A Computational Modeling Approach for the Design of Genetic Control Systems that Respond to Transcriptional Activity.

Recent progress in synthetic biology has enabled the design of complex genetic circuits that interface with innate cellular functions, such as gene transcription, and control user-defined outputs. Implementing these genetic networks in mammalian cells, however, is a cumbersome process that requires several steps of optimization and benefits from the use of predictive modeling. Combining deterministic mathematical models with software-based numerical computing platforms allows researchers to quickly design, evaluate, and optimize multiple circuit topologies to establish experimental constraints that generate the desired control systems. In this chapter, we present a systematic approach based on predictive mathematical modeling to guide the design and construction of gene activity-based sensors. This approach enables user-driven circuit optimization through iterations of sensitivity analyses and parameter scans, providing a universal method to engineer sense and respond cells for diverse applications.

Molecular characterization of carbapenemase-producing Enterobacterales in a tertiary hospital in Lima, Peru.

Carbapenemase-producing Enterobacterales (CPE) are a growing threat to global health and the economy. Understanding the interactions between resistance and virulence mechanisms of CPE is crucial for managing difficult-to-treat infections and informing outbreak prevention and control programs. Here, we report the characterization of 21 consecutive, unique clinical isolates of CPE collected in 2018 at a tertiary hospital in Lima, Peru. Isolates were characterized by phenotypic antimicrobial susceptibility testing and whole-genome sequencing to identify resistance determinants and virulence factors. Seven Klebsiella pneumoniae isolates were classified as extensively drug-resistant. The remaining Klebsiella, Enterobacter hormaechei, and Escherichia coli isolates were multidrug-resistant. Eighteen strains carried the metallo-ß-lactamase NDM-1, two the serine-carbapenemase KPC-2, and one isolate had both carbapenemases. The blaNDM-1 gene was located in the truncated ΔISAba125 element, and the blaKPC-2 gene was in the Tn4401a transposon. ST147 was the most frequent sequence type among K. pneumoniae isolates. Our findings highlight the urgent need to address the emergence of CPE and strengthen control measures and antibiotic stewardship programs in low- and middle-income settings.IMPORTANCEGenomic surveillance of antimicrobial resistance contributes to monitoring the spread of resistance and informs treatment and prevention strategies. We characterized 21 carbapenemase-producing Enterobacterales collected at a Peruvian tertiary hospital in 2018, which exhibited very high levels of resistance and carried numerous resistance genes. We detected the coexistence of carbapenemase-encoding genes (blaNDM-1 and blaKPC-2) in a Klebsiella pneumoniae isolate that also had the PmrB(R256G) mutation associated with colistin resistance. The blaKPC-2 genes were located in Tn4401a transposons, while the blaNDM-1 genes were in the genetic structure Tn125 (ΔISAba125). The presence of high-risk clones among Klebsiella pneumoniae (ST11 and ST147) and Escherichia coli (ST410) isolates is also reported. The study reveals the emergence of highly resistant bacteria in a Peruvian hospital, which could compromise the effectiveness of current treatments and control.

Cell factory engineering: Challenges and opportunities for synthetic biology applications.

The production of high-quality recombinant proteins is critical to maintaining a continuous supply of biopharmaceuticals, such as therapeutic antibodies. Engineering mammalian cell factories presents a number of limitations typically associated with the proteotoxic stress induced upon aberrant accumulation of off-pathway protein folding intermediates, which eventually culminate in the induction of apoptosis. In this review, we will discuss advances in cell engineering and their applications at different hierarchical levels of control of the expression of recombinant proteins, from transcription and translational to posttranslational modifications and subcellular trafficking. We also highlight challenges and unique opportunities to apply modern synthetic biology tools to the design of programmable cell factories for improved biomanufacturing of therapeutic proteins.

Antimicrobial Resistance Patterns and Dynamics of Extended-Spectrum ß-Lactamase-Producing Uropathogenic Escherichia coli in Cusco, Peru.

Urinary tract infections (UTIs) are a common human infection. Antibiotic resistance in extended-spectrum ß-lactamase (ESBL)-producing uropathogenic E. coli (UPEC) is a major therapeutic challenge due to limited treatment alternatives. The aim was to characterize the antimicrobial resistance (AMR) and dynamics of ESBL-producing UPEC isolates from UTI cases seen at a local hospital in Cusco, Peru. Ninety-nine isolates from respective patients were characterized against 18 different antibiotics. Latent class analysis (LCA) was used to evaluate the dynamics across the study time according to resistance patterns. The median age of patients was 51 years old, and nearly half were women. ESBL-producing UPEC isolates were slightly more frequent in outpatient services than emergency rooms, and there were higher resistance rates in males compared to females. Half of the ESBL producers were resistant to aminoglycosides and nitrofurantoin. Cefoxitin and fosfomycin resistance was 29.3% and 14.1%, respectively. Resistance to carbapenems was not observed. All isolates were multidrug-resistant bacteria, and 16.2% (16/99) were also classified as extensively drug-resistant bacteria. The resistance patterns varied across the study time and differed regarding sex and healthcare service. The study revealed high levels of AMR to commonly used antimicrobials and a dynamic circulation of ESBL-producing UPEC isolates with varying resistance patterns.

Nature inspired optimization tools for SVMs - NIOTS.

Support Vector Machines (SVMs) technique for achieving classifiers and regressors. However, to obtain models with high accuracy and low complexity, it is necessary to define the kernel parameters as well as the parameters of the training model, which are called hyperparameters. The challenge of defining the more suitable value to hyperparameters is called the Parameter Selection Problem (PSP). However, minimizing the complexity and maximizing the generalization capacity of the SVMs are conflicting criteria. Therefore, we propose the Nature Inspired Optimization Tools for SVMs (NIOTS) that offers a method to automate the search process for the best possible solution for the PSP, allowing the user to quickly obtain several sets of good solutions and choose the one most appropriate for his specific problem.•The PSP has been modeled as a Multiobjective Optimization Problem (MOP) with two objectives: (1) good precision and (2) low complexity (low number of support vectors).•The user can evaluate multiple solutions included in the Pareto front, in terms of precision and low complexity of the model.•Apart from the Adaptive Parameter with Mutant Tournament Multiobjective Differential Evolution (APMT-MODE), the user can choose other metaheuristics and also among several kernel options.

Complete Genome Sequences of Two Salmonella enterica Lytic Phages, NBSal006 and NBSal007.

The use of bacteriophages as antimicrobial agents represents a promising alternative for the control of pathogenic bacteria. Here, we present the complete genome sequences of two novel Salmonella enterica lytic bacteriophages, NBSal006 and NBSal007, candidates for Salmonella biocontrol.

Optimizing bacteriophage engineering through an accelerated evolution platform.

The emergence of antibiotic resistance has raised serious concerns within scientific and medical communities, and has underlined the importance of developing new antimicrobial agents to combat such infections. Bacteriophages, naturally occurring bacterial viruses, have long been characterized as promising antibiotic alternatives. Although bacteriophages hold great promise as medical tools, clinical applications have been limited by certain characteristics of phage biology, with structural fragility under the high temperatures and acidic environments of therapeutic applications significantly limiting therapeutic effectiveness. This study presents and evaluates the efficacy of a new accelerated evolution platform, chemically accelerated viral evolution (CAVE), which provides an effective and robust method for the rapid enhancement of desired bacteriophage characteristics. Here, our initial use of this methodology demonstrates its ability to confer significant improvements in phage thermal stability. Analysis of the mutation patterns that arise through CAVE iterations elucidates the manner in which specific genetic modifications bring forth desired changes in functionality, thereby providing a roadmap for bacteriophage engineering.

Complete Genome Sequences of Five Salmonella enterica Phages, NBSal001, NBSal002, NBSal003, NBSal004, and NBSal005.

Salmonella enterica is a Gram-negative bacterium, recognized as one of the most important foodborne pathogens in the world. Bacteriophages represent a promising alternative to the biocontrol of Salmonella Here, we report the isolation of five Salmonella bacteriophages, the sequencing of their full genomes, and initial genomic characterization.

Draft Genome Sequence of the First New Delhi Metallo-ß-Lactamase (NDM-1)-Producing Escherichia coli Strain Isolated in Peru.

We present here the draft genome sequence of the first New Delhi metallo-ß-lactamase (NDM-1)-producing Escherichia coli strain, belonging to sequence type 155 (ST155), isolated in Peru. Assembly of this draft genome resulted in 5,061,184 bp, revealing a clinically significant resistome for ß-lactams, aminoglycosides, tetracyclines, phenicols, sulfonamides, trimethoprim, and fluoroquinolones.

An experimental evaluation of the incidence of fitness-function/search-algorithm combinations on the classification performance of myoelectric control systems with iPCA tuning.

BACKGROUND: The information of electromyographic signals can be used by Myoelectric Control Systems (MCSs) to actuate prostheses. These devices allow the performing of movements that cannot be carried out by persons with amputated limbs. The state of the art in the development of MCSs is based on the use of individual principal component analysis (iPCA) as a stage of pre-processing of the classifiers. The iPCA pre-processing implies an optimization stage which has not yet been deeply explored. METHODS: The present study considers two factors in the iPCA stage: namely A (the fitness function), and B (the search algorithm). The A factor comprises two levels, namely A1 (the classification error) and A2 (the correlation factor). Otherwise, the B factor has four levels, specifically B1 (the Sequential Forward Selection, SFS), B2 (the Sequential Floating Forward Selection, SFFS), B3 (Artificial Bee Colony, ABC), and B4 (Particle Swarm Optimization, PSO). This work evaluates the incidence of each one of the eight possible combinations between A and B factors over the classification error of the MCS. RESULTS: A two factor ANOVA was performed on the computed classification errors and determined that: (1) the interactive effects over the classification error are not significative (F0.01,3,72 = 4.0659 > fAB = 0.09), (2) the levels of factor A have significative effects on the classification error (F0.02,1,72 = 5.0162 < fA = 6.56), and (3) the levels of factor B over the classification error are not significative (F0.01,3,72 = 4.0659 > fB = 0.08). CONCLUSIONS: Considering the classification performance we found a superiority of using the factor A2 in combination with any of the levels of factor B. With respect to the time performance the analysis suggests that the PSO algorithm is at least 14 percent better than its best competitor. The latter behavior has been observed for a particular configuration set of parameters in the search algorithms. Future works will investigate the effect of these parameters in the classification performance, such as length of the reduced size vector, number of particles and bees used during optimal search, the cognitive parameters in the PSO algorithm as well as the limit of cycles to improve a solution in the ABC algorithm.

Evaluating different combinations of feature selection algorithms and cost functions applied to iPCA tuning in myoelectric control systems.

A myoelectric control system extracts information from electromyographic (EMG) signals and uses it to control different types of prostheses, so that people who suffered traumatisms, paralysis or amputations can use them to execute common movements. Recent research shows that the addition of a tuning stage, using the individual component analysis (iPCA), results in improved classification performance. We propose and evaluate a set of novel configurations for the iPCA tuning, based on a biologically inspired optimization procedure, the artificial bee colony algorithm. This procedure is implemented and tested using two different cost functions, the traditional classification error and the proposed correlation factor, which involves lower computational effort. We compare the tuned system's performance, in terms of correct classifications, to that of a system tuned using two standard algorithms, the sequential forward selection and the sequential floating forward selection. The statistical analyses of the results don't find a significant difference among the classification performances associated with the search algorithms (p < 0.01). On the other hand, they establish a significant difference among the classification performances related to the cost functions (p < 0.02).

Reconfigurable systems for sequence alignment and for general dynamic programming.

Reconfigurable systolic arrays can be adapted to efficiently resolve a wide spectrum of computational problems; parallelism is naturally explored in systolic arrays and reconfigurability allows for redefinition of the interconnections and operations even during run time (dynamically). We present a reconfigurable systolic architecture that can be applied for the efficient treatment of several dynamic programming methods for resolving well-known problems, such as global and local sequence alignment, approximate string matching and longest common subsequence. The dynamicity of the reconfigurability was found to be useful for practical applications in the construction of sequence alignments. A VHDL (VHSIC hardware description language) version of this new architecture was implemented on an APEX FPGA (Field programmable gate array). It would be several magnitudes faster than the software algorithm alternatives.

Prevalencia de farmacodependencia en estudiantes de sexto ano de bachillerato de colegios oficiales y privados. Segundo semestre 1984. Barranquilla, Colombia / Prevalence of drug dependence in senior high school students from governamental and private schools. Second semester 1984. Barranquilla, Colombia

Con el fin de describir el nivel de farmacodependencia de los estudiantes de sexto ano de bachillerato de los colegios de Barranquilla, la magnitud del problema, las variables asociadas con el fenomeno y con el proposito de estructurar programas preventivos, se realizo un estudio epidemiologico de tipo descriptivo, de corte, en una muestra representativa durante el periodo del II semestre de 1984. Para la recoleccion de la informacion se elaboro un formulario, el cual fue previamente probado. Los resultados nos muestran que la prevalencia de farmacodependencia en la poblacion estudiada de 123 por mil, estuvo relacionada en mayor proporcion, con los alumnos cuyos padres eran de temperamento violento, no cumunicativos y en aquellos cuya composicion familiar era inestable. Segun clase economica, los sicofarmacos de mayor consumo fueron: la cocaina, en la clase alta y la marihuana en la clase baja. En ambas clases el "bazooko" ocupo el segundo lugar. Los resultados del trabajo nos indican que una serie de factores de riesgo se asocian al cosumo de sicofarmacos y por ello, los autores consideran que son factibles programas de prevencion