. Although comparative and identical experiments with X-rays or neutrons have not been performed, the compassion of our data with the ones available in literature suggest that the heavy ions have a high rbe and that they are several times more effective than low LET X-rays. The rbe compared to neutrons however appears to be only slightly higher.
Kale, P. G.↗
Distinct function of Chlamydomonas CTRA-CTR transporters in Cu assimilation and intracellular mobilization
Abstract Successful acclimation to copper (Cu) deficiency involves a fine balance between Cu import and export. In the green alga Chlamydomonas reinhardtii, Cu import is dependent on a transcription factor, Copper Response Regulator 1 (CRR1), responsible for activating genes in Cu-deficient cells. Among CRR1 target genes are two Cu transporters belonging to the CTR/COPT gene family (CTR1 and CTR2) and a related soluble protein (CTR3). The ancestor of these green algal proteins was likely acquired from an ancient chytrid and contained conserved cysteine-rich domains (named the CTR-associated domains, CTRA) that are predicted to be involved in Cu acquisition. We show by reverse genetics that Chlamydomonas CTR1 and CTR2 are canonical Cu importers albeit with distinct affinities, while loss of CTR3 did not result in an observable phenotype under the conditions tested. Mutation of CTR1, but not CTR2, recapitulates the poor growth of crr1 in Cu-deficient medium, consistent with a dominant role for CTR1 in high-affinity Cu(I) uptake. On the other hand, the overaccumulation of Cu(I) (20 times the quota) in zinc (Zn) deficiency depends on CRR1 and both CTR1 and CTR2. CRR1-dependent activation of CTR gene expression needed for Cu over-accumulation can be bypassed by the provision of excess Cu in the growth medium. Over-accumulated Cu is sequestered into the acidocalcisome but can become remobilized by restoring Zn nutrition. This mobilization is also CRR1-dependent, and requires activation of CTR2 expression, again distinguishing CTR2 from CTR1 and consistent with the lower substrate affinity of CTR2. One sentence summary Regulation of Cu uptake and sequestration by members of the CTR family of proteins in Chlamydomonas.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Enhancing Developer Productivity - L2 Milestone (Final Report)
This report documents the work done as part of the “Enhancing Developer Productivity” level 2 milestone. The team surveyed developers about impediments and successes; improved our CI pipeline monitoring and reporting; developed tools for line coverage reporting and analysis; improved compiler warning adherence in SIERRA; prototyped static analysis, AI, and mutation testing tooling in SIERRA; and developed a 3-5 year SIERRA plan document to help these initiatives continue past this milestone.
97 MATHEMATICS AND COMPUTING↗
Association between CT-texture-derived tumor heterogeneity, outcomes, and BRCA mutation status in patients with high-grade serous ovarian cancer
Purpose: To assess the associations between inter-site texture heterogeneity parameters derived from computed tomography (CT), survival, and BRCA mutation status in women with high-grade serous ovarian cancer (HGSOC). Materials and methods: Retrospective study of 88 HGSOC patients undergoing CT and BRCA mutation status testing prior to primary cytoreductive surgery. Associations between texture metrics—namely inter-site cluster variance (SCV), inter-site cluster prominence (SCP), inter-site cluster entropy (SE)—and overall survival (OS), progression-free survival (PFS) as well as BRCA mutation status were assessed. Results: Higher inter-site cluster variance (SCV) was associated with lower PFS (p = 0.006) and OS (p = 0.003). Higher inter-site cluster prominence (SCP) was associated with lower PFS (p = 0.02) and higher inter-site cluster entropy (SE) correlated with lower OS (p = 0.01). Higher values of all three metrics were significantly associated with lower complete surgical resection status in BRCA-negative patients (SE p = 0.039, SCV p = 0.006, SCP p = 0.02), but not in BRCA-positive patients (SE p = 0.7, SCV p = 0.91, SCP p = 0.67). None of the metrics were able to distinguish between BRCA mutation carrier and non-mutation carrier. Conclusion: The assessment of tumoral heterogeneity in the era of personalized medicine is important, as increased heterogeneity has been associated with distinct genomic abnormalities and worse patient outcomes. A radiomics approach using standard-of-care CT scans might have a clinical impact by offering a non-invasive tool to predict outcome and therefore improving treatment effectiveness. However, it was not able to assess BRCA mutation status in women with HGSOC.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Fast Evaluation of Viral Emerging Risks (FEVER): A computational tool for biosurveillance, diagnostics, and mutation typing of emerging viral pathogens
Viral pathogens can rapidly evolve, adapt to novel hosts, and evade human immunity. The early detection of emerging viral pathogens through biosurveillance coupled with rapid and accurate diagnostics are required to mitigate global pandemics. However, RNA viruses can mutate rapidly, hampering biosurveillance and diagnostic efforts. Here, we present a novel computational approach called FEVER (Fast Evaluation of Viral Emerging Risks) to design assays that simultaneously accomplish: 1) broad-coverage biosurveillance of an entire group of viruses, 2) accurate diagnosis of an outbreak strain, and 3) mutation typing to detect variants of public health importance. We demonstrate the application of FEVER to generate assays to simultaneously 1) detect sarbecoviruses for biosurveillance; 2) diagnose infections specifically caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); and 3) perform rapid mutation typing of the D614G SARS-CoV-2 spike variant associated with increased pathogen transmissibility. These FEVER assays had a high in silico recall (predicted positive) up to 99.7% of 525,708 SARS-CoV-2 sequences analyzed and displayed sensitivities and specificities as high as 92.4% and 100% respectively when validated in 100 clinical samples. The D614G SARS-CoV-2 spike mutation PCR test was able to identify the single nucleotide identity at position 23,403 in the viral genome of 96.6% SARS-CoV-2 positive samples without the need for sequencing. This study demonstrates the utility of FEVER to design assays for biosurveillance, diagnostics, and mutation typing to rapidly detect, track, and mitigate future outbreaks and pandemics caused by emerging viruses.
59 BASIC BIOLOGICAL SCIENCES↗
Benchmarking Computational Tools for Calling SNPs and Indels in Complex Microbial Populations
The NASA BioNutrients missions seek to understand the suitability of microorganisms for bioproduction during space flight. One topic of interest is the stability of microbial genomes during long-term ambient storage and subsequent rehydration and growth. To address these questions, samples from 8 species were flown to ISS for 5 years of desiccated storage at ambient temperature (Stasis Packs) and 2 species were packaged along with powdered media inside a bioreactor system to allow hydration and growth in microgravity (Production Packs). For both systems, Whole Genome Sequencing (WGS) of the DNA extracted from the returned samples and paired ground controls will be conducted to identify changes in genome stability due to time, storage conditions and growth in space. Across the technical replicates, ground controls, 10 timepoints, and multiple experimental conditions, ~300 samples have been selected for initial analysis with WGS sequencing to 100x coverage. A flexible and resource efficient mutation calling pipeline is needed to process this large dataset and allow for comparisons between species. Many bioinformatics tools for calling Indels and Single Nucleotide Variants (SNVs) are designed for use with pure isolates, where true variations from the reference genome are expected to dominate the reads aligning to the location of mutation. In contrast, DNA from the Stasis Pack (SP) samples was collected directly after recovery from desiccated storage and the Production Pack (PP) samples were collected after fermentation. In this context, reads with mutations are expected to be less frequent than reads that align with the reference genome, as each sample will include multiple lines of cells. Thus, BioNutrients samples are expected to be similar to samples from cancer cell or “pooled” sequencing approaches. In preparation for the analysis of the BioNutrients samples, we have tested three mutation calling tools (GATK for Microbes, BreSeq and DiscoSNP) designed for complex samples. A challenge of validating mutation identification pipelines is a lack of “Ground Truth” datasets, especially for complex samples. To compare these three tools, we sought to identify mutations in pre-existing WGS data collected from populations of Chlamydomonas reinhardtii that were exposed to UV mutagenesis and growth in LEO as part of the Space Algae-1 mission. Here we present a summary of these tools against the analysis originally conducted using the CRISP tool. Critical metrics are compared such as runtime, the number of SNPs, the number and size of Indels, and patterns of transversion and transitions identified by each tool are reported. By sharing these benchmarking results collected in support of the BioNutrients mission, we aim to guide others seeking to identify SNVs in similarly complex microbial samples.
Biology↗
Genome engineering of E. coli for improved styrene production and polymerization
Microbial production of exogenous organic compounds is challenging as biosynthetic pathways are often complex and produce metabolites that are toxic to the hosts. Biogenic styrene is an example of this problem, which if addressed could result in a more sustainable supply of this important component of the plastics industry. In this study, we engineered Escherichia coli for the production of styrene. We systematically optimized the production capability by first screening different pathway expression levels in E. coli strains. We then further designed and constructed a transcription regulator library targeting 54 genes with 85,420 mutations, and tested this library for increased styrene resistance and production. A series of tolerant mutants not only exhibited improved styrene tolerance but also produced higher styrene concentrations compared to the parent strain. The best producing mutant, ST05 LexA_E45I, produced a 3.45-fold increase in styrene compared to the parent strain. The produced styrene was extracted via gas stripping into dodecane and used in a direct free radical synthesis of polystyrene.
09 BIOMASS FUELS↗
The expression of genes encoding novel Sesame oleosin variants facilitates enhanced triacylglycerol accumulation in Arabidopsis leaves and seeds
Summary Triacylglycerols (TAG), accumulate within lipid droplets (LD), predominantly surrounded by OLEOSINs (OLE), that protect TAG from hydrolysis. We tested the hypothesis that identifying and removing degradation signals from OLE would promote its abundance, preventing TAG degradation and enhancing TAG accumulation. We tested whether mutating potential ubiquitin‐conjugation sites in a previously reported improved Sesamum indicum OLE ( SiO ) variant, o3‐3 Cys‐OLE ( SiCO herein), would stabilize it and increase its lipogenic potential. SiCOv1 was created by replacing all five lysines in SiCO with arginines. Separately, six cysteine residues within SiCO were deleted to create SiCOv2. SiCOv1 and SiCOv2 mutations were combined to create SiCOv3. Transient expression of SiCOv3 in Nicotiana benthamiana increased TAG by two‐fold relative to SiCO. Constitutive expression of SiCOv3 or SiCOv5 , containing the five predominant TAG‐increasing mutations from SiCOv3 , in Arabidopsis along with mouse DGAT2 ( mD ) increased TAG accumulation by 54% in leaves and 13% in seeds compared with control lines coexpressing SiCO and mD. Lipid synthesis rates increased, consistent with an increase in lipid sink strength that sequesters newly synthesized TAG, thereby relieving the constitutive BADC‐dependent inhibition of ACCase reported for WT Arabidopsis. These OLE variants represent novel factors for potentially increasing TAG accumulation in a variety of oil crops.
59 BASIC BIOLOGICAL SCIENCES↗
Data for the Expression of Genes Encoding Novel Sesame Oleosin Variants Facilitates Enhanced Triacylglycerol Accumulation in Arabidopsis Leaves and Seeds
Triacylglycerols (TAG), accumulate within lipid droplets (LD), predominantly surrounded by OLEOSINs (OLE), that protect TAG from hydrolysis. We tested the hypothesis that identifying and removing degradation signals from OLE would promote its abundance, preventing TAG degradation and enhancing TAG accumulation. We tested whether mutating potential ubiquitin-conjugation sites in a previously reported improved Sesamum indicum OLE ( SiO ) variant, o3-3 Cys-OLE ( SiCO herein), would stabilize it and increase its lipogenic potential. SiCOv1 was created by replacing all five lysines in SiCO with arginines. Separately, six cysteine residues within SiCO were deleted to create SiCOv2. SiCOv1 and SiCOv2 mutations were combined to create SiCOv3. Transient expression of SiCOv3 in Nicotiana benthamiana increased TAG by two-fold relative to SiCO. Constitutive expression of SiCOv3 or SiCOv5 , containing the five predominant TAG-increasing mutations from SiCOv3 , in Arabidopsis along with mouse DGAT2 ( mD ) increased TAG accumulation by 54% in leaves and 13% in seeds compared with control lines coexpressing SiCO and mD . Lipid synthesis rates increased, consistent with an increase in lipid sink strength that sequesters newly synthesized TAG, thereby relieving the constitutive BADC-dependent inhibition of ACCase reported for WT Arabidopsis. These OLE variants represent novel factors for potentially increasing TAG accumulation in a variety of oil crops.
Feedstock Production↗
Functional coding and non-coding variants in human BRCA1 gene and their use in genetic screening
BRCA1 is involved in double-strand DNA damage repair pathways, and mutations in the gene are associated with hereditary breast and ovarian cancers. With great help of the development of high-throughput DNA sequencing techniques numerous single-nucleotide polymorphisms (SNPs) and insertion deletion (Indel) mutations are detected on both coding and non-coding/regulatory regions of the BRCA1. Mutations may cause pathogenic or benign changes on the protein function or affect its expression. In the last decade, use of genetic screening tests to detect mutations on such genes has become greatly popular. However, it is very important to know the effect of the detected mutations, which is mostly possible by the use of predictive softwares, and also the related family history to be able to correctly analyse the screening results and to inform the patient. Therefore, use of in silico and in vitro techniques to score the pathogenicity of detected variants on genes like BRCA1 is now of great importance. Otherwise, results obtained from screening tests and family history cannot be analysed precisely.
62 RADIOLOGY AND NUCLEAR MEDICINE↗
Knockout of ABC transporter gene ABCA2 confers resistance to Bt toxin Cry2Ab in Helicoverpa zea
Evolution of pest resistance reduces the benefits of widely cultivated genetically engineered crops that produce insecticidal proteins derived from Bacillus thuringiensis (Bt). Better understanding of the genetic basis of pest resistance to Bt crops is needed to monitor, manage, and counter resistance. Previous work shows that in several lepidopterans, resistance to Bt toxin Cry2Ab is associated with mutations in the gene encoding the ATP-binding cassette protein ABCA2. The results here show that mutations introduced by CRISPR/Cas9 gene editing in the Helicoverpa zea (corn earworm or bollworm) gene encoding ABCA2 (HzABCA2) can cause resistance to Cry2Ab. Disruptive mutations in HzABCA2 facilitated the creation of two Cry2Ab-resistant strains. A multiple concentration bioassay with one of these strains revealed it had > 200-fold resistance to Cry2Ab relative to its parental susceptible strain. All Cry2Ab-resistant individuals tested had disruptive mutations in HzABCA2. We identified five disruptive mutations in HzABCA2 gDNA. The most common mutation was a 4-bp deletion in the expected Cas9 guide RNA target site. The results here indicate that HzABCA2 is a leading candidate for monitoring Cry2Ab resistance in field populations of H. zea.
60 APPLIED LIFE SCIENCES↗
Functional characterization of natural variants found on the major stress inducible 70-kDa heat shock gene, HSPA1A, in humans
Highlights: • Mutations, R36C, I74T, and F592S, lower the rate of ATP hydrolysis of HSPA1A. • S16P, R36C, I480N, and F592S alter the interaction of HSPA1A and protein substrates. • R36C increases while the I480N decreases the refolding of heat-denatured luciferase. • R36C, I480N, and F592S failed to protect cells from aggregated protein stress. In this report, we investigated the effects of natural single nucleotide polymorphisms on the function of HSPA1A, the major stress-inducible Hsp70 gene in humans. We first established that all mutant proteins retain their ability to hydrolyze ATP, but three of them had a significantly lower rate of ATP hydrolysis as compared to the wild-type (WT) protein. We also used Isothermal Titration Calorimetry and found that although all mutants bind to protein substrate with dissociation constants similar to the WT protein, four of them had increased reaction entropies. We also tested whether these mutations affect the ability of HSPA1A to refold heat-denatured luciferase. These assays revealed that one mutation resulted in significantly lower levels while a second one resulted in higher levels of the refolded enzyme. We then determined whether the mutations affected the ability of HSPA1A to prevent apoptosis caused by poly-glutamine carrying huntingtin proteins. This assay determined that three of the mutations caused increased cell apoptosis as compared to the WT. Our results reveal that although none of these naturally occurring mutations exists on positions of known function, some alter the molecular chaperone activities of HSPA1A most probably by affecting the allosteric communication between its two major domains.
60 APPLIED LIFE SCIENCES↗