Identification of LINE retrotransposons and long non-coding RNAs expressed in the octopus brain.

BACKGROUND: Transposable elements (TEs) widely contribute to the evolution of genomes allowing genomic innovations, generating germinal and somatic heterogeneity, and giving birth to long non-coding RNAs (lncRNAs). These features have been associated to the evolution, functioning, and complexity of the nervous system at such a level that somatic retrotransposition of long interspersed element (LINE) L1 has been proposed to be associated to human cognition. Among invertebrates, octopuses are fascinating animals whose nervous system reaches a high level of complexity achieving sophisticated cognitive abilities. The sequencing of the genome of the Octopus bimaculoides revealed a striking expansion of TEs which were proposed to have contributed to the evolution of its complex nervous system. We recently found a similar expansion also in the genome of Octopus vulgaris. However, a specific search for the existence and the transcription of full-length transpositionally competent TEs has not been performed in this genus. RESULTS: Here, we report the identification of LINE elements competent for retrotransposition in Octopus vulgaris and Octopus bimaculoides and show evidence suggesting that they might be transcribed and determine germline and somatic polymorphisms especially in the brain. Transcription and translation measured for one of these elements resulted in specific signals in neurons belonging to areas associated with behavioral plasticity. We also report the transcription of thousands of lncRNAs and the pervasive inclusion of TE fragments in the transcriptomes of both Octopus species, further testifying the crucial activity of TEs in the evolution of the octopus genomes. CONCLUSIONS: The neural transcriptome of the octopus shows the transcription of thousands of putative lncRNAs and of a full-length LINE element belonging to the RTE class. We speculate that a convergent evolutionary process involving retrotransposons activity in the brain has been important for the evolution of sophisticated cognitive abilities in this genus.

Effect of the aqueous matrix on the inactivation of E. coli by permaleic acid.

In this work permaleic acid (PMA) was investigated as possible disinfecting agent and compared to peracetic acid (PAA) in real tap water and wastewater. Preliminary tests in lysogeny broth (LB) were also performed. PMA was synthesized from maleic anhydride and hydrogen peroxide and, for the first time, its antimicrobial activity was evaluated with respect to the growth inhibition of E. coli. The effect of the pH and bivalent ions, typically occurring in real water matrices (namely, Mg2+ and Ca2+), was also investigated. pKa values for PMA were calculated for the first time by DFT calculations. The concentration of bivalent ions strongly affected disinfection efficiency with PMA (Ca2+=0.33 mgL-1 and Mg2+=0.35 mgL-1: 100% E. coli reduction > log 5; Ca2+=13.3 mg L-1 and Mg2+=25.6 mg L-1: E. coli reduction < log 1, after 60 min), and such results were supported by DFT modelling outcomes (pKa2 of PMA 7.3) and disinfection tests in presence of EDTA chelating agent. More alkaline pH conditions drastically decreased PMA disinfection (pH = 5: > log 5 E.coli reduction; pH = 9: < log 1 E.coli reduction, after 60 min). PMA disinfection efficiency is strongly affected by the target water quality, the concentration of metal bivalent ions and the initial pH.

The survey and reference assisted assembly of the Octopus vulgaris genome.

The common octopus, Octopus vulgaris, is an active marine predator known for the richness and plasticity of its behavioral repertoire, and remarkable learning and memory capabilities. Octopus and other coleoid cephalopods, cuttlefish and squid, possess the largest nervous system among invertebrates, both for cell counts and body to brain size. O. vulgaris has been at the center of a long-tradition of research into diverse aspects of its biology. To leverage research in this iconic species, we generated 270 Gb of genomic sequencing data, complementing those available for the only other sequenced congeneric octopus, Octopus bimaculoides. We show that both genomes are similar in size, but display different levels of heterozygosity and repeats. Our data give a first quantitative glimpse into the rate of coding and non-coding regions and support the view that hundreds of novel genes may have arisen independently despite the close phylogenetic distance. We furthermore describe a reference-guided assembly and an open genomic resource (CephRes-gdatabase), opening new avenues in the study of genomic novelties in cephalopods and their biology.

FTIR and NDIR spectroscopies as valuable alternatives to IRMS spectrometry for the δ(13)C analysis of food.

The (13)C/(12)C carbon isotope ratio is a chemical parameter with many important applications in several scientific area and the technique of choice currently used for the δ(13)C determination is the isotope ratio mass spectrometry (IRMS). This latter is highly accurate (0.1‰) and sensitive (up to 0.01‰), but at the same time expensive and complex. The objective of this work was to assess the reliability of FTIR and NDIRS techniques for the measurement of carbon stable isotope ratio of food sample, in comparison to IRMS. IRMS, NDIRS and FTIR were used to analyze samples of food, such as oil, durum, cocoa, pasta and sugar, in order to determine the natural abundance isotopic ratio of carbon in a parallel way. The results were comparable, showing a close relationship among the three techniques. The main advantage in using FTIR and NDIRS is related to their cheapness and easy-to-operate in comparison to IRMS.

Bactericidal and Fungicidal Activity in the Gas Phase of Sodium Dichloroisocyanurate (NaDCC).

Sodium dichloroisocyanurate (NaDCC) is usually employed as a disinfectant for the treatment of water, environmental surfaces and medical equipment principally for its effectiveness as a microbicide agent. In this study, we explore the possibility of a new use for NaDCC by investigating the microbicidal activity of chlorine, which derives from the hydrolysis of NaDCC mediated by air humidity, and by testing its effect on the neutralization of microbes present in domestic waste. NaDCC was inserted in a plastic garbage can where LB agar plates, with different dilutions of a known title of four different microorganisms (Escherichia coli, Staphylococcus aureus, Debaryomyces hansenii and Aspergillus brasiliensis), were weakly inserted. The molecular chlorine (Cl2) levels present in the garbage can were quantified using an iodometric titration. The gas emitted in the garbage can presented a strong microbicide effect, inhibiting the proliferation of all four microorganisms and for four consecutive weeks, thus showing that NaDCC hydrolysis, mediated by air humidity, is able to ensure the decontamination of restricted environments, avoiding the proliferation of both Gram-positive and Gram-negative bacteria as well as fungi.

Learning and memory in Octopus vulgaris: a case of biological plasticity.

Here we concisely summarize major aspects of the learning capabilities of the cephalopod mollusc Octopus vulgaris, a solitary living marine invertebrate. We aim to provide a backdrop against which neurobiology of these animals can be further interpreted and thus soliciting further interest for one of the most advanced members of invertebrate animals.

Selection and validation of a set of reliable reference genes for quantitative RT-PCR studies in the brain of the Cephalopod Mollusc Octopus vulgaris.

BACKGROUND: Quantitative real-time polymerase chain reaction (RT-qPCR) is valuable for studying the molecular events underlying physiological and behavioral phenomena. Normalization of real-time PCR data is critical for a reliable mRNA quantification. Here we identify reference genes to be utilized in RT-qPCR experiments to normalize and monitor the expression of target genes in the brain of the cephalopod mollusc Octopus vulgaris, an invertebrate. Such an approach is novel for this taxon and of advantage in future experiments given the complexity of the behavioral repertoire of this species when compared with its relatively simple neural organization. RESULTS: We chose 16S, and 18S rRNA, actB, EEF1A, tubA and ubi as candidate reference genes (housekeeping genes, HKG). The expression of 16S and 18S was highly variable and did not meet the requirements of candidate HKG. The expression of the other genes was almost stable and uniform among samples. We analyzed the expression of HKG into two different set of animals using tissues taken from the central nervous system (brain parts) and mantle (here considered as control tissue) by BestKeeper, geNorm and NormFinder. We found that HKG expressions differed considerably with respect to brain area and octopus samples in an HKG-specific manner. However, when the mantle is treated as control tissue and the entire central nervous system is considered, NormFinder revealed tubA and ubi as the most suitable HKG pair. These two genes were utilized to evaluate the relative expression of the genes FoxP, creb, dat and TH in O. vulgaris. CONCLUSION: We analyzed the expression profiles of some genes here identified for O. vulgaris by applying RT-qPCR analysis for the first time in cephalopods. We validated candidate reference genes and found the expression of ubi and tubA to be the most appropriate to evaluate the expression of target genes in the brain of different octopuses. Our results also underline the importance of choosing a proper normalization strategy when analyzing gene expression by qPCR taking into appropriate account the experimental setting and variability of the sample of animals (and tissues), thus providing a set of HGK which expression appears to be unaffected by the experimental factor(s).

The octopus vertical lobe modulates short-term learning rate and uses LTP to acquire long-term memory.

Analyzing the processes and neuronal circuitry involved in complex behaviors in phylogenetically remote species can help us understand the evolution and function of these systems. Cephalopods, with their vertebrate-like behaviors but much simpler brains, are ideal for such an analysis. The vertical lobe (VL) of Octopus vulgaris is a pivotal brain station in its learning and memory system. To examine the organization of the learning and memory circuitry and to test whether the LTP that we discovered in the VL is involved in behavioral learning, we tetanized the VL to induce a global synaptic enhancement of the VL pathway. The effects of tetanization on learning and memory of a passive avoidance task were compared to those of transecting the same pathway. Tetanization accelerated and transection slowed short-term learning to avoid attacking a negatively reinforced object. However, both treatments impaired long-term recall the next day. Our results suggest that the learning and memory system in the octopus, as in mammals [9], is separated into short- and long-term memory sites. In the octopus, the two memory sites are not independent; the VL, which mediates long-term memory acquisition through LTP, also modulates the circuitry controlling behavior and short-term learning.