THE STUDY OF THREE GRAPEVINE CLONES TO UNCOVER THE GENETIC TRAITS RESPONSIBLE FOR THE LOW SUSCEPTIBILITY TO FLAVESCENCE DORéE

Flavescence dorée (FD) is one of the most destructive grapevine yellows diseases and a quarantine pest in the European Community. It is caused by phytoplasmas, which are transmitted in vineyard by the leafhopper Scaphoideus titanus. Inter and intraspecific differences in susceptibility to FD have already been observed among grapevine varieties and clones of the same variety. Grapevine varieties and clones completely resistant to FD have not been uncovered yet, however these differences suggest the presence of genetic traits in grapevine related to high or low susceptibility to FD. Cultivated grapevines are clonally propagated and the genome of each cultivar is preserved, except for the accumulation of mutations over time that can generate distinguishable clones with several notable phenotypes. The differences between the genome of clones of the same variety are less than those between different varieties; thus, in order to highlight the genetic features responsible for the different phenotypes, the study of the genomes of clones with different susceptibility to FD can be a valid technique to achieve the goal. The aim of this work is to find out the genetic traits responsible for the different susceptibility to FD among three Chardonnay clones, analyzing the diversity in their genomes and transcriptomic profiles. The clones were sequenced by accurate whole genome techniques, Hi-Fi reads sequencing on PacBio platform coupled with Illumina, and then the genomes were de novo assembled. Moreover, two of them were experimentally infected in field by means of the insect vector and the transcriptomic profiles in the early stage of FD infection were analyzed. In particular, the clones were compared in absence of the disease and the vector, in presence of the healthy vector and with the FD infective vector. The results obtained from the preliminary genome comparison showed higher similarity between the three clones than compared with the reference genome from variety Pinot noir, while the analysis to identify the genomic differences among clones are still in progress. The transcriptomic profiles showed interesting differences in some pathways expressed in presence of healthy vectors, while the clones shared a similar expression profile before being in contact with the vectors as well as after the challenge with the FD infective vectors. These findings might suggest the involvement of antibiosis mechanisms in the partial resistance of the specific Chardonnay clone to FD. The results obtained, and those that will be achieved in future, are useful for new breeding programs and clonal selection. Grapevine plants more resistant to FD will permit to decrease the insecticides used to control the disease in vineyards. Moreover, the knowledge of the molecular and metabolic mechanisms involved in scarcely susceptible clones could pave the way for the development, for example, of biostimulants capable to induce such defenses even in the most susceptible plants

Biochemical and molecular changes in peach fruit exposed to cold stress conditions

Storage or transportation temperature is very important for preserving the quality of fruit. However, low temperature in sensitive fruit such as peach can induce loss of quality. Fruit exposed to a specific range of temperatures and for a longer period can show chilling injury (CI) symptoms. The susceptibility to CI at low temperature varies among cultivars and genetic backgrounds. Along with agronomic management, appropriate postharvest management can limit quality losses. The importance of correct temperature management during postharvest handling has been widely demonstrated. Nowadays, due to long-distance markets and complex logistics that require multiple actors, the management of storage/transportation conditions is crucial for the quality of products reaching the consumer. Peach fruit exposed to low temperatures activate a suite of physiological, metabolomic, and molecular changes that attempt to counteract the negative effects of chilling stress. In this review an overview of the factors involved, and plant responses is presented and critically discussed. Physiological disorders associated with CI generally only appear after the storage/transportation, hence early detection methods are needed to monitor quality and detect internal changes which will lead to CI development. CI detection tools are assessed: they need to be easy to use, and preferably non-destructive to avoid loss of products. Graphical Abstract

Bacterial community of Industrial raw Sausage Packaged in Modified Atmosphere throughout the Shelf Life

Ten lots of industrial raw sausages in modified atmosphere (CO2 30%, O2 70%), produced in the same plant over 7\u202fmonths, were analyzed at the day after production (S samples) and at the end of shelf life (E samples), after 12\u202fdays storage at 7\u202f\ub0C to simulate thermal abuse. Quality of the products was generally compromised by storage at 7\u202f\ub0C, with only 3 E samples without alterations. During the shelf life, the pH decreased for the accumulation of acetic and lactic acids. A few biogenic amines accumulated, remaining below acceptable limits. The profile of volatile compounds got enriched with alcohols, ketones, and acids (e.g. ethanol, 2,3-butanediol, 2,3-butandione, butanoic acid) originated by bacterial metabolism. Throughout the shelf life, aerobic bacteria increased from 4.7 log to 6.6\u202flog\u202fcfu/g, and lactic acid bacteria (LAB) from 3.7 to 8.1\u202flog\u202fcfu/g. Staphylococci, enterobacteria, and pseudomonads passed from 3.7, 3.0, and 1.7 to 5.5, 4.8, and 3.0\u202flog\u202fcfu/g, respectively. Dominant cultivable LAB, genotyped by RAPD-PCR, belonged to the species Lactobacillus curvatus/graminis and Lactobacillus sakei, with lower amounts of Leuconostoc carnosum and Leuconostoc mesenteroides. Brochothrix thermosphacta was the prevailing species among aerobic bacteria. The same biotypes ascribed to several different species where often found in E samples of diverse batches, suggesting a recurrent contamination from the plant of production. Profiling of 16S rRNA gene evidenced that microbiota of S samples clustered in two main groups where either Firmicutes or Bacteroidetes prevailed, albeit with taxa generally associated to the gastro-intestinal tract of mammals. The microbial diversity was lower in E samples than in S ones. Even though a common profile could not be identified, most E samples clustered together and were dominated by Firmicutes, with Lactobacillaceae and Listeriaceae as the most abundant families (mostly ascribed to Lactobacillus and Brochothrix, respectively). In a sole E sample Proteobacteria (especially Serratia) was the major phylum

Fruitomics: The importance of combining sensory and chemical analyses in assessing cold storage responses of six peach (Prunus persica L. Batsch) cultivars

Cold storage is used to extend peach commercial life, but can affect quality. Quality changes are assessed through the content of nutritionally relevant compounds, aroma, physical characters and/or sensorially. Here, six peach and nectarine cultivars were sampled at commercial harvest and after 7 days of 1 °C storage. A trained panel was used to evaluate sensorial characters, while carotenoids, phenolics, vitamin C, total sugars, and qualitative traits including firmness, titrable acidity and soluble solid content were integrated with volatile organic compound (VOC) analysis previously reported. The different analyses reveal interesting patterns of correlation, and the six cultivars responded differently to cold storage. Sensory parameters were correlated with 64 VOCs and seven intrinsic characters. Acidity, firmness, and 10 VOCs were strongly negatively correlated with harmony and sweetness, but positively correlated with bitterness, astringency, and crunchiness. In contrast, Brix, b-carotene, and six VOCs were positively correlated with harmony and sweetness

High-Throughput Sequencing Technologies and new Approaches in Food Microbiology

Recent investigation approaches, based on High-Throughput Sequencing (HTS) technologies, allow to develop in-depth analysis of food microbiota/microbiome. HTS, which identify the modern Next Generation Sequencing (NGS) techniques, contribute to food investigation advances by allowing to produce a larger volume of data at a price that is decreasing. This contribute offers an overview about the latest and most innovative techniques for analyzing food microbiota. Furthermore, the impact on food microbiology of omics approaches based on HTS is discussed. Relevant metagenomics, metatranscriptomics, metaproteomics studies concerning different food application fields are treated. The current scenario and pregnant omics and multi-omics works are highlighted, showing the usefulness to adopt an integrated multi-omics approach in different food microbiology areas, especially in food quality and safety. In this context, nowadays, food is more and more considered not only as a source of energy but also as an affordable way to prevent diseases. Finally, some technical limitations of multi-omics methods are outlined. If in the past an integrative omics approach was not feasible because of the lack of expertise and technical limitations, the current technological advances offer high performances in terms of standardization to investigate a wide data set coming different platforms

Obesity: the Role of Leptin

In Chapter One, Dr Med Ioannis Iakovou examines whether the link between weight and bone mineral density is caused by or directly correlated with leptin and adiponectin. Afterwards, Chapter Two by Martha A. Ramirez, Adrian A. Arellano, Fang Xie, Elizabeth A. Benavides, Robin A. Katchko, Luis Ayala, Alexandra Calderon, Rita A. Flores, Jean M. Escudero, Duane H. Keisler, Randy L. Stanko, and Michelle R. Garcia investigates the link between leptin and infertility issues caused by defects of abnormalitie sin the corpus luteum. Chapter Three by Professor Jaak Jürimäe, PhD investigates the link between leptin and energy intake and expenditure by athletes. In Chapter Four, Renata Saucedo, PhD, Jorge Valencia, PhD, Claudia Gutierrez, and Arturo Zarate, PhD examine the connection between increased leptin levels and insulin resistance. Next, Tiziana Maria Sirangelo analyzes the role between leptin and obesity, explaining that leptin plays a crucial role in the regulation of food intake in Chapter Five. In Chapter Six, Federico Sireci, MD, Francesco Cappello, Frank Rikki Canevari, MD, Francesco Dispenza, MD, Salvatore Gallina, PhD, Pietro Salvago, MD, and Francesco Martines study the peptidergic immunohistochemical manifestation of leptin in laryngeal SCCs

Food Microbiology and Multi-Omics Approaches

Microbial functions in food have got more and more attention from the researchers so that the investigation in food microbiology has drastically changed. It is well established that traditional culture methods for analyzing food microbiota are very limited. High-throughput sequencing (HTS) and omic technologies allow to deep understand the behaviour of microorganisms in foods. We discuss different sequencing approaches and several HTS investigations of food microbiota. Furthermore, we focus on the four major types of omics approaches, genomics, transcriptomics, proteomics, and metabolomics and on their impact on food microbiology. However, most of the studies based on next generation sequencing just give a partial representation of the food-based ecosystem, and it is emerging the need to adopt omic combination approaches, referred to as multi-omic approach, which show more evidence for biological mechanisms. At the moment, only a few examples that combine different omic approaches have been found in food microbiology study. The current scenario and examples of recent works are discussed, showing the usefulness to adopt this integrated approach. Certain limitations are also outlined

Biochemical and molecular changes in peach fruit exposed to cold stress conditions

Storage or transportation temperature is very important for preserving the quality of fruit. However, low temperature in sensitive fruit such as peach can induce loss of quality. Fruit exposed to a specific range of temperatures and for a longer period can show chilling injury (CI) symptoms. The susceptibility to CI at low temperature varies among cultivars and genetic backgrounds. Along with agronomic management, appropriate postharvest management can limit quality losses. The importance of correct temperature management during postharvest handling has been widely demonstrated. Nowadays, due to long-distance markets and complex logistics that require multiple actors, the management of storage/transportation conditions is crucial for the quality of products reaching the consumer. Peach fruit exposed to low temperatures activate a suite of physiological, metabolomic, and molecular changes that attempt to counteract the negative effects of chilling stress. In this review an overview of the factors involved, and plant responses is presented and critically discussed. Physiological disorders associated with CI generally only appear after the storage/transportation, hence early detection methods are needed to monitor quality and detect internal changes which will lead to CI development. CI detection tools are assessed: they need to be easy to use, and preferably non-destructive to avoid loss of products

Multi-Omics and Genome Editing Studies on Plant Cell Walls to Improve Biomass Quality

Biomass is one of the most important sources of renewable energy and plays an important role in reducing our reliance on fossil fuels. Efficient biomass production is essential to obtain large amounts of sustainable energy with minimal environmental cost. However, the biochemical and molecular processes behind the synthesis of the main components of biomass are still not fully understood. This review provides a comprehensive summary of the most relevant studies on cell wall biosynthesis and degradation mechanisms, focusing on the lignocellulosic component, in which the conversion process to fermentable sugars is expensive, due to its recalcitrant nature. A focus is placed on multi-omics research involving genomics, transcriptomics, proteomics, metabolomics, and phenomics, since multi-omics approaches offer a unique opportunity to investigate the biological pathways underlying the genotype traits characterizing cell wall energy crops. Furthermore, our study highlights the advances in genome editing approaches and proposes the modification of the genes that are involved in the complex cell wall structure as a feasible solution to an efficient biomass production. Several key points for future research activities based on these emerging technologies are also discussed, focusing on the combination of multi-omics and gene editing approaches, which offer potential for improved biomass valorization and the development of tangible bioproducts