New insights into the operative network of FaEO,an enone oxidoreductase from <Emphasis Type="Italic">Fragaria x ananassa</Emphasis> Duch.

The 2-methylene-furan-3-one reductase or Fragaria x ananassa Enone Oxidoreductase (FaEO) catalyses the last reductive step in the biosynthesis of 4-hydroxy-2,5-dimethyl-3(2H)-furanone, a major component in the characteristic flavour of strawberries. In the present work, we describe the association between FaEO and the vacuolar membrane of strawberry fruits. Even if FaEO lacks epitopes for stable or transient membrane-interactions, it contains a calmodulin-binding region, suggesting that in vivo FaEO may be associated with the membrane via a peripheral protein complex with calmodulin. Moreover, we also found that FaEO occurs in dimeric form in vivo and, as frequently observed for calmodulin-regulated proteins, it may be expressed in different isoforms by alternative gene splicing. Further mass spectrometry analysis confirmed that the isolated FaEO consists in the already known isoform and that it is the most characteristic during ripening. Finally, a characterization by absorption spectroscopy showed that FaEO has specific flavoprotein features. The relevance of these findings and their possible physiological implications are discussed.     

From protein-protein interactions to protein co-expression networks: a new perspective to evaluate large-scale proteomic data

The reductionist approach of dissecting biological systems into their constituents has been successful in the first stage of the molecular biology to elucidate the chemical basis of several biological processes. This knowledge helped biologists to understand the complexity of the biological systems evidencing that most biological functions do not arise from individual molecules; thus, realizing that the emergent properties of the biological systems cannot be explained or be predicted by investigating individual molecules without taking into consideration their relations. Thanks to the improvement of the current -omics technologies and the increasing understanding of the molecular relationships, even more studies are evaluating the biological systems through approaches based on graph theory. Genomic and proteomic data are often combined with protein-protein interaction (PPI) networks whose structure is routinely analyzed by algorithms and tools to characterize hubs/bottlenecks and topological, functional, and disease modules. On the other hand, co-expression networks represent a complementary procedure that give the opportunity to evaluate at system level including organisms that lack information on PPIs. Based on these premises, we introduce the reader to the PPI and to the co-expression networks, including aspects of reconstruction and analysis. In particular, the new idea to evaluate large-scale proteomic data by means of co-expression networks will be discussed presenting some examples of application. Their use to infer biological knowledge will be shown, and a special attention will be devoted to the topological and module analysis.     

Sequencing of Australian wild rice genomes reveals ancestral relationships with domesticated rice

The related A genome species of the Oryza genus are the effective gene pool for rice. Here, we report draft genomes for two Australian wild A genome taxa: O. rufipogon‐like population, referred to as Taxon A, and O. meridionalis‐like population, referred to as Taxon B. These two taxa were sequenced and assembled by integration of short‐ and long‐read next‐generation sequencing (NGS) data to create a genomic platform for a wider rice gene pool. Here, we report that, despite the distinct chloroplast genome, the nuclear genome of the Australian Taxon A has a sequence that is much closer to that of domesticated rice (O. sativa) than to the other Australian wild populations. Analysis of 4643 genes in the A genome clade showed that the Australian annual, O. meridionalis, and related perennial taxa have the most divergent (around 3 million years) genome sequences relative to domesticated rice. A test for admixture showed possible introgression into the Australian Taxon A (diverged around 1.6 million years ago) especially from the wild indica/O. nivara clade in Asia. These results demonstrate that northern Australia may be the centre of diversity of the A genome Oryza and suggest the possibility that this might also be the centre of origin of this group and represent an important resource for rice improvement.     

RAC3 influences the chemoresistance of colon cancer cells through autophagy and apoptosis inhibition

Background

RAC3 coactivator overexpression has been implicated in tumorigenesis, contributing to inhibition of apoptosis and autophagy. Both mechanisms are involved in resistance to treatment with chemotherapeutic agents. The aim of this study was to investigate its role in chemoresistance of colorectal cancer.

Methods

The sensitivity to 5-fluorouracil and oxaliplatin in colon cancer cells HT-29, HCT 116 and Lovo cell lines, expressing high or low natural levels of RAC3, was investigated using viability assays.

Results

In HCT 116 cells, we found that although 5-fluorouracil was a poor inducer of apoptosis, autophagy was strongly induced, while oxaliplatin has shown a similar ability to induce both of them. However, in HCT 116 cells expressing a short hairpin RNA for RAC3, we found an increased sensitivity to both drugs if it is compared with control cells. 5-Fluorouracil and oxaliplatin treatment lead to an enhanced caspase 3-dependent apoptosis and produce an increase of autophagy. In addition, both process have shown to be trigged faster than in control cells, starting earlier after stimulation.

Conclusions

Our results suggest that RAC3 expression levels influence the sensitivity to chemotherapeutic drugs. Therefore, the knowledge of RAC3 expression levels in tumoral samples could be an important contribution to design new improved therapeutic strategies in the future.

     

Iron overload down-regulates the expression of the HIV-1 Rev cofactor eIF5A in infected T lymphocytes

Background

Changes in iron metabolism frequently accompany HIV-1 infection. However, while many clinical and in vitro studies report iron overload exacerbates the development of infection, many others have found no correlation. Therefore, the multi-faceted role of iron in HIV-1 infection remains enigmatic.

Methods

RT-qPCR targeting the LTR region, gag, Tat and Rev were performed to measure the levels of viral RNAs in response to iron overload. Spike-in SILAC proteomics comparing i) iron-treated, ii) HIV-1-infected and iii) HIV-1-infected/iron treated T lymphocytes was performed to define modifications in the host cell proteome. Data from quantitative proteomics were integrated with the HIV-1 Human Interaction Database for assessing any viral cofactors modulated by iron overload in infected T lymphocytes.

Results

Here, we demonstrate that the iron overload down-regulates HIV-1 gene expression by decreasing the levels of viral RNAs. In addition, we found that iron overload modulates the expression of many viral cofactors. Among them, the downregulation of the REV cofactor eIF5A may correlate with the iron-induced inhibition of HIV-1 gene expression. Therefore, we demonstrated that eiF5A downregulation by shRNA resulted in a significant decrease of Nef levels, thus hampering HIV-1 replication.

Conclusions

Our study indicates that HIV-1 cofactors influenced by iron metabolism represent potential targets for antiretroviral therapy and suggests eIF5A as a selective target for drug development.

     

Intestinal Dysbiosis and Yeast Isolation in Stool of Subjects with Autism Spectrum Disorders

High frequency of gastrointestinal yeast presence in ASD subjects was shown through a simple cultural approach (Candida spp. in 57.5 % of ASDs and no controls); the identification of aggressive form (pseudo-hyphae presenting) of Candida spp. at light microscope means that adhesion to intestinal mucosa is facilitated. Dysbiosis appears sustained by lowered Lactobacillus spp. and decreased number of Clostridium spp. Absence of C. difficilis and its toxins in both ASDs and controls is also shown. Low-mild gut inflammation and augmented intestinal permeability were demonstrated together with the presence of GI symptoms. Significant linear correlation was found between disease severity (CARs score) and calprotectin and Clostridium spp. presence. Also GI symptoms, such as constipation and alternating bowel, did correlate (multivariate analyses) with the increased permeability to lactulose. The present data provide rationale basis to a possible specific therapeutic intervention in restoring gut homeostasis in ASDs.     

Feeding ecology of the Sicilian pond turtle <Emphasis Type="Italic">Emys trinacris</Emphasis> (Testudines,Emydidae) influenced by seasons and invasive aliens species

Feeding ecology of a species is the result of its evolutionary history, biology, physiology and local constraints, such as prey availability, intra- and inter-specific interactions and environmental characteristics. In this study we investigated the still unknown diet of the Sicilian pond turtle, with special emphasis to the relationships with recently introduced alien species in the “Lake Preola and Gorghi Tondi” Nature Reserve (Sicily, Italy). A total of 83 faecal samples were collected in three different periods. Emys trinacris seems an opportunistic and generalist species. The main prey taxa were aquatic invertebrates, including the invasive Procambarus clarkii, while non-aquatic preys are found sporadically. Plant matter, mainly leaves and roots of aquatic forms, was also found in high frequency with a high occurrence of fruits and seeds in spring. We did not find a significant difference in diet composition within sex and age, while an evident divergence was found between periods and sites. In particular, we noticed a decrease in prey abundance and in food-niche breadth from pre-reproductive period to post-reproductive period. Moreover a very clear difference was found between a site with allochthonous fishes and a site fish-free, with a more abundant and wide diet spectrum in the last one, as a result of the increased availability of prey. We highlighted the importance to take any possible actions to avoid the spread of fishes in other basins and to study the indirect impact of Procambarus clarkii, as possible vector of harmful trace element.     

Effects of three global change drivers on terrestrial C:N:P stoichiometry: a global synthesis

Over the last few decades, there has been an increasing number of controlled‐manipulative experiments to investigate how plants and soils might respond to global change. These experiments typically examined the effects of each of three global change drivers [i.e., nitrogen (N) deposition, warming, and elevated CO₂] on primary productivity and on the biogeochemistry of carbon (C), N, and phosphorus (P) across different terrestrial ecosystems. Here, we capitalize on this large amount of information by performing a comprehensive meta‐analysis (>2000 case studies worldwide) to address how C:N:P stoichiometry of plants, soils, and soil microbial biomass might respond to individual vs. combined effects of the three global change drivers. Our results show that (i) individual effects of N addition and elevated CO₂ on C:N:P stoichiometry are stronger than warming, (ii) combined effects of pairs of global change drivers (e.g., N addition + elevated CO₂, warming + elevated CO₂) on C:N:P stoichiometry were generally weaker than the individual effects of each of these drivers, (iii) additive interactions (i.e., when combined effects are equal to or not significantly different from the sum of individual effects) were more common than synergistic or antagonistic interactions, (iv) C:N:P stoichiometry of soil and soil microbial biomass shows high homeostasis under global change manipulations, and (v) C:N:P responses to global change are strongly affected by ecosystem type, local climate, and experimental conditions. Our study is one of the first to compare individual vs. combined effects of the three global change drivers on terrestrial C:N:P ratios using a large set of data. To further improve our understanding of how ecosystems might respond to future global change, long‐term ecosystem‐scale studies testing multifactor effects on plants and soils are urgently required across different world regions.     

M-wave properties during progressive motor unit activation by transcutaneous stimulation.

The aim of this study was to interpret changes in experimentally recorded M waves with progressive motor unit (MU) activation based on simulation of the surface electromyogram. Activation order during transcutaneous electrical stimulation was analyzed by investigating M-wave average rectified value, spectral properties, and conduction velocity (CV) during electrically elicited contractions. M-waves were detected from the biceps brachii muscle of 10 healthy male subjects by a linear adhesive array of eight electrodes. Electrical stimulation was delivered to the motor point at either constant current intensity (40, 60, 80, and 100% of the supramaximal stimulation current) or with linearly increasing current. A model of surface electromyogram generation that varied activation order based on MU size and location was used to interpret the experimental results. From the experimental and model analysis, it was found that 1) MUs tended to be activated from low to high CV and from the superficial to the deep muscle layers with increasing transcutaneous electrical stimulation of the biceps brachii muscle, and 2) characteristic spectral frequencies of the M-wave were affected by many factors other than average CV (such as the activation order by MU location or the spread of the MU innervation zones and CVs), thus decreasing with a concomitant increase in CV during progressive MU activation.     

Natural polyphenols as proteasome modulators and their role as anti-cancer compounds

The purpose of this review is to discuss the effect of natural antioxidant compounds as modulators of the 20S proteasome, a multi-enzymatic multi-catalytic complex present in the cytoplasm and nucleus of eukaryotic cells and involved in several cellular activities such as cell-cycle progression, proliferation and the degradation of oxidized and damaged proteins. From this perspective, proteasome inhibition is a promising approach to anticancer therapy and such natural antioxidant effectors can be considered as potential relevant adjuvants and pharmacological models in the study of new drugs.