1,721,052 research outputs found
Effect of preillumination on photomotile responses of the marine ciliate Fabrea salina
No full textFabrea salina is a marine ciliate that shows photomotile responses such as positive phototaxis and a step-down photophobic reaction. We found that preilluminated F. salina cells show a phototactic response significantly greater than that of dark-adapted cells when exposed to the same phototactic light stimulus. In particular, positive phototaxis is strongly enhanced by preillumination. This enhancement effect depends on the preillumination light irradiance, on the total preillumination dose, and on the duration of the dark interval between preillumination and the phototaxis measurement. Our results show that the determining factor is the tot preillumination dose given to the sample. The enhancement effect shows an asymptotic behavior over a certain range of energy values (10-200 W/m(2)). Further, the effect is transient; after 120 s in the dark, the cells lose any memory of the preillumination, independent of the preillumination energy received. These results are tentatively discussed in terms of light-driven membrane potential or membrane channel conductances
A compression-based approach for coding sequences identification in prokaryotic genomes
No full textTo identify coding regions in genomic sequences represents the first step toward further analysis of the biological function carried on by the different functional elements in a genome. The present paper presents a novel method for the classification of coding and non-coding regions in prokaryotic genomes, based on a suitable defined compression index of a DNA sequence. The proposed approach has been applied on some prokaryotic complete genomes, obtaining optimal scores of correctly recognized coding and non-coding regions. Several false-positive and false-negative cases have been investigated in detail, discovering that this approach can fail in the presence of highly-structured coding regions (e.g., genes coding for modular proteins) or quasi-random non-coding regions (regions hosting non-functional fragments of copies of functional genes; regions hosting promoters or other protein-binding sequences, etc.)
BpMatch: An Efficient Algorithm for a Segmental Analysis of Genomic Sequences
No full textHere, we propose BpMatch: an algorithm that, working on a suitably modified suffix-tree data structure, is able to compute, in a fast and efficient way, the coverage of a source sequence S on a target sequence T, by taking into account direct and reverse segments, eventually overlapped. Using BpMatch, the operator should define a priori, the minimum length l of a segment and the minimum number of occurrences minRep, so that only segments longer than l and having a number of occurrences greater than minRep are considered to be significant. BpMatch outputs the significant segments found and the computed segment-based distance. On the worst case, assuming the alphabet dimension d is a constant, the time required by BpMatch to calculate the coverage is O(l(2)n). On the average, by setting l >= 2 log(d)(n), the time required to calculate the coverage is only O(n). BpMatch, thanks to the minRep parameter, can also be used to perform a self-covering: to cover a sequence using segments coming from itself, by avoiding the trivial solution of having a single segment coincident with the whole sequence. The result of the self-covering approach is a spectral representation of the repeats contained in the sequence. BpMatch is freely available on: www.sourceforge.net/projects/bpmatch/
A computational approach to the functional screening of genomes
No full textComparative genomics usually involves managing the functional aspects of genomes, by simply comparing gene by gene functions. Following this approach, Mushegian and Koonin proposed a hypothetical minimal genome, Minimal
Gene Set (MGS), aiming for a possible oldest ancestor genome. They obtained MGS by comparing the genomes of two
simple bacteria and eliminating duplicated or functionally identical genes. The authors raised the fundamental
question of whether a hypothetical organism possessing MGS is able to live or not. We attacked this viability problem
specifying in silico the metabolic pathways of the MGS-based prokaryote. We then performed a dynamic simulation of cellular metabolic activities in order to check whether the MGS-prokaryote reaches some equilibrium state and
produces the necessary biomass. We assumed these two conditions to be necessary for a living organism. Our
simulations clearly show that the MGS does not express an organism that is able to live. We then iteratively proceeded
with functional replacements in order to obtain a genome composition that gives rise to equilibrium. We ruled out 76
of the original 254 genes in the MGS, because they resulted in duplication from a functional point of view. We also
added seven genes not present in the MGS. These genes encode for enzymes involved in critical nodes of the metabolic
network. These modifications led to a genome composed of 187 elements expressing a virtually living organism,
Virtual Cell (ViCe), that exhibits homeostatic capabilities and produces biomass. Moreover, the steady-state distribution of the concentrations of virtual metabolites that resulted was similar to that experimentally measured
in bacteria. We conclude then that ViCe is able to ‘‘live in silico.’
Phototactic orientation mechanism in the ciliate Fabrea salina, as inferred from numerical simulations
No full textA Simple Protein Synthesis Model for the PURE System Operation
No full textThe encapsulation of transcription-translation (TX-TL) cell-free machinery inside lipid vesicles (liposomes) is a key element in synthetic cell technology. The PURE system is a TX-TL kit composed of well-characterized parts, whose concentrations are fine tunable, which works according to a modular architecture. For these reasons, the PURE system perfectly fulfils the requirements of synthetic biology and is widely used for constructing synthetic cells. In this work, we present a simplified mathematical model to simulate the PURE system operations. Based on Michaelis-Menten kinetics and differential equations, the model describes protein synthesis dynamics by using 9 chemical species, 6 reactions and 16 kinetic parameters. The model correctly predicts the time course for messenger RNA and protein production and allows quantitative predictions. By means of this model, it is possible to foresee how the PURE system species affect the mechanism of proteins synthesis and therefore help in understanding scenarios where the concentration of the PURE system components has been modified purposely or as a result of stochastic fluctuations (for example after random encapsulation inside vesicles). The model also makes the determination of response coefficients for all species involved in the TX-TL mechanism possible and allows for scrutiny on how chemical energy is consumed by the three PURE system modules
Optimizing soluble protein extraction and two-dimensional polyacrylamide gel electrophoresis quality for extremophile ciliates
No full textAn efficient protein extraction methodology is quite important for sample preparation and subsequent 2D-PAGE and mass spectrometry analysis. Cell lysis is the first step in protein extraction and purification. Many techniques are available for cell disruption, including physical and detergent-based methods. Here we report on a very fast and efficient detergent-free TRIS-based method to extract the soluble fraction proteins of extremophile ciliates, comparing it with a detergent-based protocol. This comparison has been carried out by means of 2D-PAGE and subsequent MALDI-compatible silver staining of protein samples obtained from the intensely pigmented hypersaline ciliate Fabrea salina and the Antarctic hypotrich ciliate Euplotes focardii. Our results indicate that this fast and easy extraction method allows to obtain more clear crude extracts and more spot-abundant polyacrylamide gels
A TASTE OF YEAST MOBILOMICS
No full textMobilomics calls for detecting all the mobile elements in a genome so as to understand their dynamic behavior. We devise and apply a method that extends a pairwise strain comparison tool for mobile genetic elements (MGE) inference, and perform experiments on a whole dataset of 39 complete genomes of as many yeast (S.cerevisiae) strains. We locate a priori all the MGEs regions that are annotated in the reference sequence at hand, and map all the putative MGEs in all the other (non-annotated) strains. Interestingly, evolutionary relation among the strains based on the presence/absence of candidate MGEs, turns out to be quite close to that inferred by classic phylogenetic methods based on SNPs analysis
DigesTip: A new device for a rapid and efficient in-solution protein digestion
No full textDigesTip is a new device for in-solution protein digestion, based on a patent pending technology, able to immobilize enzymes (trypsin, in this case) on a solid surface, keeping their activity preserved. DigesTip is a standard pipette tip, usable both by human and by robots. Its main performances are: very short digestion time (1 min) and usability with low protein sample concentrations (5 μg/mL). DigesTip obtains a clear signal in MS measurements and its usage rules out several preparative steps
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