May sediments affect the inhibiting properties of NaCl on CH4 and CO2 hydrates formation? an experimental report.

The equilibria of methane and carbon dioxide clathrate hydrates were measured in presence of a pure-quartz porous sand, with and without NaCl. Two different salt concentrations were tested: 0.030 and 0.037 wt%. Results were compared with phase equilibrium data already present in literature for these species. Despite salt, the porous medium was found to promote the process, mainly for the increased surface/volume ratio and for the improved heat transfer. In presence of salt, sand affected the process differently as a function of temperature: at values higher than 3 – 5 °C, it promoted the process, while for values lower than this range, but still greater than the ice-point, it acted as an inhibitor. However, these results can be considered true only for temperatures above the ice point. Due to similarity of ice water with clathrate hydrates, Raman microscale measurements were performed to gather information about the influence of sediments, salt, and temperature on OH-stretching vibrations of water. The obtained results allowed to clarify how the addition of NaCl, and or sediments to liquid water, under different temperature conditions (15 °C and −15 °C), influenced the water hydrogen bonds. Specifically, the changes of OH-stretching vibrations, when correlated with the NaCl concentrations, demonstrated that the presence of sediments partially inhibited the salt effects in the ice water probably due to hydrophilic interactions with the silanol groups of sediments. SEM measurements showed morphological information on sediments and on ice in different experimental conditions

Thermodynamic assessment and microscale Raman spectroscopy of binary CO2/CH4 hydrates produced during replacement applications in natural reservoirs

The present research deals with the micro – scale characterization of sI hydrates containing a binary mixture of methane and carbon dioxide. The application of replacement strategies in natural hydrate reservoirs, always leads to the formation of “mixed” hydrates, whose mechanical and chemical properties are different from those of pure CH4 and CO2 hydrates. As a function of the technique used for the process and due to the variability of the systems, a wide range of different compositions and morphologies can be obtained and the current literature must be expanded, in order to achieve a wide and accurate experimental database of CO2/CH4 hydrate properties. In this work, binary CO2/CH4 hydrates binary CO2/CH4 hydrates were produced in a small – scale reactor and then supercooled, in order to favour their extraction from the reactor and their stability at environmental conditions for a certain period of time. The gas hydrates, prepared with CO2 hydrates of pure water and with CH4 and CO2 mixtures, also in the presence of specific sands, were ex situ analysed by the use Raman-spectroscopy that confirmed the gas uptake in the hydrate structures by identification of the fingerprint of CH4 and CO2 occupancy in the hydrates. The characteristic of water inside the gas hydrates and the interaction between the host molecules and the lattice of water molecules was clarified. The different gas hydrates, analysed by Field Emission Scanning Electron Microscopy instrument equipped with “Coolstage head” under high vacuum condition, differed in morphology and surface features. The analysis of water Raman spectra of the different GHs permitted to describe the relation between symmetric and asymmetric OHs bands, but also provided information about the characteristics of water inside the different GHs, showing that the least ordered water structure was that of GHs containing sand, while the most ordered one was present on binary CO2/CH4 hydrates

Systematic analysis of mRNA 5' coding sequence incompleteness in Danio rerio: an automated EST-based approach

<p>Abstract</p> <p>Background</p> <p>All standard methods for cDNA cloning are affected by a potential inability to effectively clone the 5' region of mRNA. The aim of this work was to estimate mRNA open reading frame (ORF) 5' region sequence completeness in the model organism <it>Danio rerio </it>(zebrafish).</p> <p>Results</p> <p>We implemented a novel automated approach (<it>5'_ORF_Extender</it>) that systematically compares available expressed sequence tags (ESTs) with all the zebrafish experimentally determined mRNA sequences, identifies additional sequence stretches at 5' region and scans for the presence of all conditions needed to define a new, extended putative ORF. Our software was able to identify 285 (3.3%) mRNAs with putatively incomplete ORFs at 5' region and, in three example cases selected (<it>selt1a</it>, <it>unc119.2</it>, <it>nppa</it>), the extended coding region at 5' end was cloned by reverse transcription-polymerase chain reaction (RT-PCR).</p> <p>Conclusion</p> <p>The implemented method, which could also be useful for the analysis of other genomes, allowed us to describe the relevance of the "5' end mRNA artifact" problem for genomic annotation and functional genomic experiment design in zebrafish.</p> <p>Open peer review</p> <p>This article was reviewed by Alexey V. Kochetov (nominated by Mikhail Gelfand), Shamil Sunyaev, and Gáspár Jékely. For the full reviews, please go to the Reviewers' Comments section.</p

Uncertainty principle of genetic information in a living cell

BACKGROUND: Formal description of a cell's genetic information should provide the number of DNA molecules in that cell and their complete nucleotide sequences. We pose the formal problem: can the genome sequence forming the genotype of a given living cell be known with absolute certainty so that the cell's behaviour (phenotype) can be correlated to that genetic information? To answer this question, we propose a series of thought experiments. RESULTS: We show that the genome sequence of any actual living cell cannot physically be known with absolute certainty, independently of the method used. There is an associated uncertainty, in terms of base pairs, equal to or greater than μs (where μ is the mutation rate of the cell type and s is the cell's genome size). CONCLUSION: This finding establishes an "uncertainty principle" in genetics for the first time, and its analogy with the Heisenberg uncertainty principle in physics is discussed. The genetic information that makes living cells work is thus better represented by a probabilistic model rather than as a completely defined object

Sequence, "subtle" alternative splicing and expression of the CYYR1 (cysteine/tyrosine-rich 1) mRNA in human neuroendocrine tumors

BACKGROUND: CYYR1 is a recently identified gene located on human chromosome 21 whose product has no similarity to any known protein and is of unknown function. Analysis of expressed sequence tags (ESTs) have revealed high human CYYR1 expression in cells belonging to the diffuse neuroendocrine system (DNES). These cells may be the origin of neuroendocrine (NE) tumors. The aim of this study was to conduct an initial analysis of sequence, splicing and expression of the CYYR1 mRNA in human NE tumors. METHODS: The CYYR1 mRNA coding sequence (CDS) was studied in 32 NE tumors by RT-PCR and sequence analysis. A subtle alternative splicing was identified generating two isoforms of CYYR1 mRNA differing in terms of the absence (CAG(- )isoform, the first described mRNA for CYYR1 locus) or the presence (CAG(+ )isoform) of a CAG codon. When present, this specific codon determines the presence of an alanine residue, at the exon 3/exon 4 junction of the CYYR1 mRNA. The two mRNA isoform amounts were determined by quantitative relative RT-PCR in 29 NE tumors, 2 non-neuroendocrine tumors and 10 normal tissues. A bioinformatic analysis was performed to search for the existence of the two CYYR1 isoforms in other species. RESULTS: The CYYR1 CDS did not show differences compared to the reference sequence in any of the samples, with the exception of an NE tumor arising in the neck region. Sequence analysis of this tumor identified a change in the CDS 333 position (T instead of C), leading to the amino acid mutation P111S. NE tumor samples showed no significant difference in either CYYR1 CAG(- )or CAG(+ )isoform expression compared to control tissues. CYYR1 CAG(- )isoform was significantly more expressed than CAG(+ )isoform in NE tumors as well as in control samples investigated. Bioinformatic analysis revealed that only the genomic sequence of Pan troglodytes CYYR1 is consistent with the possible existence of the two described mRNA isoforms. CONCLUSION: A new "subtle" splicing isoform (CAG(+)) of CYYR1 mRNA, the sequence and the expression of this gene were defined in a large series of NE tumors

Digital Dermatoglyphics in Italians

Finger prints of 420 male and female subjects from Bologna (Italy) were analyzed. Sexual dimorphism and bilateral asymmetry were observed in the group. Differences in the frequency distribution of fingertip patterns in Italy with regards to the regional average were examined and biological distances were computed by Distance Coefficients, R and Xz. An increase in the frequency of whorls from north to south Italy and an increase in biological distance with increasing geographical distance were found

UniGene Tabulator: a full parser for the UniGene format

Summary: UniGene Tabulator 1.0 provides a solution for full parsing of UniGene flat file format; it implements a structured graphical representation of each data field present in UniGene following import into a common database managing system usable in a personal computer. This database includes tables related for sequence, protein similarity, sequence-tagged site (STS) and transcript map interval (TXMAP) data, plus a summary table where each record represents a UniGene cluster. UniGene Tabulator enables full local management of UniGene data, allowing parsing, querying, indexing, retrieving, exporting and analysis of UniGene data in a relational database form, usable on Macintosh (OS X 10.3.9 or later) and Windows (2000, with service pack 4, XP, with service pack 2, or later) operating systems-based computers. Availability: the current release, including both the FileMaker runtime applications, are freely available a