Question 3: The Worlds of the Prebiotic and Never Born Proteins

Starting from the statement that no reliable methods are known to produce high molecular weight polypeptides under prebiotic conditions, a possible approach, at least to understand the differences between extant proteins and the possible large number of never born proteins, could be biological. Using the phage display method a large library of totally random amino acidic sequences was obtained. Consequently, different experiments to directly consider the frequency of stable folds were performed, and the interesting results obtained from such new approach are discussed in terms of contingency, contributing to the discussion on the selection mechanism of extant proteins. Presented at the International School of Complexity – 4th Course: Basic Questions on the Origins of Life; “Ettore Majorana” Foundation and Centre for Scientific Culture, Erice, Italy, 1–6 October 2006.     

Daily Rhythms of Serum Leptin in Ewes: Effects of Feeding,Pregnancy and Lactation

The aim of the present study was to test whether serum concentrations of leptin in ewes vary with a daily rhythm. For this purpose, we examined 24 h serum leptin profiles of ewes exposed to natural photoperiodic conditions and subjected to two different feeding schedules (regular feeding and fasting). The results show for the first time the existence of daily rhythm of plasma leptin in regularly fed ewes, with a minimum during the light phase and a peak during the dark phase. Daily rhythms of serum leptin persisted after 50 h of fasting, although fasting shifted the peak of the rhythm to the beginning of the light phase and significantly reduced daily leptin production. To gain a better understanding of the role of leptin in the temporal organization of physiological events related to pregnancy and lactation, we measured serum leptin profiles throughout 24 h in ewes either during pregnancy or lactation. Daily leptin rhythms were found to persist during pregnancy and lactation, but both physiological conditions altered leptin concentrations. Maternal serum leptin concentration rose between early and mid pregnancy, then decreased in the late pregnancy and during lactation. Daily serum leptin concentration was significantly lower in nonpregnant, nonlactating ewes, compared either to lactating or to early pregnant ewes.     

Contribution of Genome-Wide Association Studies to Scientific Research: A Pragmatic Approach to Evaluate Their Impact

The factual value of genome-wide association studies (GWAS) for the understanding of multifactorial diseases is a matter of intense debate. Practical consequences for the development of more effective therapies do not seem to be around the corner. Here we propose a pragmatic and objective evaluation of how much new biology is arising from these studies, with particular attention to the information that can help prioritize therapeutic targets. We chose multiple sclerosis (MS) as a paradigm disease and assumed that, in pre-GWAS candidate-gene studies, the knowledge behind the choice of each gene reflected the understanding of the disease prior to the advent of GWAS. Importantly, this knowledge was based mainly on non-genetic, phenotypic grounds. We performed single-gene and pathway-oriented comparisons of old and new knowledge in MS by confronting an unbiased list of candidate genes in pre-GWAS association studies with those genes exceeding the genome-wide significance threshold in GWAS published from 2007 on. At the single gene level, the majority (94 out of 125) of GWAS-discovered variants had never been contemplated as plausible candidates in pre-GWAS association studies. The 31 genes that were present in both pre- and post-GWAS lists may be of particular interest in that they represent disease-associated variants whose pathogenetic relevance is supported at the phenotypic level (i.e. the phenotypic information that steered their selection as candidate genes in pre-GWAS association studies). As such they represent attractive therapeutic targets. Interestingly, our analysis shows that some of these variants are targets of pharmacologically active compounds, including drugs that are already registered for human use. Compared with the above single-gene analysis, at the pathway level GWAS results appear more coherent with previous knowledge, reinforcing some of the current views on MS pathogenesis and related therapeutic research. This study presents a pragmatic approach that helps interpret and exploit GWAS knowledge.     

Influence of Ionization State on the Activation of Temocapril by hCES1: A Molecular‐Dynamics Study

Temocapril is a prodrug whose hydrolysis by carboxylesterase 1 (CES1) yields the active ACE inhibitor temocaprilat. This molecular‐dynamics (MD) study uses a resolved structure of the human CES1 (hCES1) to investigate some mechanistic details of temocapril hydrolysis. The ionization constants of temocapril (pK1 and pK3) and temocaprilat (pK1, pK2, and pK3) were determined experimentally and computationally using commercial algorithms. The constants so obtained were in good agreement and revealed that temocapril exists mainly in three ionic forms (a cation, a zwitterion, and an anion), whereas temocaprilat exists in four major ionic forms (a cation, a zwitterion, an anion, and a dianion). All these ionic forms were used as ligands in 5‐ns MS simulations. While the cationic and zwitterionic forms of temocapril were involved in an ion‐pair bond with Glu255 suggestive of an inhibitor behavior, the anionic form remained in a productive interaction with the catalytic center. As for temocaprilat, its cation appeared trapped by Glu255, while its zwitterion and anion made a slow departure from the catalytic site and a partial egress from the protein. Only its dianion was effectively removed from the catalytic site and attracted to the protein surface by Lys residues. A detailed mechanism of product egress emerges from the simulations.     

Influence of fatty acid‐free diet on mammary tumor development and growth rate in HER‐2/neu transgenic mice

Numerous investigations have found a relationship between higher risk of cancer and increased intake of fats, while results of clinical studies of fat reduction and breast cancer recurrence have been mixed. A diet completely free of fats cannot be easily administered to humans, but experimental studies in mice can be done to determine whether this extreme condition influences tumor development. Here, we examined the effects of a FA‐free diet on mammary tumor development and growth rate in female FVB‐neu proto‐oncogene transgenic mice that develop spontaneous multifocal mammary tumors after a long latency period. Mice were fed a fatty acid‐free diet beginning at 112, 35, and 30 days of age. In all these experiments, tumor appearance was delayed, tumor incidence was reduced and the mean number of palpable mammary tumors per mouse was lower, as compared to standard diet‐fed mice. By contrast, tumor growth rate was unaffected in mice fed the fatty acid‐free diet. Plasma of mice fed the fatty acid‐free diet revealed significantly higher contents of oleic, palmitoleic and 20:3ω9 acids and lower contents of linoleic and palmitic acids. In conclusion, these findings indicate that a FA‐free diet reduces tumor incidence and latency but not tumor growth rate, suggesting that a reduction in dietary FAs in humans may have a protective effect on tumorigenesis but not on tumors once they appear. J. Cell. Physiol. 228: 242–249, 2013. © 2012 Wiley Periodicals, Inc.     

Assay for apoptosis using the mitochondrial probes, Rhodamine123 and 10-N-nonyl acridine orange

Apoptosis plays a pivotal role in the regulation of cell turnover, and a defect or an excess of apoptosis has been implicated in several human diseases. Apoptosis is activated from an extracellular death signal, or from an internal pathway starting from the endoplasmatic reticulum or the mitochondria. To investigate the mitochondrial compartment during apoptosis, we have established a protocol using fluorochromes and flow cytometry to probe the structure and function of mitochondria kinetically. The protocol could be applied to whole cells or to isolated mitochondria. In the first case, cells are counterstained with ethidium bromide (EB) to evaluate plasma membrane function. The presence of the electrochemical gradient in the mitochondria is probed with Rhodamine123 (Rh123), whereas the structure and the integrity of mitochondria are assessed using 10-N-nonyl-acridine orange (NAO). Not considering the time requested for cell/mitochondria preparation and the activation of apoptosis, the protocol lasts <1 h.     

Pilocarpine-induced status epilepticus in rats involves ischemic and excitotoxic mechanisms

The neuron loss characteristic of hippocampal sclerosis in temporal lobe epilepsy patients is thought to be the result of excitotoxic, rather than ischemic, injury. In this study, we assessed changes in vascular structure, gene expression, and the time course of neuronal degeneration in the cerebral cortex during the acute period after onset of pilocarpine-induced status epilepticus (SE). Immediately after 2 hr SE, the subgranular layers of somatosensory cortex exhibited a reduced vascular perfusion indicative of ischemia, whereas the immediately adjacent supragranular layers exhibited increased perfusion. Subgranular layers exhibited necrotic pathology, whereas the supergranular layers were characterized by a delayed (24 h after SE) degeneration apparently via programmed cell death. These results indicate that both excitotoxic and ischemic injuries occur during pilocarpine-induced SE. Both of these degenerative pathways, as well as the widespread and severe brain damage observed, should be considered when animal model-based data are compared to human pathology.     

Fluorescence decay of dyed protozoa: differences between stressed and non‐stressed cysts

Several series of tests have shown that fresh, intact samples of Giardia duodenalis and Cryptosporidium parvum (oo)cysts are not marked by fluorescent probes such as carboxyfluorcein‐succinimidyl‐diacetate‐ester (CFDA‐SE), C12‐resazurin and SYTOX® Green, probably because of their robust cell walls. These dyes fail to indicate the viability of such protozoa and allow negative responses to be recorded from living and infectious samples. Cryptosporidium parvum showed stronger isolation from chemicals, with living oocysts remaining unstained by the probe for up to 90 days after extraction. However, in further fluorescence decay (FD) experiments run with G. duodenalis samples stained using CFDA‐SE (comprising living, non‐stressed but aged cysts, heat‐killed samples and UV‐C‐stressed samples) each showed a different FD decay profile, here studied in seven series of tests of five replicates each. The FD profiles were fitted by double‐exponential decay kinetics, with the decay constant k₂ being five times higher than k₁. This FD procedure is fast and can be easily reproduced in 10 steps, taking ~ 1 h of laboratory work for already purified samples. Copyright © 2015 John Wiley & Sons, Ltd.