Design, modeling and simulation of bacterial biosensors for detecting heavy metals in irrigation water for precision agriculture.

Sensors used in precision agriculture for the detection of heavy metals in irrigation water are generally expensive and sometimes their deployment and maintenance represent a permanent investment to keep them in operation, leaving a lasting polluting footprint in the environment at the end of their lifespan. This represents an area of opportunity to design new biological devices that can replace part, or all of the sensors currently used. In this article, a novel workflow is proposed to fully carry out the complete process of design, modeling, and simulation of reprogrammable microorganisms .

Discovery of possible gene relationships through the application of self-organizing maps to DNA microarray databases.

DNA microarrays and cell cycle synchronization experiments have made possible the study of the mechanisms of cell cycle regulation of Saccharomyces cerevisiae by simultaneously monitoring the expression levels of thousands of genes at specific time points. On the other hand, pattern recognition techniques can contribute to the analysis of such massive measurements, providing a model of gene expression level evolution through the cell cycle process. In this paper, we propose the use of one of such techniques--an unsupervised artificial neural network called a Self-Organizing Map (SOM)-which has been successfully applied to processes involving very noisy signals, classifying and organizing them, and assisting in the discovery of behavior patterns without requiring prior knowledge about the process under analysis.

Genetic programming as alternative for predicting development effort of individual software projects.

Statistical and genetic programming techniques have been used to predict the software development effort of large software projects. In this paper, a genetic programming model was used for predicting the effort required in individually developed projects. Accuracy obtained from a genetic programming model was compared against one generated from the application of a statistical regression model.

Use of evolved artificial regulatory networks to simulate 3D cell differentiation.

Cell differentiation has a crucial role in both artificial and natural developments. This paper presents results from simulations in which a genetic algorithm (GA) was used to evolve artificial regulatory networks (ARNs) to produce predefined 3D cellular structures through the selective activation and inhibition of genes. The ARNs used in this work are extensions of a model previously used to create 2D geometrical patterns.

A cell pattern generation model based on an extended artificial regulatory network.

Cell pattern generation has a fundamental role in both artificial and natural development. This paper presents results from a model in which a genetic algorithm (GA) was used to evolve an artificial regulatory network (ARN) to produce predefined 2D cell patterns through the selective activation and inhibition of genes. The ARN used in this work is an extension of a model previously used to create simple geometrical patterns.

Biofunctional domains of the Mycoplasma pneumoniae P30 adhesin.

The P30 adhesin genes of spontaneous, hemadsorption-negative (HA-) class II Mycoplasma pneumoniae mutants that displayed P30 adhesin-deficient protein profiles were analyzed. One subclass of P30-deficient mutants possessed the entire p3O structural gene without alterations (825 nucleotides, encoding 275 amino acids with a predicted molecular mass of 29,743 Da [S. F.

Possible origin of sequence divergence in the P1 cytadhesin gene of Mycoplasma pneumoniae.

Specific regions of the P1 adhesin structural gene of Mycoplasma pneumoniae hybridize to various parts of the mycoplasma genome, indicating their multiple-copy nature. In addition, restriction fragment length polymorphisms and sequence divergence have been observed in the P1 gene, permitting the classification of clinical isolates of M. pneumoniae into two groups, I and II.

Characterization of the gene for a 30-kilodalton adhesion-related protein of Mycoplasma pneumoniae.

A previously identified trypsin-resistant surface protein of Mycoplasma pneumoniae clusters at the tip organelle of virulent mycoplasmas and appears to be essential for cytadherence and virulence. Monoclonal antibodies generated against this protein were used to identify positive recombinant clones from M. pneumoniae genomic DNA libraries.

Sequence divergency of the cytadhesin gene of Mycoplasma pneumoniae.

The Mycoplasma pneumoniae cytadhesin P1 genes from two groups of clinical isolates that display restriction fragment length polymorphisms were cloned and sequenced. Within each group the nucleotide sequences were identical, but two major differences were detected between the groups. These two stretches of sequence divergence were located in multiple-copy regions of the P1 gene and resulted in considerable amino acid changes.

Spontaneous mutation results in loss of the cytadhesin (P1) of Mycoplasma pneumoniae.

The cytadhesin (P1) structural gene of a spontaneous mutant of Mycoplasma pneumoniae which displayed a P1-negative phenotype was analyzed. An extra adenine was discovered in a stretch of normally seven adenines near the N-terminal region of the mutant P1 structural gene. The frameshift mutation resulted in the early termination of protein translation.

DNA and protein sequence homologies between the adhesins of Mycoplasma genitalium and Mycoplasma pneumoniae.

Mycoplasma genitalium and Mycoplasma pneumoniae are morphologically and serologically related pathogens that colonize the human host. Their successful parasitism appears to be dependent on the product, an adhesin protein, of a gene that is carried by each of these mycoplasmas. Here we describe the cloning and determine the sequence of the structural gene for the putative adhesin of M.

Regions of Mycoplasma pneumoniae cytadhesin P1 structural gene exist as multiple copies.

The Mycoplasma pneumoniae cytadhesin P1 structural gene with flanking regions was labeled by nick translation and used as a probe to analyze gene copy number in M. pneumoniae. Multiple bands of genomic DNA were hybridized by the probe.