A roadmap of tissue culture and biotechnology in European hazelnut (Corylus avellana L.)

The increasing interest in European hazelnut (Corylus avellana L.) cultivation registered in the last years has led to a significant increase in worldwide hazelnut growing areas, also involving regions characterized by a marginal presence of hazelnut orchards. Despite this increasement, world production still relies on the cultivation of few varieties, most of which are particularly suitable to the environment where they have been selected. Therefore, it is necessary to develop new cultivars with high environmental plasticity capable of providing constant and high-quality productions in the new environments and under the climatic change conditions of traditional growing areas. Over the years, many molecular markers for genetic breeding programs have been developed and omics sciences also provided further information about the genetics of this species. These data could be of support to the application of new plant breeding techniques (NPBTs), which would allow the development of cultivars with the desired characteristics in a shorter time than traditional techniques. However, the application of these methodologies is subordinated to the development of effective regeneration protocols which, to date, have been set up exclusively for seed-derived explants. A further aspect to be exploited is represented by the possibility of cultivating hazelnut cells and tissues in vitro to produce secondary metabolites of therapeutic interest. This review aims to consolidate the state of the art on biotechnologies and in vitro culture techniques applied on this species, also describing the various studies that over time allowed the identification of genomic regions that control traits of interest.

Bioactive compounds as an alternative for the sugarcane industry: Towards an integrative approach

Here, a comprehensive review of sugarcane industrialization and its relationship with bioactive compounds (BCs) detected in various products and by-products generated during its processing is presented. Furthermore, it is discussed how these compounds have revealed important antioxidant, antineoplastic, antidiabetic, and antimicrobial activities. From this bibliographic research highlights the significance of two types of BCs of natural origin (phenolic compounds (PCs) and terpenoids) and a group of compounds synthesized during industrial transformation processes (Maillard reaction products (MRPs)). It was found that most of the studies about the BCs from sugarcane have been conducted by identifying, isolating, and analyzing ones or a few compounds at a specific period, this being a conventional approach. However, given the complexity of the synthesis processes of all these BCs and the biological activities they can manifest in a specific biological context, novel approaches are needed to address these analyses holistically. To overcome this challenge, integrating massive and multiscale methods, such as omics sciences, seems necessary to enrich these studies. This work is intended to contribute to the state of the art that could support future research about the exploration, characterization, or evaluation of different bioactive molecules from sugarcane and its derivatives.

Recent trends on omics and bioinformatics approaches to study SARS-CoV-2: A bibliometric analysis and mini-review

BACKGROUND

The successful sequencing of SARS-CoV-2 cleared the way for the use of omics technologies and integrative biology research for combating the COVID-19 pandemic. Currently, many research groups have slowed down their respective projects to concentrate efforts in the study of the biology of SARS-CoV-2. In this bibliometric analysis and mini-review, we aimed to describe how computational methods or omics approaches were used during the first months of the COVID-19 pandemic.

METHODS

We analyzed bibliometric data from Scopus, BioRxiv, and MedRxiv (dated June 19th, 2020) using quantitative and knowledge mapping approaches. We complemented our analysis with a manual process of carefully reading the selected articles to identify either the omics or bioinformatic tools used and their purpose.

RESULTS

From a total of 184 articles, we found that metagenomics and transcriptomics were the main sources of data to perform phylogenetic analysis aimed at corroborating zoonotic transmission, identifying the animal origin and taxonomic allocation of SARS-CoV-2. Protein sequence analysis, immunoinformatics and molecular docking were used to give insights about SARS-CoV-2 targets for drug and vaccine development. Most of the publications were from China and USA. However, China, Italy and India covered the top 10 most cited papers on this topic.

CONCLUSION

We found an abundance of publications using omics and bioinformatics approaches to establish the taxonomy and animal origin of SARS-CoV-2. We encourage the growing community of researchers to explore other lesser-known aspects of COVID-19 such as virus-host interactions and host response.

Current trends in plant growth-promoting microorganisms research for sustainable food security

The use of intensive non-sustainable agricultural practices for satisfying global food demand is degrading the agro-ecosystems, leading to their inability to produce efficient and equitable sources of calories. Microbial communities play an important role in the improvement of soil fertility and plant development; thus, the genetic and metabolic diversity of microbiota in agro-ecosystems is a promising alternative for designing microbial inoculants to not only produce enough food but also mitigates the economic, health, social, and environmental issues caused by conventional agriculture. This Special Issue has been launched to compile and inspire high-impact recent advancements on bioprospecting beneficial microorganisms as a sustainable strategy to warranty global food security.

Application of "omics" sciences to the prediction of bone metastases from breast cancer: State of the art

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Breast cancer (BC) is the first cause of cancer-related death in women.

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Most patients with advanced BC develop bone metastases (BM).

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Omics technologies have been applied to identify putative BM “predicting” biomarkers.

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Prospective studies are needed before any clinical application of such biomarkers.

Breast cancer (BC) is the most frequent malignancy and the first cause of cancer-related death in women.

The majority of patients with advanced BC develop skeletal metastases which may ultimately lead to serious complications, termed skeletal-related events, that often dramatically impact on quality of life and survival.

Therefore, the identification of biomarkers able to stratify BC patient risk to develop bone metastases (BM) is fundamental to define personalized diagnostic and therapeutic strategies, possibly at the earliest stages of the disease.

In this regard, the advent of “omics” sciences boosted the investigation of several putative biomarkers of BC osteotropism, including deregulated genes, proteins and microRNAs.

The present review revisits the current knowledge on BM development in BC and the most recent studies exploring potential BM-predicting biomarkers, based on the application of omics sciences to the study of primary breast malignancies.

Homicide and concealment of the corpse. Autopsy case series and review of the literature

INTRODUCTION

The concealment of the body following a homicide undermines different moments of the forensic and medico-legal investigations. The aim of the present study is to provide an overview of the literature and the forensic casuistry of the Institute of Legal Medicine of Padova for analyzing and discussing diverse methodological approaches for the forensic pathologist dealing with covered-up homicides.

MATERIAL AND METHODS

A literature review, updated until September 2019, was performed, and a literature pool of forensic cases was built. In-house cases were included by conducting a retrospective analysis of the forensic caseworks of Padova of the last 20 years. Data regarding epidemiology, methodology of assessment, methods of concealment, and answers to medico-legal issues were extracted for both data sets.

RESULTS AND DISCUSSION

Seventy-eight papers were included in the literature review (78.2% being case reports or case series, 17% retrospective studies, and 6% experimental studies or reviews). Literature and in-house data sets consisted of 145 and 13 cases, respectively. Death scene investigation, radiology, toxicology, and additional analyses were performed in 20-54% of literature and 62-77% of in-house cases. Cover-up by multiple methods prevailed. Death was caused by head trauma in about 40% of cases (both data sets), strangulation in 21% of literature, and 7% of in-house cases, and was undetermined in 17% of literature and 7% of in-house cases.

CONCLUSIONS

The methodology of ascertainment should be case-specific and based on a multidisciplinary and multimodal evaluation of all data, including those gained through novel radiological and/or analytical techniques.

New molecular approaches to Alzheimer's disease

Alzheimer's disease is a neurodegenerative disorder and the most common and devastating form of dementia. It affects mainly older people, accounting for 50-80% of dementia cases. The age is the main associated risk factor and based on the onset age, early-onset (EOAD) or late-onset (LOAD) forms are distinguished. AD has a strong impact both on the life-style of patients and their families and on the society, due to the high costs related to social and medical care. So far, despite the great advances in understanding of the AD pathogenesis, there is no a cure for this form of dementia and current available treatments are limited to temporarily relieve symptoms. In this review, firstly we give an overview of the current knowledge of the genetic basis of both forms of AD with a particular emphasis on the insights in the understanding of the pathogenic mechanisms of this disorder. Then we discuss the promising relevance of "omics sciences" and the open challenges of the application of Big Data in promoting precision medicine for AD.

Towards precision medicine: The application of omics technologies in asthma management

Asthma is a chronic obstructive respiratory disease characterised by bronchial inflammation. Its biological and clinical features have been widely explored and a number of pharmacological treatments are currently available. Currently several aspects of asthma pathophysiological background remain unclear, and this is represent a limitation for the traditional asthma phenotype approach. In this scenario, the identification of new molecular and clinical biomarkers may be helpful in order to better understand the disease, define specific diagnostic tools and highlight relevant novel targets for pharmacological treatments. Omics technologies offer innovative research tools for addressing the above mentioned goals. However, there is still a lot to do both in the fields of basic research and in the clinical application. Recently, genome-wide association studies, microRNAs and proteomics are contributing to enrich the available data for the identification of new asthma biomarkers. A precise approach to the patient with asthma, particularly with severe uncontrolled asthma, requires new and specific therapeutic targets, but also proper tools able to drive the clinician in tailoring the treatment. On the other hand, there is a need of predictors to treatment's response, particularly in the field of biological drugs, whose sustainability implies a correct and precise selection of the patients. Translating acquired omics knowledge in clinical practice may address the unmet needs described above, but large-scale studies are required in order to confirm their relevance and effectiveness in daily practice. Thus in our opinion the application of omics is still lagging in the real-life setting.

Evolving Relevance of Neuroproteomics in Alzheimer's Disease

Substantial progress in the understanding of the biology of Alzheimer's disease (AD) has been achieved over the past decades. The early detection and diagnosis of AD and other age-related neurodegenerative diseases, however, remain a challenging scientific frontier. Therefore, the comprehensive discovery (relating to all individual, converging or diverging biochemical disease mechanisms), development, validation, and qualification of standardized biological markers with diagnostic and prognostic functions with a precise performance profile regarding specificity, sensitivity, and positive and negative predictive value are warranted.Methodological innovations in the area of exploratory high-throughput technologies, such as sequencing, microarrays, and mass spectrometry-based analyses of proteins/peptides, have led to the generation of large global molecular datasets from a multiplicity of biological systems, such as biological fluids, cells, tissues, and organs. Such methodological progress has shifted the attention to the execution of hypothesis-independent comprehensive exploratory analyses (opposed to the classical hypothesis-driven candidate approach), with the aim of fully understanding the biological systems in physiology and disease as a whole. The systems biology paradigm integrates experimental biology with accurate and rigorous computational modelling to describe and foresee the dynamic features of biological systems. The use of dynamically evolving technological platforms, including mass spectrometry, in the area of proteomics has enabled to rush the process of biomarker discovery and validation for refining significantly the diagnosis of AD. Currently, proteomics-which is part of the systems biology paradigm-is designated as one of the dominant matured sciences needed for the effective exploratory discovery of prospective biomarker candidates expected to play an effective role in aiding the early detection, diagnosis, prognosis, and therapy development in AD.