Expression profiles have been successfully
determined by using hybridization- and tagbased technologies, even though such
approaches suffer from limits and
drawbacks and lack information about rare
RNA species, emerging as contributors to
pathological phenotypes in humans (1-8).
The introduction of next generation
sequencing (NGS) technologies, revealing
mammalian transcriptomes' complexity, has
shown that a small fraction of transcribed
sequences (<2%) is represented by mRNA
(9). However, the unprecedented level of
sensitivity in the data produced by NGS
platforms brings with it the power to make
several biological observations, at the cost
of a considerable effort in the development
of new bioinformatics tools and
computational strategies to deal with these
massive data files.
Indeed, for these large-scale
analyses, data transferring, processing and
handling may represent a computational
bottleneck. Another issue is the availability
of software required to perform one or
more downstream analysis (1).
To this purpose, in this paper we
describe the computational strategies used
to analyze different aspects of a wholetranscriptome. In particular, we illustrate
the results of the analysis performed on a
dataset obtained from a strand-specific
RNA sequenicng of ribosomal-depleted
samples, isolated from a cell type impaired
in the Down syndrome
Bioventing is a subsoil bio-remediation technique which improves the activity of bacteria to transform contaminants into less hazardous compounds by inflating air through wells. The mathematical model describes the bacteria population dynamics and the dynamics of a multiphase, multicomponent fluid in porous media and in this paper a simple version of it will be described. A critical point of the design problem is to choose well positions and air flow rates to optimise the biodegradation process. The numerical simulation and some initial optimisation design results for the simple model proposed will be reported. The decontamination time required for different flow rates and for different well spatial configurations will be compared.
subsoil decontamination
bioventing
optimal design
porous media
