Large scale purification and structural properties of yeast aspartyl-tRNA synthetase

ABSTRACTThermus thermophilusis an extremely thermophilic bacterium that is widely used as a model thermophile, in large part due to its amenability to genetic manipulation. Here we describe a system for the introduction of genomic point mutations or deletions using a counterselectable marker consisting of a conditionally lethal mutant allele ofpheSencoding the phenylalanyl-tRNA synthetase α-subunit. Mutant PheS with an A294G amino acid substitution renders cells sensitive to the phenylalanine analogp-chlorophenylalanine. Insertion of the mutantpheSallele via a linked kanamycin resistance gene into a chromosomal locus provides a gene replacement intermediate that can be removed by homologous recombination usingp-chlorophenylalanine as a counterselective agent. This selection is suitable for the sequential introduction of multiple mutations to produce a final strain unmarked by an antibiotic resistance gene. We demonstrated the utility of this method by constructing strains bearing either a point mutation in or a precise deletion of therrsBgene encoding 16S rRNA. We also used this selection to identify spontaneous, large-scale deletions in the pTT27 megaplasmid, apparently mediated by either of theT. thermophilusinsertion elements ISTth7and ISTth8. One such deletion removed 121 kb, including 118 genes, or over half of pTT27, including multiple sugar hydrolase genes, and facilitated the development of a plasmid-encoded reporter system based on β-galactosidase. The ability to introduce mutations ranging from single base substitutions to large-scale deletions provides a potentially powerful tool for engineering the genome ofT. thermophilusand possibly other thermophiles as well.IMPORTANCEThermus thermophilusis an extreme thermophile that has played an important part in the development of both biotechnology and basic biological research. Its suitability as a genetic model system is established by its natural competence for transformation, but the scarcity of genetic tools limits the kinds of manipulations that can currently be performed. We have developed a counterselectable marker that allows the introduction of unmarked deletions and point mutations into theT. thermophilusgenome. We find that this marker can also be used to select large chromosomal deletions apparently resulting from aberrant transposition of endogenous insertion sequences. This system has the potential to advance the genetic manipulation of this important model organism.

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Practical Method for Damage Evaluation Based on Point Estimate Considering Uncertainty of Structural Properties

Applied Mechanics and Materials ◽

10.4028/www.scientific.net/amm.802.255 ◽

2015 ◽

Vol 802 ◽

pp. 255-260

Author(s):

Kahori Iiyama ◽

Masataka Hoso ◽

Takanori Ishida ◽

Kohei Fujita ◽

Yoshihiro Yamazaki ◽

...

Keyword(s):

Structural Properties ◽

Model Uncertainty ◽

Structural Damage ◽

Large Scale ◽

Practical Method ◽

Point Estimate ◽

Damage Evaluation ◽

Building Structures ◽

Large Scale Simulation ◽

Seismic Simulation

This study introduces a practical method for evaluating structural damage based on a large-scale simulation targeting expansive areas, like whole cities. In such a seismic simulation that deals with numerous building structures, it is desirable to estimate the damage based on a stochastic evaluation considering the uncertainty of structural properties. This is because an accurate modeling of numerous building structures, according to each designed value, would require a great deal of time. However, a damage evaluation considering the model uncertainty generally involves numerous calculations and is inadequate for such a large-scale simulation. Therefore, we propose a method using the point estimate technique which can estimate the probability of damage under model uncertainty from a small number of calculations. The applicability and usefulness of the proposed method is evaluated by comparing it to the method based on a Monte Carlo simulation.

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Adding function to the genome of AfricanSalmonellaST313

10.1101/450098 ◽

2018 ◽

Author(s):

Rocío Canals ◽

Disa L. Hammarlöf ◽

Carsten Kröger ◽

Siân V. Owen ◽

Wai Yee Fong ◽

...

Keyword(s):

Large Scale ◽

Global Gene Expression ◽

Growth Conditions ◽

Trna Synthetase ◽

Sub Saharan Africa ◽

Phenotypic Differences ◽

Metabolic Genes ◽

Lineage 2 ◽

Global Gene Expression Analysis ◽

Sub Saharan

AbstractSalmonellaTyphimurium ST313 causes invasive nontyphoidalSalmonella(iNTS) disease in sub-Saharan Africa, targeting susceptible HIV+, malarial or malnourished individuals. An in-depth genomic comparison between the ST313 isolate D23580, and the well-characterized ST19 isolate 4/74 that causes gastroenteritis across the globe, revealed extensive synteny. To understand how the 856 nucleotide variations generated phenotypic differences, we devised a large-scale experimental approach that involved the global gene expression analysis of strains D23580 and 4/74 grown in sixteen infection-relevant growth conditions. Comparison of transcriptional patterns identified virulence and metabolic genes that were differentially expressed between D23580 versus 4/74, many of which were validated by proteomics. We also uncovered theS.Typhimurium D23580 and 4/74 genes that showed expression differences during infection of murine macrophages. Our comparative transcriptomic data are presented in a new enhanced version of theSalmonellaexpression compendium SalComD23580:bioinf.gen.tcd.ie/cgi-bin/salcom_v2.pl. We discovered that the ablation of melibiose utilization was caused by 3 independent SNP mutations in D23580 that are shared across ST313 lineage 2, suggesting that the ability to catabolise this carbon source has been negatively selected during ST313 evolution. The data revealed a novel plasmid maintenance system involving a plasmid-encoded CysS cysteinyl-tRNA synthetase, highlighting the power of large-scale comparative multi-condition analyses to pinpoint key phenotypic differences between bacterial pathovariants.

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Bilevel Integer Programs with Stochastic Right-Hand Sides

INFORMS Journal on Computing ◽

10.1287/ijoc.2020.1055 ◽

2021 ◽

Author(s):

Junlong Zhang ◽

Osman Y. Özaltın

Keyword(s):

Structural Properties ◽

Large Scale ◽

Value Function ◽

Integer Program ◽

Value Functions ◽

Integer Programs ◽

Solution Algorithms ◽

Right Hand ◽

Solution Methods ◽

The Value Function

We develop an exact value function-based approach to solve a class of bilevel integer programs with stochastic right-hand sides. We first study structural properties and design two methods to efficiently construct the value function of a bilevel integer program. Most notably, we generalize the integer complementary slackness theorem to bilevel integer programs. We also show that the value function of a bilevel integer program can be characterized by its values on a set of so-called bilevel minimal vectors. We then solve the value function reformulation of the original bilevel integer program with stochastic right-hand sides using a branch-and-bound algorithm. We demonstrate the performance of our solution methods on a set of randomly generated instances. We also apply the proposed approach to a bilevel facility interdiction problem. Our computational experiments show that the proposed solution methods can efficiently optimize large-scale instances. The performance of our value function-based approach is relatively insensitive to the number of scenarios, but it is sensitive to the number of constraints with stochastic right-hand sides. Summary of Contribution: Bilevel integer programs arise in many different application areas of operations research including supply chain, energy, defense, and revenue management. This paper derives structural properties of the value functions of bilevel integer programs. Furthermore, it proposes exact solution algorithms for a class of bilevel integer programs with stochastic right-hand sides. These algorithms extend the applicability of bilevel integer programs to a larger set of decision-making problems under uncertainty.

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Online Social Networks (OSN) Evolution Model Based on Homophily and Preferential Attachment

Symmetry ◽

10.3390/sym10110654 ◽

2018 ◽

Vol 10 (11) ◽

pp. 654 ◽

Cited By ~ 1

Author(s):

Jebran Khan ◽

Sungchang Lee

Keyword(s):

Social Networks ◽

Structural Properties ◽

Online Social Networks ◽

Large Scale ◽

Preferential Attachment ◽

Real Life ◽

Synthetic Data ◽

Evolution Model ◽

Scale Invariant ◽

Scale Free

In this paper, we propose a new scale-free social networks (SNs) evolution model that is based on homophily combined with preferential attachments. Our model enables the SN researchers to generate SN synthetic data for the evaluation of multi-facet SN models that are dependent on users’ attributes and similarities. Homophily is one of the key factors for interactive relationship formation in SN. The synthetic graph generated by our model is scale-invariant and has symmetric relationships. The model is dynamic and sustainable to changes in input parameters, such as number of nodes and nodes’ attributes, by conserving its structural properties. Simulation and evaluation of models for large-scale SN applications need large datasets. One way to get SN data is to generate synthetic data by using SN evolution models. Various SN evolution models are proposed to approximate the real-life SN graphs in previous research. These models are based on SN structural properties such as preferential attachment. The data generated by these models is suitable to evaluate SN models that are structure dependent but not suitable to evaluate models which depend on the SN users’ attributes and similarities. In our proposed model, users’ attributes and similarities are utilized to synthesize SN graphs. We evaluated the resultant synthetic graph by analyzing its structural properties. In addition, we validated our model by comparing its measures with the publicly available real-life SN datasets and previous SN evolution models. Simulation results show our resultant graph to be a close representation of real-life SN graphs with users’ attributes.

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Recent Treatment of Interstitial Lung Disease with Idiopathic Inflammatory Myopathies

Clinical Medicine Insights Circulatory Respiratory and Pulmonary Medicine ◽

10.4137/ccrpm.s23313 ◽

2015 ◽

Vol 9s1 ◽

pp. CCRPM.S23313 ◽

Cited By ~ 11

Author(s):

Hidenaga Kawasumi ◽

Takahisa Gono ◽

Yasushi Kawaguchi ◽

Hisashi Yamanaka

Keyword(s):

Interstitial Lung Disease ◽

Lung Disease ◽

Large Scale ◽

Randomized Clinical Trials ◽

Calcineurin Inhibitors ◽

Disease Recurrence ◽

Trna Synthetase ◽

Therapeutic Strategies ◽

Asian Patients ◽

Disease Subtype

Interstitial lung disease (ILD) is a prognostic factor for poor outcome in polymyositis (PM)/dermatomyositis (DM). The appropriate management of ILD is very important to improve the prognosis of patients with PM/DM. ILD activity and severity depend on the disease subtype. Therefore, clinicians should determine therapeutic strategies according to the disease subtype in each patient with PM/DM. Anti–melanoma differentiation-associated gene 5 antibody and hyperferritinemia predict the development and severity of rapidly progressive (RP) ILD, particularly in East Asian patients. Combination therapy with corticosteroids, intravenous cyclophosphamide pulse, and calcineurin inhibitors should be administered in RP-ILD. In contrast, patients with anti–aminoacyl-tRNA synthetase (ARS) show better responses to corticosteroids alone. However, ILDs with anti-ARS often display disease recurrence or become refractory to corticosteroid monotherapy. Recent studies have demonstrated that the administration of tacrolimus or rituximab in addition to corticosteroids may be considered in ILD patients with anti-ARS. Large-scale, multicenter randomized clinical trials should be conducted in the future to confirm that the aforementioned agents exhibit efficacy in ILD patients with PM/DM. The pathophysiology of ILD with PM/DM should also be elucidated in greater detail to develop effective therapeutic strategies for patients with ILD in PM/DM.

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Large-scale isolation of prolyl-tRNA synthetase fromPhaseolus aureus

Biotechnology and Bioengineering ◽

10.1002/bit.260090307 ◽

1967 ◽

Vol 9 (3) ◽

pp. 343-356 ◽

Cited By ~ 6

Author(s):

P. Dunnill ◽

P. M. Dunnill ◽

M. Houldsworth ◽

A. Boddy ◽

M. D. Lilly

Keyword(s):

Large Scale ◽

Trna Synthetase

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Sensitivity of Bistatic TanDEM-X Data to Stand Structural Parameters in Temperate Forests

Remote Sensing ◽

10.3390/rs11242966 ◽

2019 ◽

Vol 11 (24) ◽

pp. 2966

Author(s):

Stefan Erasmi ◽

Malte Semmler ◽

Peter Schall ◽

Michael Schlund

Keyword(s):

Sensitivity Analysis ◽

Structural Properties ◽

Large Scale ◽

Vertical Structure ◽

Temperate Forests ◽

Forest Type ◽

Structural Parameters ◽

Stem Volume ◽

Forest Stands ◽

Canopy Volume

Synthetic aperture radar (SAR) satellite data provide a valuable means for the large-scale and long-term monitoring of structural components of forest stands. The potential of TanDEM-X interferometric SAR (InSAR) for the assessment of forest structural properties has been widely verified. However, present studies are mostly restricted to homogeneous forests and do not account for stratification in assessing model performance. A systematic sensitivity analysis of the TanDEM-X SAR signal to forest structural parameters was carried out with emphasis on different strata of forest stands (location of the study site, forest type, and development stage). Forest structure was parameterized by forest height metrics and stem volume. Results show that X-band volume coherence is highly sensitive to the forest canopy. Volume scattering within the canopy is dependent on the vertical heterogeneity of the forest stand. In general, TanDEM-X coherence is more sensitive to forest vertical structure compared to backscatter. The relations between TanDEM-X volume coherence and forest structural properties were significant at the level of a single test site as well as across sites in temperate forests in Germany. Forest type does not affect the overall relationship between the SAR signal and the forests’ vertical structure. The prediction of forest structural parameters based on the outcome of the sensitivity analysis yielded model accuracies between 15% (relative root mean square error) for Lorey’s height and 32% for stem volume. The global database of single-polarized bistatic TanDEM-X data provides an important source for mapping structural parameters in temperate forests at large scale, irrespective of forest type.

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Multi-Omics Database Analysis of Aminoacyl-tRNA Synthetases in Cancer

Genes ◽

10.3390/genes11111384 ◽

2020 ◽

Vol 11 (11) ◽

pp. 1384

Author(s):

Justin Wang ◽

Ingrid Vallee ◽

Aditi Dutta ◽

Yu Wang ◽

Zhongying Mo ◽

...

Keyword(s):

Tumor Suppressor ◽

Survival Data ◽

Large Scale ◽

Mrna Translation ◽

Trna Synthetase ◽

The Cancer Genome Atlas ◽

Individual Gene ◽

Trna Synthetases ◽

Aminoacyl Trna Synthetases ◽

Cancer Types

Aminoacyl-tRNA synthetases (aaRSs) are key enzymes in the mRNA translation machinery, yet they possess numerous non-canonical functions developed during the evolution of complex organisms. The aaRSs and aaRS-interacting multi-functional proteins (AIMPs) are continually being implicated in tumorigenesis, but these connections are often limited in scope, focusing on specific aaRSs in distinct cancer subtypes. Here, we analyze publicly available genomic and transcriptomic data on human cytoplasmic and mitochondrial aaRSs across many cancer types. As high-throughput technologies have improved exponentially, large-scale projects have systematically quantified genetic alteration and expression from thousands of cancer patient samples. One such project is the Cancer Genome Atlas (TCGA), which processed over 20,000 primary cancer and matched normal samples from 33 cancer types. The wealth of knowledge provided from this undertaking has streamlined the identification of cancer drivers and suppressors. We examined aaRS expression data produced by the TCGA project and combined this with patient survival data to recognize trends in aaRSs’ impact on cancer both molecularly and prognostically. We further compared these trends to an established tumor suppressor and a proto-oncogene. We observed apparent upregulation of many tRNA synthetase genes with aggressive cancer types, yet, at the individual gene level, some aaRSs resemble a tumor suppressor while others show similarities to an oncogene. This study provides an unbiased, overarching perspective on the relationship of aaRSs with cancers and identifies certain aaRS family members as promising therapeutic targets or potential leads for developing biological therapy for cancer.

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