pH plays a role in the mode of action of trimethoprim on Escherichia coli

Metabolomics-based approaches were applied to understand interactions of trimethoprim with Escherichia coli K-12 at sub-minimum inhibitory concentrations (MIC≈0.2, 0.03 and 0.003 mg L-1). Trimethoprim inhibits dihydrofolate reductase and thereby is an indirect inhibitor of nucleic acid synthesis. Due to the basicity of trimethoprim, two pH levels (5 and 7) were selected which mimicked healthy urine pH. This also allowed investigation of the effect on bacterial metabolism when trimethoprim exists in different ionization states. UHPLC-MS was employed to detect trimethoprim molecules inside the bacterial cell and this showed that at pH 7 more of the drug was recovered compared to pH 5; this correlated with classical growth curve measurements. FT-IR spectroscopy was used to establish recovery of reproducible phenotypes under all 8 conditions (3 drug levels and control in 2 pH levels) and GC-MS was used to generate global metabolic profiles. In addition to finding direct mode-of-action effects where nucleotides were decreased at pH 7 with increasing trimethoprim levels, off-target pH-related effects were observed for many amino acids. Additionally, stress-related effects were observed where the osmoprotectant trehalose was higher at increased antibiotic levels at pH 7. This correlated with glucose and fructose consumption and increase in pyruvate-related products as well as lactate and alanine. Alanine is a known regulator of sugar metabolism and this increase may be to enhance sugar consumption and thus trehalose production. These results provide a wider view of the action of trimethoprim. Metabolomics indicated alternative metabolism areas to be investigated to further understand the off-target effects of trimethoprim

Metabolic Profiling of Geobacter sulfurreducens during Industrial Bioprocess Scale-Up

During the industrial scale-up of bioprocesses it is important to establish that the biological system has not changed significantly when moving from small laboratory-scale shake flasks or culturing bottles to an industrially relevant production level. Therefore, during upscaling of biomass production for a range of metal transformations, including the production of biogenic magnetite nanoparticles by Geobacter sulfurreducens, from 100-ml bench-scale to 5-liter fermentors, we applied Fourier transform infrared (FTIR) spectroscopy as a metabolic fingerprinting approach followed by the analysis of bacterial cell extracts by gas chromatography-mass spectrometry (GC-MS) for metabolic profiling. FTIR results clearly differentiated between the phenotypic changes associated with different growth phases as well as the two culturing conditions. Furthermore, the clustering patterns displayed by multivariate analysis were in agreement with the turbidimetric measurements, which displayed an extended lag phase for cells grown in a 5-liter bioreactor (24 h) compared to those grown in 100-ml serum bottles (6 h). GC-MS analysis of the cell extracts demonstrated an overall accumulation of fumarate during the lag phase under both culturing conditions, coinciding with the detected concentrations of oxaloacetate, pyruvate, nicotinamide, and glycerol-3-phosphate being at their lowest levels compared to other growth phases. These metabolites were overlaid onto a metabolic network of G. sulfurreducens, and taking into account the levels of these metabolites throughout the fermentation process, the limited availability of oxaloacetate and nicotinamide would seem to be the main metabolic bottleneck resulting from this scale-up process. Additional metabolite-feeding experiments were carried out to validate the above hypothesis. Nicotinamide supplementation (1 mM) did not display any significant effects on the lag phase of G. sulfurreducens cells grown in the 100-ml serum bottles. However, it significantly improved the growth behavior of cells grown in the 5-liter bioreactor by reducing the lag phase from 24 h to 6 h, while providing higher yield than in the 100-ml serum bottles

Spread, circulation, and evolution of the Middle East respiratory syndrome coronavirus

The Middle East respiratory syndrome coronavirus (MERS-CoV) was first documented in the Kingdom of Saudi Arabia (KSA) in 2012 and, to date, has been identified in 180 cases with 43% mortality. In this study, we have determined the MERS-CoV evolutionary rate, documented genetic variants of the virus and their distribution throughout the Arabian peninsula, and identified the genome positions under positive selection, important features for monitoring adaptation of MERS-CoV to human transmission and for identifying the source of infections. Respiratory samples from confirmed KSA MERS cases from May to September 2013 were subjected to whole-genome deep sequencing, and 32 complete or partial sequences (20 were ≥99% complete, 7 were 50 to 94% complete, and 5 were 27 to 50% complete) were obtained, bringing the total available MERS-CoV genomic sequences to 65. An evolutionary rate of 1.12 × 10−3 substitutions per site per year (95% credible interval [95% CI], 8.76 × 10−4; 1.37 × 10−3) was estimated, bringing the time to most recent common ancestor to March 2012 (95% CI, December 2011; June 2012). Only one MERS-CoV codon, spike 1020, located in a domain required for cell entry, is under strong positive selection. Four KSA MERS-CoV phylogenetic clades were found, with 3 clades apparently no longer contributing to current cases. The size of the population infected with MERS-CoV showed a gradual increase to June 2013, followed by a decline, possibly due to increased surveillance and infection control measures combined with a basic reproduction number (R0) for the virus that is less than 1

Superhero Costumes as a Method for Treating Children with Selective Mutism: A Case Study

This chapter describes a creative method for treating children with selective mutism. It is a case study of a 5 year, 8 month old child who has been silent since the first day of school for 2.5 years. No one, for 2.5 years, has ever heard him speak. He used to stare at his classmates as they played but did not participate. His mother described his language as normal and behavior as quiet. When the researcher first saw him he was wearing a “Superman” costume. The researcher used the child’s ambition to be superman as a platform to think creatively to treat his deficiency. He spoke in 1 hour and 30 minutes. The single session treatment successfully treated the child and he was observed afterwards for 2 months, no relapses, and he continued speaking. To maintain the success, the teacher and the student-teacher were advised to use the “descriptive language approach.” He was observed regularly

Visible Rank and Codes with Locality

We propose a framework to study the effect of local recovery requirements of codeword symbols on the dimension of linear codes, based on a combinatorial proxy that we call \emph{visible rank}. The locality constraints of a linear code are stipulated by a matrix $H$ of $\star$'s and $0$'s (which we call a "stencil"), whose rows correspond to the local parity checks (with the $\star$'s indicating the support of the check). The visible rank of $H$ is the largest $r$ for which there is a $r \times r$ submatrix in $H$ with a unique generalized diagonal of $\star$'s. The visible rank yields a field-independent combinatorial lower bound on the rank of $H$ and thus the co-dimension of the code. We prove a rank-nullity type theorem relating visible rank to the rank of an associated construct called \emph{symmetric spanoid}, which was introduced by Dvir, Gopi, Gu, and Wigderson~\cite{DGGW20}. Using this connection and a construction of appropriate stencils, we answer a question posed in \cite{DGGW20} and demonstrate that symmetric spanoid rank cannot improve the currently best known $\widetilde{O}(n^{(q-2)/(q-1)})$ upper bound on the dimension of $q$-query locally correctable codes (LCCs) of length $n$. We also study the $t$-Disjoint Repair Group Property ($t$-DRGP) of codes where each codeword symbol must belong to $t$ disjoint check equations. It is known that linear $2$-DRGP codes must have co-dimension $\Omega(\sqrt{n})$. We show that there are stencils corresponding to $2$-DRGP with visible rank as small as $O(\log n)$. However, we show the second tensor of any $2$-DRGP stencil has visible rank $\Omega(n)$, thus recovering the $\Omega(\sqrt{n})$ lower bound for $2$-DRGP. For $q$-LCC, however, the $k$'th tensor power for $k\le n^{o(1)}$ is unable to improve the $\widetilde{O}(n^{(q-2)/(q-1)})$ upper bound on the dimension of $q$-LCCs by a polynomial factor.Comment: 22 pages; Appeared in RANDOM'21; The current version includes Theorem 5, which is a solution to Question 2 that was asked in the earlier versio

Multiple metabolomics of uropathogenic E. coli reveal different information content in terms of metabolic potential compared to virulence factors.

No single analytical method can cover the whole metabolome and the choice of which platform to use may inadvertently introduce chemical selectivity. In order to investigate this we analysed a collection of uropathogenic Escherichia coli. The selected strains had previously undergone extensive characterisation using classical microbiological methods for a variety of metabolic tests and virulence factors. These bacteria were analysed using Fourier transform infrared (FT-IR) spectroscopy; gas chromatography mass spectrometry (GC-MS) after derivatisation of polar non-volatile analytes; as well as reversed-phase liquid chromatography mass spectrometry in both positive (LC-MS(+ve)) and negative (LC-MS(-ve)) electrospray ionisation modes. A comparison of the discriminatory ability of these four methods with the metabolic test and virulence factors was made using Procrustes transformations to ascertain which methods produce congruent results. We found that FT-IR and LC-MS(-ve), but not LC-MS(+ve), were comparable with each other and gave highly similar clustering compared with the virulence factors tests. By contrast, FT-IR and LC-MS(-ve) were not comparable to the metabolic tests, and we found that the GC-MS profiles were significantly more congruent with the metabolic tests than the virulence determinants. We conclude that metabolomics investigations may be biased to the analytical platform that is used and reflects the chemistry employed by the methods. We therefore consider that multiple platforms should be employed where possible and that the analyst should consider that there is a danger of false correlations between the analytical data and the biological characteristics of interest if the full metabolome has not been measured

Implementation of Fourier transform infrared spectroscopy for the rapid typing of uropathogenic Escherichia coli.

In this paper, we demonstrate that Fourier transform infrared (FT-IR) spectroscopy is able to discriminate rapidly between uropathogenic Escherichia coli (UPEC) of key lineages with only relatively simple sample preparation. A total of 95 bacteria from six different epidemiologically important multilocus sequence types (ST10, ST69, ST95, ST73, ST127 and ST131) were used in this project and principal component-discriminant function analysis (PC-DFA) of these samples produced clear separate clustering of isolates, based on the ST. Analysis of data using partial least squares-discriminant analysis (PLS-DA), incorporating cross-validation, indicated a high prediction accuracy of 91.19% for ST131. These results suggest that FT-IR spectroscopy could be a useful method for the rapid identification of members of important UPEC STs

Randomly punctured Reed--Solomon codes achieve list-decoding capacity over linear-sized fields

Reed--Solomon codes are a classic family of error-correcting codes consisting of evaluations of low-degree polynomials over a finite field on some sequence of distinct field elements. They are widely known for their optimal unique-decoding capabilities, but their list-decoding capabilities are not fully understood. Given the prevalence of Reed-Solomon codes, a fundamental question in coding theory is determining if Reed--Solomon codes can optimally achieve list-decoding capacity. A recent breakthrough by Brakensiek, Gopi, and Makam, established that Reed--Solomon codes are combinatorially list-decodable all the way to capacity. However, their results hold for randomly-punctured Reed--Solomon codes over an exponentially large field size $2^{O(n)}$, where $n$ is the block length of the code. A natural question is whether Reed--Solomon codes can still achieve capacity over smaller fields. Recently, Guo and Zhang showed that Reed--Solomon codes are list-decodable to capacity with field size $O(n^2)$. We show that Reed--Solomon codes are list-decodable to capacity with linear field size $O(n)$, which is optimal up to the constant factor. We also give evidence that the ratio between the alphabet size $q$ and code length $n$ cannot be bounded by an absolute constant. Our proof is based on the proof of Guo and Zhang, and additionally exploits symmetries of reduced intersection matrices. With our proof, which maintains a hypergraph perspective of the list-decoding problem, we include an alternate presentation of ideas of Brakensiek, Gopi, and Makam that more directly connects the list-decoding problem to the GM-MDS theorem via a hypergraph orientation theorem

Low-Degree Polynomials Are Good Extractors

We prove that random low-degree polynomials (over $\mathbb{F}_2$) are unbiased, in an extremely general sense. That is, we show that random low-degree polynomials are good randomness extractors for a wide class of distributions. Prior to our work, such results were only known for the small families of (1) uniform sources, (2) affine sources, and (3) local sources. We significantly generalize these results, and prove the following. 1. Low-degree polynomials extract from small families. We show that a random low-degree polynomial is a good low-error extractor for any small family of sources. In particular, we improve the positive result of Alrabiah, Chattopadhyay, Goodman, Li, and Ribeiro (ICALP 2022) for local sources, and give new results for polynomial sources and variety sources via a single unified approach. 2. Low-degree polynomials extract from sumset sources. We show that a random low-degree polynomial is a good extractor for sumset sources, which are the most general large family of sources (capturing independent sources, interleaved sources, small-space sources, and more). This extractor achieves polynomially small error, and its min-entropy requirement is tight up to a square. Our results on sumset extractors imply new complexity separations for linear ROBPs, and the tools that go into its proof have further applications, as well. The two main tools we use are a new structural result on sumset-punctured Reed-Muller codes, paired with a novel type of reduction between randomness extractors. Using the first new tool, we strengthen and generalize the extractor impossibility results of Chattopadhyay, Goodman, and Gurumukhani (ITCS 2024). Using the second, we show the existence of sumset extractors for min-entropy $k=O(\log(n/\varepsilon))$, resolving an open problem of Chattopadhyay and Liao (STOC 2022).Comment: 42 page

Development of Two Charge-Transfer Complex Spectrophotometric Methods for Determination of Tofisopam in Tablet Dosage Form

Purpose: To develop an easy, fast and sensible spectrophotometric method for determination of tofisopam in tablet dosage form.Methods: Tofisopam as n-electron donor is react with two π-acceptors namely: chloranilic acid (ChA), and 7,7,8,8 tetracyanoquinodimethane (TCNQ) to form charge-transfer complexes. The obtained complexes were tested spectrophotometrically at 520 and 824 nm for ChA and TCNQ, respectively. The optimal conditions affecting the reaction status were surveyed and optimized, and the results compared with Japanese Pharmacopeia method.Results: The calibration curve were obeyed Beer`s low in the ranges 25 – 125 and 30 – 150 μg/mL for ChA and TCNQ, respectively. The lower limit of detection was 8.0 and 10.0 μg/m for ChA and TCNQ, respectively. The slope and intercept of the calibration graphs were 0.0025 and 0.011, and 0.0115 and -0.237 for ChA and TCNQ, respectivelyConclusion: The proposed methods have successfully been applied to determination of tofisopam with good accuracy and precision. The methods are accurate as the Japanese pharmacopeial method amd may be applied for routine analysis in quality control laboratories.Keywords: Charge-transfer complex, Tofisopam, Chloranilic acid, Tetracyanoquinodimethane, Spectrophotometr