From soil remediation to biofuel. Process simulation of bioethanol production from Arundo donax

A range of energy crops can be grown on marginal land (i.e. land that is not suitable for food crop production or contaminated site) to provide feedstocks for bioenergy, non-food products and biofuels. The food versus fuel debate had a significant negative impact in Europe on first generation biofuels production from food crops (i.e. wheat, rapeseed, etc). A new approach involving the use of marginal land for the production of lignocellulosic species for the production of bioethanol is now pursued in Italy and in many other countries, where the demand for high quality water resources, arable land, food and fossil fuels is rapidly growing. With an emerging “feed versus fuel debate” there is a pressing need to find options for the use of marginal lands and wastewaters or saline ground waters to produce second generation biofuel or bio paper crops. Arundo donax was selected as a potential crop for use in these areas, since it produces more cellulosic biomass and sequesters more contaminants, using less land and pesticides than any other alternative crops reported in the literature. The objective of this paper is to evaluate economically a simplified process for the production of second generation bioethanol from A. donax. Process calculations and economic analyses are performed using the software SuperPro Designer®

Understanding the molecular basis of folding cooperativity through a comparative analysis of a multidomain protein and its isolated domains

Although cooperativity is a well-established and general property of folding, our current understanding of this feature in multi-domain folding is still relatively limited. In fact, there are contrasting results indicating that the constituent domains of a multi-domain protein may either fold independently on each other or exhibit inter-dependent supradomain phenomena. To address this issue, here we present the comparative analysis of the folding of a tandem repeat protein, comprising two contiguous PDZ domains, in comparison to that of its isolated constituent domains. By analyzing in detail the equilibrium and kinetics of folding at different experimental conditions, we demonstrate that, despite each of the PDZ domains in isolation being capable of independent folding, at variance with previously characterized PDZ tandem repeats, the full-length construct folds and unfolds as a single co-operative unit. By exploiting quantitatively the comparison of the folding of the tandem repeat to those observed for its constituent domains, as well as by characterizing a truncated variant lacking a short auto-inhibitory segment, we successfully rationalize the molecular basis of the observed cooperativity and attempt to infer some general conclusions for multi-domain systems

Folding and Binding Mechanisms of the SH2 Domain from Crkl

SH2 domains are structural modules specialized in the recognition and binding of target sequences containing a phosphorylated tyrosine residue. They are mostly incorporated in the 3D structure of scaffolding proteins that represent fundamental regulators of several signaling pathways. Among those, Crkl plays key roles in cell physiology by mediating signals from a wide range of stimuli, and its overexpression is associated with several types of cancers. In myeloid cells expressing the oncogene BCR/ABL, one interactor of Crkl-SH2 is the focal adhesion protein Paxillin, and this interaction is crucial in leukemic transformation. In this work, we analyze both the folding pathway of Crkl-SH2 and its binding reaction with a peptide mimicking Paxillin, under different ionic strength and pH conditions, by using means of fluorescence spectroscopy. From a folding perspective, we demonstrate the presence of an intermediate along the reaction. Moreover, we underline the importance of the electrostatic interactions in the early event of recognition, occurring between the phosphorylated tyrosine of the Paxillin peptide and the charge residues of Crkl-SH2. Finally, we highlight a pivotal role of a highly conserved histidine residue in the stabilization of the binding complex. The experimental results are discussed in light of previous works on other SH2 domains

Catalase Takes Part in Rat Liver Mitochondria Oxidative Stress Defense

Highly purified rat liver mitochondria (RLM) when exposed to tert-butylhydroperoxide undergo matrix swelling, membrane potential collapse, and oxidation of glutathione and pyridine nucleotides, all events attributable to the induction of mitochondrial permeability transition. Instead, RLM, if treated with the same or higher amounts of H2O2 or tyramine, are insensitive or only partially sensitive, respectively, to mitochondrial permeability transition. In addition, the block of respiration by antimycin A added to RLM respiring in state 4 conditions, or the addition of H2O2, results in O2 generation, which is blocked by the catalase inhibitors aminotriazole or KCN. In this regard, H2O2 decomposition yields molecular oxygen in a 2:1 stoichiometry, consistent with a catalytic mechanism with a rate constant of 0.0346 s(-1). The rate of H2O2 consumption is not influenced by respiratory substrates, succinate or glutamate-malate, nor by N-ethylmaleimide, suggesting that cytochrome c oxidase and the glutathione-glutathione peroxidase system are not significantly involved in this process. Instead, H2O2 consumption is considerably inhibited by KCN or aminotriazole, indicating activity by a hemoprotein. All these observations are compatible with the presence of endogenous heme-containing catalase with an activity of 825 +/- 15 units, which contributes to mitochondrial protection against endogenous or exogenous H2O2. Mitochondrial catalase in liver most probably represents regulatory control of bioenergetic metabolism, but it may also be proposed for new therapeutic strategies against liver diseases. The constitutive presence of catalase inside mitochondria is demonstrated by several methodological approaches as follows: biochemical fractionating, proteinase K sensitivity, and immunogold electron microscopy on isolated RLM and whole rat liver tissue

P19-derived neuronal cells express H1, H2, and H3 histamine receptors: a biopharmaceutical approach to evaluate antihistamine agents

Histamine is a biogenic amine implicated in various biological and pathological processes. Convenient cellular models are needed to screen and develop new antihistamine agents. This report aimed to characterize the response of neurons differentiated from mouse P19 embryonal carcinoma cells to histamine treatment, and to investigate the modulation of this response by antihistamine drugs, vegetal diamine oxidase, and catalase. The exposure of P19 neurons to histamine reduced cell viability to 65% maximally. This effect involves specific histamine receptors, since it was prevented by treatment with desloratadine and cimetidine, respectively, H-1 and H-2 antagonists, but not by the H-3 antagonist ciproxifan. RT-PCR analysis showed that P19 neurons express H-1 and H-2 receptors, and the H-3 receptor, although it seemed not involved in the histamine effect on these cells. The H-4 receptor was not expressed. H-1 and H-2 antagonists as well as vegetal diamine oxidase diminished the intracellular Ca2+ mobilization triggered by histamine. The treatment with vegetal diamine oxidase or catalase protected against mortality and a significant reduction of H2O2 level, generated from the cells under the histamine action, was found upon treatments with desloratadine, cimetidine, vegetal diamine oxidase, or catalase. Overall, the results indicate the expression of functional histamine receptors and open the possibility of using P19 neurons as model system to study the roles of histamine and related drugs in neuronal pathogenesis. This model is less expensive to operate and can be easily implemented by current laboratories of analysis and by Contract Research Organizations

Whole genome amplification and real-time PCR in forensic casework

<p>Abstract</p> <p>Background</p> <p>WGA (Whole Genome Amplification) in forensic genetics can eliminate the technical limitations arising from low amounts of genomic DNA (gDNA). However, it has not been used to date because any amplification bias generated may complicate the interpretation of results. Our aim in this paper was to assess the applicability of MDA to forensic SNP genotyping by performing a comparative analysis of genomic and amplified DNA samples. A 26-SNPs TaqMan panel specifically designed for low copy number (LCN) and/or severely degraded genomic DNA was typed on 100 genomic as well as amplified DNA samples.</p> <p>Results</p> <p>Aliquots containing 1, 0.1 and 0.01 ng each of 100 DNA samples were typed for a 26-SNPs panel. Similar aliquots of the same DNA samples underwent multiple displacement amplification (MDA) before being typed for the same panel. Genomic DNA samples showed 0% PCR failure rate for all three dilutions, whilst the PCR failure rate of the amplified DNA samples was 0% for the 1 ng and 0.1 ng dilutions and 0.077% for the 0.01 ng dilution. The genotyping results of both the amplified and genomic DNA samples were also compared with reference genotypes of the same samples obtained by direct sequencing. The genomic DNA samples showed genotype concordance rates of 100% for all three dilutions while the concordance rates of the amplified DNA samples were 100% for the 1 ng and 0.1 ng dilutions and 99.923% for the 0.01 ng dilution. Moreover, ten artificially-degraded DNA samples, which gave no results when analyzed by current forensic methods, were also amplified by MDA and genotyped with 100% concordance.</p> <p>Conclusion</p> <p>We investigated the suitability of MDA material for forensic SNP typing. Comparative analysis of amplified and genomic DNA samples showed that a large number of SNPs could be accurately typed starting from just 0.01 ng of template. We found that the MDA genotyping call and accuracy rates were only slightly lower than those for genomic DNA. Indeed, when 10 pg of input DNA was used in MDA, we obtained 99.923% concordance, indicating a genotyping error rate of 1/1299 (7.7 × 10^-4). This is quite similar to the genotyping error rate of STRs used in current forensic analysis. Such efficiency and accuracy of SNP typing of amplified DNA suggest that MDA can also generate large amounts of genome-equivalent DNA from a minimal amount of input DNA. These results show for the first time that MDA material is suitable for SNP-based forensic protocols and in general when samples fail to give interpretable STR results.</p

In silico and in vitro comparative analysis to select, validate and test SNPs for human identification

<p>Abstract</p> <p>Background</p> <p>The recent advances in human genetics have recently provided new insights into phenotypic variation and genome variability. Current forensic DNA techniques involve the search for genetic similarities and differences between biological samples. Consequently the selection of ideal genomic biomarkers for human identification is crucial in order to ensure the highest stability and reproducibility of results.</p> <p>Results</p> <p>In the present study, we selected and validated 24 SNPs which are useful in human identification in 1,040 unrelated samples originating from three different populations (Italian, Benin Gulf and Mongolian). A Rigorous <it>in silico </it>selection of these markers provided a list of SNPs with very constant frequencies across the populations tested as demonstrated by the F_stvalues. Furthermore, these SNPs also showed a high specificity for the human genome (only 5 SNPs gave positive results when amplified in non-human DNA).</p> <p>Conclusion</p> <p>Comparison between <it>in silico </it>and <it>in vitro </it>analysis showed that current SNPs databases can efficiently improve and facilitate the selection of markers because most of the analyses performed (F_st, r², heterozigosity) in more than 1,000 samples confirmed available population data.</p

Bollettino Sismico Italiano: maggio - agosto 2015

Nel secondo quadrimestre 2015 si sono verificati 7 eventi di magnitudo superiore a 4: il 9 maggio un evento di ML 4.5 è stato localizzato nel basso Tirreno ad una profondità di circa 217 km; l’11 maggio un terremoto di Mw 4.4 nel Mar Ionio a circa 47 km di profondità; il 29 maggio un Mw 4.2 nel Mar Adriatico di fronte a San Benedetto del Tronto; il 2 agosto un evento di magnitudo ML4.0 nel Mar Tirreno, al largo della costa calabra occidentale, ad una profondità di circa 247 km e il 3 agosto un terremoto di magnitudo ML 4.0 tra le province di Cosenza e Catanzaro a sud della Sila, seguito da una sequenza di oltre 80 repliche di piccola magnitudo. L’8 agosto 2015 si è verificato un terremoto di ML 4.1 alle Isole Eolie, ed infine il 29 agosto un evento di Mw 4.0 vicino al confine della Slovenia con il Friuli Venezia Giulia, seguito da una sequenza sismica che è continuata anche dopo il 31 agosto.Istituto Nazionale di Geofisica e Vulcanologia - Dipartimento di Protezione CivilePublished4IT. Banche dat

Bollettino Sismico Italiano: settembre - dicembre 2015

Nel terzo quadrimestre 2015 si sono verificati 5 terremoti con M>4 nel territorio Italiano. In particolare il 14 ed il 16 ottobre si sono verificati due eventi profondi del basso Tirreno il primo con M=4.2 a 300 km di profondità, il secondo con M=4.4 a circa 250 km di profondità. Due terremoti M4.2 e M4.4 sono avvenuti il 6 dicembre nel Mar Adriatico a nord delle Isole Tremiti. Associati a questi si sono verificati alcuni eventi di magnitudo sopra a 3.5: si è trattata di una vera e propria sequenza sismica durata pochi giorni. L’ultimo evento di magnitudo superiore a 4 si è verificato a NE di Palermo nel basso Tirreno il 20 dicembre con una M=4.2. E’ infine da segnalare un terremoto con M = 4.8 che si è verificato il 1 Novembre in Slovenia, al confine con la Croazia.Istituto Nazionale di Geofisica e Vulcanologia - Dipartimento di Protezione CivilePublished4IT. Banche dat

Bollettino Sismico Italiano: maggio - agosto 2016

Il 24 agosto 2016 un terremoto di magnitudo 6.0 ha dato inizio ad una sequenza sismica in Italia centrale, che ha generato decine di migliaia di eventi sismici. Per l’analisi e revisione di questa sequenza si rimanda ad un uscita speciale del BSI prevista per fine 2017(S_BSI_CI). In questo quadrimestre e nel successivo gli eventi nella zona della sequenza sono quelli localizzati nella sala di sorveglianza. Solo gli eventi con M>= 3.5, e pochi altri (vedi Marchetti et al. Annals of Geophys. DOI: 10.4401/ag6116) sono stati rivisti dal BSI.Nel secondo quadrimestre 2016 si sono verificati sedici eventi di magnitudo superiore a 4.0 (ML) rivisti dagli analisti del BSI uno vicino alle coste tunisine quindi fuori dal territorio nazionale; l’evento di Mw 4.1 che è avvenuto il 30 maggio in provincia di Terni vicino al Lago di Bolsena (lat=42.7, lon=11.98 ad una profondità di 8 km) e 14 eventi nella zona della sequenza nell’ultima settimana del quadrimestre: il 24 agosto 2016 si è verificato l’evento di magnitudo ML=6.0 (Mw=6.0) che ha iniziato una sequenza sismica per la quale sono stati localizzati decine di migliaia di terremoti e che alla fine di ottobre 2016 ha generato eventi persino più forti (fino a Mw=6.5) della prima scossa.Istituto Nazionale di Geofisica e Vulcanologia - Dipartimento di Protezione CivilePublished4IT. Banche dat