CNR Institute of Biophysics

Pisa, Italy

CNR Institute of Biophysics

Pisa, Italy
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Zifarelli G.,CNR Institute of Biophysics | Pusch M.,CNR Institute of Biophysics
FEBS Letters | Year: 2010

Nitrate compartmentalization in intracellular organelles has been long recognized as critical for plant physiology but the molecular identity of the proteins involved remained unclear for a long time. In Arabidopsis thaliana, AtClC-a has been recently shown to be a NO3-/H+ antiporter critical for nitrate transport into the vacuoles. AtClC-a is a member of the CLC protein family, whose animal and bacterial members, comprising both channels and H+-coupled antiporters, have been previously implicated exclusively in Cl- transport. Despite the different NO3- over Cl- selectivity of AtClC-a compared to the other CLC antiporters, it has similar transport properties.Other CLC homologues have been cloned in Arabidopsis, tobacco, rice and soybean. © 2009 Federation of European Biochemical Societies.

Marchetti C.,CNR Institute of Biophysics
BioMetals | Year: 2014

There is increasing evidence that toxic metals play a role in diseases of unknown etiology. Their action is often mediated by membrane proteins, and in particular neurotransmitter receptors. This brief review will describe recent findings on the direct interaction of metal ions with ionotropic γ-aminobutyric acid (GABAA) and glutamate receptors, the main inhibitory and excitatory neurotransmitter receptors in the mammalian central nervous system, respectively. Both hyper and hypo function of these receptors are involved in neurological and psychotic syndromes and modulation by metal ions is an important pharmacological issue. The focus will be on three xenobiotic metals, lead (Pb), cadmium (Cd) and nickel (Ni) that have no biological function and whose presence in living organisms is only detrimental, and two trace metals, zinc (Zn) and copper (Cu), which are essential for several enzymatic functions, but can mediate toxic actions if deregulated. Despite limited access to the brain and tight control by metalloproteins, exogenous metals interfere with receptor performances by mimicking physiological ions and occupying one or more modulatory sites on the protein. These interactions will be discussed as a potential cause of neuronal dysfunction. © Springer Science+Business Media 2014.

The aim of this study was to describe monthly series of the Standardized Precipitation Index obtained from four weather stations of the State of São Paulo, Brazil. The analyses were carried out by evaluating the normality assumption of the SPI distributions, the spectral features of these series and, the presence of climatic trends in these datasets. It was observed that the Pearson type III distribution was better than the gamma 2-parameter distribution in providing monthly SPI series closer to the normality assumption inherent to the use of this standardized index. The spectral analyses carried out in the timefrequency domain did not allow us to establish a dominant mode in the analyzed series. In general, the Mann-Kendall and the Pettitt tests indicated the presence of no significant trend in the SPI series. However, both trend tests have indicated that the temporal variability of this index, observed at the months of October over the last 60 years, cannot be seen as the result of a purely random process. This last inference is due to the concentration of decreasing trends, with a common beginning (1983/84) in the four locations of the study.

Drought is a slow-moving hazard that occurs in virtually all countries of the world. In the light of this, several indices have been developed to improve the detection of drought's onset, as well as quantifying other features of this phenomenon. The Standardized Precipitation Index (SPI) is often used in order to characterize meteorological droughts. In addition, this index is largely used by Brazilian's agricultural institutions. In order to add important information to the drought literature, this review article described a general definition of drought, evaluated it from a statistical point of view, and also described the SPI strengths and limitations. An adaptation of the SPI that aims to develop a probability-based agricultural drought index was also presented. The results obtained herein, associated with several studies carried out throughout the world, demonstrated that the SPI is not an agricultural index. It is just a mathematical approach developed to transforming skewed distributions into the Gaussian form. If this standardization cannot be achieved, the use of this index becomes meaningless. Therefore, a normality test should be used in establishing a temporal lower limit for the SPI computations. It was also verified that for periods in which the probability associated with the zero precipitation value is close to 0.5, the SPI may erroneously indicate the end of an existing drought (or a decrease in its severity) in the presence of a decrease in the actual evapotranspiration values.

Moran O.,CNR Institute of Biophysics
International Journal of Biochemistry and Cell Biology | Year: 2014

The cystic fibrosis transmembrane conductance regulator (CFTR) is a multidomain membrane protein forming an anion selective channel. Mutations in the gene encoding CFTR cause cystic fibrosis (CF). The intracellular side of CFTR constitutes about 80% of the total mass of the protein. This region includes domains involved in ATP-dependent gating and regulatory protein kinase-A phosphorylation sites. The high-resolution molecular structure of CFTR has not yet been solved. However, a range of lower resolution structural data, as well as functional biochemical and electrophysiological data, are now available. This information has enabled the proposition of a working model for the structural architecture of the intracellular domains of the CFTR protein. This article is part of a Directed Issue entitled: Cystic Fibrosis: From o-mics to cell biology, physiology, and therapeutic advances. © 2014 Elsevier Ltd.

Moran O.,CNR Institute of Biophysics
Journal of Theoretical Biology | Year: 2010

Mutations of the cystic fibrosis transmembrane conductance regulator (CFTR) cause cystic fibrosis, a hereditary lethal disease. CFTR is a chloride channel expressed in the apical membrane of epithelia. It is activated by cAMP dependent phosphorylation and gated by the binding of ATP. The impaired chloride transport of some types of cystic fibrosis mutations could be pharmacologically solved by the use of chemical compounds called potentiators. Here it is undertaken the construction of a model of the CFTR activation pathways, and the possible modification produced by a potentiator application. The model yields a novel mechanism for the potentiator action, describing the activatory and inhibitory activities on two different positions in the CFTR activation pathway. © 2009 Elsevier Ltd.

The climatic variability is the main factor responsible for the oscillations and frustrations of the coffee grain yield in Brazil. The relationships between the climatic parameters and the agricultural production are quite complex, because environmental factors affect the growth and the development of the plants under different forms during the growth stages of the coffee crop. Agrometeorological models related to the growth, development and productivity can supply information for the soil water monitoring and yield forecast, based on the water stress. A soil water balance during different growth stages of the coffee crop, can quantify the effect of the available soil water on the decrease of the final yield. Other climatic factors can reduce the productivity, such as adverse air temperatures happened during different growth stages. Solar radiation and relative humidity influence many physiological processes of the coffee tree but are not generally thought to play an important role as thermal and rainfall conditions in defining potential yield or ecological limitations for this crop. According to the last report of the Intergovernmental Panel on Climate Change (IPCC, 2007), the global temperature is supposed to increase 1.1oC to 6.4oC and the rainfall 15% in the tropical areas of Brazil. Some Global warming projections as presented by IPCC will cause a strong decrease in the coffee production in Brazil. According to the literature besides the reduction of suitable areas for coffee production, the crop will tend to move South and uphill regions. This review article analyze the effect that these possible scenarios would have in the agro-climatic coffee zoning in Brazil, and adaptive solutions, such as agronomic mitigations and development of cultivars adapted to high temperatures is considered.

Morandini P.,CNR Institute of Biophysics
Plant Biotechnology Journal | Year: 2013

Which factors limit metabolite accumulation in plant cells? Are theories on flux control effective at explaining the results? Many biotechnologists cling to the idea that every pathway has a rate limiting enzyme and target such enzymes first in order to modulate fluxes. This often translates into large effects on metabolite concentration, but disappointing small increases in flux. Rate limiting enzymes do exist, but are rare and quite opposite to what predicted by biochemistry. In many cases however, flux control is shared among many enzymes. Flux control and concentration control can (and must) be distinguished and quantified for effective manipulation. Flux control for several 'building blocks' of metabolism is placed on the demand side, and therefore increasing demand can be very successful. Tampering with supply, particularly desensitizing supply enzymes, is usually not very effective, if not dangerous, because supply regulatory mechanisms function to control metabolite homeostasis. Some important, but usually unnoticed, metabolic constraints shape the responses of metabolic systems to manipulation: mass conservation, cellular resource allocation and, most prominently, energy supply, particularly in heterotrophic tissues. The theoretical basis for this view shall be explored with recent examples gathered from the manipulation of several metabolites (vitamins, carotenoids, amino acids, sugars, fatty acids, polyhydroxyalkanoates, fructans and sugar alcohols). Some guiding principles are suggested for an even more successful engineering of plant metabolism. © 2013 Society for Experimental Biology, Association of Applied Biologists and Blackwell Publishing Ltd.

Kusch J.,Universitatsklinikum Jena | Zifarelli G.,CNR Institute of Biophysics
Biophysical Journal | Year: 2014

Ion channels and transporters are membrane proteins whose functions are driven by conformational changes. Classical biophysical techniques provide insight into either the structure or the function of these proteins, but a full understanding of their behavior requires a correlation of both these aspects in time. Patch-clamp and voltage-clamp fluorometry combine spectroscopic and electrophysiological techniques to simultaneously detect conformational changes and ionic currents across the membrane. Since its introduction, patch-clamp fluorometry has been responsible for invaluable advances in our knowledge of ion channel biophysics. Over the years, the technique has been applied to many different ion channel families to address several biophysical questions with a variety of spectroscopic approaches and electrophysiological configurations. This review illustrates the strength and the flexibility of patch-clamp fluorometry, demonstrating its potential as a tool for future research. © 2014 Biophysical Society.

Sgarbossa A.,CNR Institute of Biophysics
International Journal of Molecular Sciences | Year: 2012

Biomolecular self-assembly is a fundamental process in all organisms. As primary components of the life molecular machinery, proteins have a vast array of resources available to them for self-assembly in a functional structure. Protein self-assembly, however, can also occur in an aberrant way, giving rise to non-native aggregated structures responsible for severe, progressive human diseases that have a serious social impact. Different neurodegenerative disorders, like Huntington's, Alzheimer's, and spongiform encephalopathy diseases, have in common the presence of insoluble protein aggregates, generally termed 'amyloid', that share several physicochemical features: a fibrillar morphology, a predominantly beta-sheet secondary structure, birefringence upon staining with the dye Congo red, insolubility in common solvents and detergents, and protease resistance. Conformational constrains, hydrophobic and stacking interactions can play a key role in the fibrillogenesis process and protein-protein and peptide-peptide interactions-resulting in self-assembly phenomena of peptides yielding fibrils-that can be modulated and influenced by natural biomolecules. Small organic molecules, which possess both hydrophilic and hydrophobic moieties able to bind to peptide/protein molecules through hydrogen bonds and hydrophobic and aromatic interactions, are potential candidates against amyloidogenesis. In this review some significant case examples will be critically discussed. © 2012 by the authors; licensee MDPI, Basel, Switzerland.

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