A Genome-Wide Analysis of Promoter-Mediated Phenotypic Noise in Escherichia coli

Gene expression is subject to random perturbations that lead to fluctuations in the rate of protein production. As a consequence, for any given protein, genetically identical organisms living in a constant environment will contain different amounts of that particular protein, resulting in different phenotypes. This phenomenon is known as “phenotypic noise.” In bacterial systems, previous studies have shown that, for specific genes, both transcriptional and translational processes affect phenotypic noise. Here, we focus on how the promoter regions of genes affect noise and ask whether levels of promoter-mediated noise are correlated with genes' functional attributes, using data for over 60% of all promoters in Escherichia coli. We find that essential genes and genes with a high degree of evolutionary conservation have promoters that confer low levels of noise. We also find that the level of noise cannot be attributed to the evolutionary time that different genes have spent in the genome of E. coli. In contrast to previous results in eukaryotes, we find no association between promoter-mediated noise and gene expression plasticity. These results are consistent with the hypothesis that, in bacteria, natural selection can act to reduce gene expression noise and that some of this noise is controlled through the sequence of the promoter region alon

Excited-State Electronic Structure with Configuration Interaction Singles and Tamm–Dancoff Time-Dependent Density Functional Theory on Graphical Processing Units

Excited-state calculations are implemented in a development version of the GPU-based TeraChem software package using the configuration interaction singles (CIS) and adiabatic linear response Tamm–Dancoff time-dependent density functional theory (TDA-TDDFT) methods. The speedup of the CIS and TDDFT methods using GPU-based electron repulsion integrals and density functional quadrature integration allows full ab initio excited-state calculations on molecules of unprecedented size. CIS/6-31G and TD-BLYP/6-31G benchmark timings are presented for a range of systems, including four generations of oligothiophene dendrimers, photoactive yellow protein (PYP), and the PYP chromophore solvated with 900 quantum mechanical water molecules. The effects of double and single precision integration are discussed, and mixed precision GPU integration is shown to give extremely good numerical accuracy for both CIS and TDDFT excitation energies (excitation energies within 0.0005 eV of extended double precision CPU results)

Evaluation of Discrimination Performance in Case for Multiple Non-Discriminated Samples: Classification of Honeys by Fluorescent Fingerprinting

In this study we develop a variant of fluorescent sensor array technique based on addition of fluorophores to samples. A correct choice of fluorophores is critical for the successful application of the technique, which calls for the necessity of comparing different discrimination protocols. We used 36 honey samples from different sources to which various fluorophores were added (tris-(2,2′-bipyridyl) dichlororuthenium(II) (Ru(bpy)32+), zinc(II) 8-hydroxyquinoline-5-sulfonate (8-Ox-Zn), and thiazole orange in the presence of two types of deoxyribonucleic acid). The fluorescence spectra were obtained within 400–600 nm and treated by principal component analysis (PCA). No fluorophore allowed for the discrimination of all samples. To evaluate the discrimination performance of fluorophores, we introduced crossing number (CrN) calculated as the number of mutual intersections of confidence ellipses in the PCA scores plots, and relative position (RP) characterized by the pairwise mutual location of group centers and their most distant points. CrN and RP parameters correlated with each other, with total sensitivity (TS) calculated by Mahalanobis distances, and with the overall rating based on all metrics, with coefficients of correlation over 0.7. Most of the considered parameters gave the first place in the discrimination performance to Ru(bpy)32+ fluorophore

Generation of an induced pluripotent stem cell line HPCASRi002-A from a patient with neonatal severe primary hyperparathyroidism caused by a compound heterozygous mutation in the CASR gene

Neonatal severe primary hyperparathyroidism (NSHPT) is a rare autosomal recessive disorder of calcium homeostasis that manifests shortly after birth with hypercalcemia and bone disease. NSHPT, in most cases, is attributed to mutations in the calcium-sensing receptor (CASR) gene. We reprogrammed dermal fibroblasts derived from a patient with NSHPT carrying a compound heterozygous mutation in the CASR gene into induced pluripotent stem cells (iPSCs). The established iPSCs expressed pluripotency markers, maintained normal karyotype and differentiated into all three germ layers. This line is a valuable resource for modeling of hyperparathyroidism related to CASR mutations

A pre-catalytic non-covalent step governs DNA polymerase β fidelity

DNA polymerase beta (pol beta) selects the correct deoxyribonucleoside triphosphate for incorporation into the DNA polymer. Mistakes made by pol beta lead to mutations, some of which occur within specific sequence contexts to generate mutation hotspots. The adenomatous polyposis coli (APC) gene is mutated within specific sequence contexts in colorectal carcinomas but the underlying mechanism is not fully understood. In previous work, we demonstrated that a somatic colon cancer variant of pol beta, K289M, misincorporates deoxynucleotides at significantly increased frequencies over wild-type pol beta within a mutation hotspot that is present several times within the APC gene. Kinetic studies provide evidence that the rate-determining step of pol beta catalysis is phosphodiester bond formation and suggest that substrate selection is governed at this step. Remarkably, we show that, unlike WT, a pre-catalytic step in the K289M pol beta kinetic pathway becomes slower than phosphodiester bond formation with the APC DNA sequence but not with a different DNA substrate. Based on our studies, we propose that precatalytic conformational changes are of critical importance for DNA polymerase fidelity within specific DNA sequence contexts.Open access journalThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at [email protected]

Structure of Cyclic Nucleoside Phosphonate Ester Prodrugs: An Inquiry

The configuration at phosphorus in cyclic (<i>S</i>)-HPMPC (<b>1</b>, cidofovir) and (<i>S</i>)-HPMPA (<b>2</b>) phenyl ester (<b>5</b> and <b>6</b>, respectively) diastereomers (<b>(</b><i><b>R</b></i>_<b>p</b><b>)</b><i><b>-</b></i><b>5</b>, <b>(</b><i><b>R</b></i>_<b>p</b><b>)</b><i><b>-</b></i><b>6</b>, <b>(</b><i><b>S</b></i>_<b>p</b><b>)</b><i><b>-</b></i><b>6</b>) was determined by X-ray crystallography and correlated to their ¹H and ³¹P NMR spectra in solution. <b>(</b><i><b>R</b></i>_<b>p</b><b>)</b><i><b>-</b></i><b>5</b> and <b>(</b><i><b>R</b></i>_<b>p</b><b>)</b><i><b>-</b></i><b>6</b> have chair conformations with the nucleobase substituent equatorial and the P-OPh axial. Perhaps surprisingly, <b>(</b><i><b>S</b></i>_<b>p</b><b>)</b><i><b>-</b></i><b>6</b> is (<i>a</i>, <i>a</i>) in the crystal and exists largely as an equilibrium of (<i>a</i>, <i>a</i>)/(<i>e</i>, <i>e</i>) conformers in chloroform or acetonitrile

Structure of Cyclic Nucleoside Phosphonate Ester Prodrugs: An Inquiry

The configuration at phosphorus in cyclic (<i>S</i>)-HPMPC (<b>1</b>, cidofovir) and (<i>S</i>)-HPMPA (<b>2</b>) phenyl ester (<b>5</b> and <b>6</b>, respectively) diastereomers (<b>(</b><i><b>R</b></i>_<b>p</b><b>)</b><i><b>-</b></i><b>5</b>, <b>(</b><i><b>R</b></i>_<b>p</b><b>)</b><i><b>-</b></i><b>6</b>, <b>(</b><i><b>S</b></i>_<b>p</b><b>)</b><i><b>-</b></i><b>6</b>) was determined by X-ray crystallography and correlated to their ¹H and ³¹P NMR spectra in solution. <b>(</b><i><b>R</b></i>_<b>p</b><b>)</b><i><b>-</b></i><b>5</b> and <b>(</b><i><b>R</b></i>_<b>p</b><b>)</b><i><b>-</b></i><b>6</b> have chair conformations with the nucleobase substituent equatorial and the P-OPh axial. Perhaps surprisingly, <b>(</b><i><b>S</b></i>_<b>p</b><b>)</b><i><b>-</b></i><b>6</b> is (<i>a</i>, <i>a</i>) in the crystal and exists largely as an equilibrium of (<i>a</i>, <i>a</i>)/(<i>e</i>, <i>e</i>) conformers in chloroform or acetonitrile

Structure of Cyclic Nucleoside Phosphonate Ester Prodrugs: An Inquiry

The configuration at phosphorus in cyclic (<i>S</i>)-HPMPC (<b>1</b>, cidofovir) and (<i>S</i>)-HPMPA (<b>2</b>) phenyl ester (<b>5</b> and <b>6</b>, respectively) diastereomers (<b>(</b><i><b>R</b></i>_<b>p</b><b>)</b><i><b>-</b></i><b>5</b>, <b>(</b><i><b>R</b></i>_<b>p</b><b>)</b><i><b>-</b></i><b>6</b>, <b>(</b><i><b>S</b></i>_<b>p</b><b>)</b><i><b>-</b></i><b>6</b>) was determined by X-ray crystallography and correlated to their ¹H and ³¹P NMR spectra in solution. <b>(</b><i><b>R</b></i>_<b>p</b><b>)</b><i><b>-</b></i><b>5</b> and <b>(</b><i><b>R</b></i>_<b>p</b><b>)</b><i><b>-</b></i><b>6</b> have chair conformations with the nucleobase substituent equatorial and the P-OPh axial. Perhaps surprisingly, <b>(</b><i><b>S</b></i>_<b>p</b><b>)</b><i><b>-</b></i><b>6</b> is (<i>a</i>, <i>a</i>) in the crystal and exists largely as an equilibrium of (<i>a</i>, <i>a</i>)/(<i>e</i>, <i>e</i>) conformers in chloroform or acetonitrile