Genome Sequencing of Ancient Plant Remains: Findings, Uses and Potential Applications for the Study and Improvement of Modern Crops

The advent of new sequencing technologies is revolutionizing the studies of ancient DNA (aDNA). In the last 30 years, DNA extracted from the ancient remains of several plant species has been explored in small-scale studies, contributing to understand the adaptation, and migration patterns of important crops. More recently, NGS technologies applied on aDNA have opened up new avenues of research, allowing investigation of the domestication process on the whole-genome scale. Genomic approaches based on genome-wide and targeted sequencing have been shown to provide important information on crop evolution and on the history of agriculture. Huge amounts of next-generation sequencing (NGS) data offer various solutions to overcome problems related to the origin of the material, such as degradation, fragmentation of polynucleotides, and external contamination. Recent advances made in several crop domestication studies have boosted interest in this research area. Remains of any nature are potential candidates for aDNA recovery and almost all the analyses that can be made on fresh DNA can also be performed on aDNA. The analysis performed on aDNA can shed light on many phylogenetic questions concerning evolution, domestication, and improvement of plant species. It is a powerful instrument to reconstruct patterns of crop adaptation and migration. Information gathered can also be used in many fields of modern agriculture such as classical breeding, genome editing, pest management, and product promotion. Whilst unlocking the hidden genome of ancient crops offers great potential, the onus is now on the research community to use such information to gain new insight into agriculture

Dissection of genetic and environmental factors involved in tomato organoleptic quality

Background: One of the main tomato breeding objectives is to improve fruit organoleptic quality. However, this task is made somewhat challenging by the complex nature of sensory traits and the lack of efficient selection criteria. Sensory quality depends on numerous factors, including fruit colour, texture, aroma, and composition in primary and secondary metabolites. It is also influenced by genotypic differences, the nutritional regime of plants, stage of ripening at harvest and environmental conditions. In this study, agronomic, biochemical and sensory characterization was performed on six Italian heirlooms grown in different environmental conditions.Result: We identified a number of links among traits contributing to fruit organoleptic quality and to the perception of sensory attributes. PCA analysis was used to highlight some biochemical, sensory and agronomic discriminating traits: this statistical test allowed us to identify which sensory attributes are more closely linked to environmental conditions and those, instead, linked to the genetic constitution of tomato. Sweetness, sourness, saltiness and tomato flavour are not only grouped in the same PCA factor, but also result in a clear discrimination of tomato ecotypes in the three different fields. The three different traditional varieties cluster on the basis of attributes like juiciness, granulosity, hardness and equatorial diameter, and are therefore more closely related to the genetic background of the cultivar.Conclusion: This finding suggests that a different method should be undertaken to improve sensory traits related to taste perception and texture. Our results might be used to ascertain in what direction to steer breeding in order to improve the flavour characteristics of tomato ecotypes

A novel synthetic peptide from a tomato defensin exhibits antibacterial activities against Helicobacter pylori

Defensins are a class of cysteine-rich proteins, which exert broad spectrum antimicrobial activity. In this work, we used a bioinformatic approach to identify putative defensins in the tomato genome. Fifteen proteins had a mature peptide that includes the well-conserved tetradisulfide array. We selected a representative member of the tomato defensin family; we chemically synthesized its gamma-motif and tested its antimicrobial activity. Here, we demonstrate that the synthetic peptide exhibits potent antibacterial activity against Gram-positive bacteria, such as Staphylococcus aureus A170, Staphylococcus epidermidis, and Listeria monocytogenes, and Gram-negative bacteria, including Salmonella enterica serovar Paratyphi, Escherichia coli, and Helicobacter pylori. In addition, the synthetic peptide shows minimal (<5%) hemolytic activity and absence of cytotoxic effects against THP-1 cells. Finally, SolyC exerts an anti-inflammatory activity in vitro, as it downregulates the level of the proinflammatory cytokines TNF-alpha and IFN-gamma

Biological and geochemical markers of the geographical origin and genetic identity of potatoes

There is a growing interest in agriculture productions combining safety and quality attributes with clear regional identity. In the last few years several methods have been employed for food authentication and traceability. In this study we tested geochemical data for elemental concentrations of Mn, Cu, Zn, Rb, Stand Cd and strontium isotope ratio in combination with biological data of 11 secondary metabolites and DNA as markers for the authentication of the origin of early potatoes at small geographical scale levels in Italy. DNA fingerprints through 12 SSR (simple sequence repeat) primer pairs allowed cultivar identification, confirming the discrimination power of molecular markers. Element concentrations, strontium isotope ratio and secondary metabolite data, through multivariate statistics (partial least squares discriminant analysis. PLS-DA), made it possible to clearly assign all the potato samples to the respective administrative regions of cultivation. The validation of the models was successful. It included external prediction tests on 20% of the data randomly selected from each administrative province and a study on the robustness of these multivariate data treatments to uncertainties on measurement results

Use of network analysis to capture key traits affecting tomato organoleptic quality

The long-term objective of tomato breeders is to identify metabolites that contribute to defining the target flavour and to design strategies to enhance it. This paper reports the results of network analysis, based on metabolic phenotypic and sensory data, to highlight important relationships among such traits. This tool allowed a reduction in data set complexity, building a network consisting of 35 nodes and 74 links corresponding to the 74 significant (positive or negative) correlations among the variables studied. A number of links among traits contributing to fruit organoleptic quality and to the perception of sensory attributes were identified. Modular partitioning of the characteristics involved in fruit organoleptic perception captured the essential fruit parameters that regulate interactions among different class traits. The main feature of the network was the presence of three nodes interconnected among themselves (dry matter, pH, and °Brix) and with other traits, and nodes with widely different linkage degrees. Identification of strong associations between some metabolic and sensory traits, such as citric acid with tomato smell, glycine with tomato smell, and granulosity with dry matter, suggests a basis for more targeted investigations in the future

New Spherically Symmetric Solutions in f(R)-gravity by Noether Symmetries

Spherical symmetry for f(R)-gravity is discussed by searching for Noether symmetries. The method consists in selecting conserved quantities in form of currents that reduce dynamics of f(R)-models compatible with symmetries. In this way we get a general method to obtain constants of motion without setting a priori the form of f(R). In this sense, the Noether symmetry results a physical criterium. Relevant cases are discussed.Comment: 9 pages, accepted for publication in General Relativity and Gravitatio

Manipulation of β-carotene levels in tomato fruits results in increased ABA content and extended shelf-life

Tomato fruit ripening is controlled by the hormone ethylene and by a group of transcription factors, acting upstream of ethylene. During ripening, the linear carotene lycopene accumulates at the expense of cyclic carotenoids. Fruit-specific overexpression of LYCOPENE β-CYCLASE (LCYb) resulted in increased β-carotene (provitamin A) content. Unexpectedly, LCYb-overexpressing fruits also exhibited a diverse array of ripening phenotypes, including delayed softening and extended shelf life. These phenotypes were accompanied, at the biochemical level, by an increase of abscisic acid (ABA) content, decreased ethylene production, increased density of cell wall material containing linear pectins with a low degree of methylation, and a thicker cuticle with a higher content of cutin monomers and triterpenoids. The levels of several primary metabolites and phenylpropanoid compounds were also altered in the transgenic fruits, which could be attributed to delayed fruit ripening and/or to ABA. Network correlation analysis and pharmacological experiments with the ABA biosynthesis inhibitor, abamine, indicated that altered ABA levels were a direct effect of the increased β-carotene content and were in turn responsible for the extended shelf life phenotype. Thus, manipulation of -carotene levels results not only in an improvement of the nutritional value of tomato fruits, but also of their shelf life

Hybrid topoisomerase i and HDAC inhibitors as dual action anticancer agents

Recent studies have shown that HDAC inhibitors act synergistically with camptothecin derivatives in combination therapies. To exploit this synergy, new hybrid molecules targeting simultaneously topoisomerase I and HDAC were designed. In particular, a selected multivalent agent containing a camptothecin and a SAHA-like template showed a broad spectrum of antiproliferative activity, with IC50 values in the nanomolar range. Preliminary in vivo results indicated a strong antitumor activity on human mesothelioma primary cell line MM473 orthotopically xenografted in CD-1 nude mice and very high tolerability

EEG microstate complexity for aiding early diagnosis of Alzheimer’s disease

This is the final version. Available from Nature Research via the DOI in this record. The dynamics of the resting brain exhibit transitions between a small number of discrete networks, each remaining stable for tens to hundreds of milliseconds. These functional microstates are thought to be the building blocks of spontaneous consciousness. The electroencephalogram (EEG) is a useful tool for imaging microstates, and EEG microstate analysis can potentially give insight into altered brain dynamics underpinning cognitive impairment in disorders such as Alzheimer’s disease (AD). Since EEG is non-invasive and relatively inexpensive, EEG microstates have the potential to be useful clinical tools for aiding early diagnosis of AD. In this study, EEG was collected from two independent cohorts of probable AD and cognitively healthy control participants, and a cohort of mild cognitive impairment (MCI) patients with four-year clinical follow-up. The microstate associated with the frontoparietal working-memory/attention network was altered in AD due to parietal inactivation. Using a novel measure of complexity, we found microstate transitioning was slower and less complex in AD. When combined with a spectral EEG measure, microstate complexity could classify AD with sensitivity and specificity &gt; 80%, which was tested on an independent cohort, and could predict progression from MCI to AD in a small preliminary test cohort of 11 participants. EEG microstates therefore have potential to be a non-invasive functional biomarker of AD.Engineering and Physical Sciences Research Council (EPSRC)Wellcome TrustAlzheimer’s SocietyGarfield Weston FoundationUniversity of BristolUniversity of San Marino and IS