Computing in Biotechnology: Omics and Beyond

Bioinspired Hybrid Nanostructured PEEK Implant with Enhanced Antibacterial and Anti-inflammatory Synergy

Implant-associated infections and excessive immune responses are two major postsurgical issues for successful implantation. However, conventional strategies including antibiotic treatment and inflammatory regulation are always compromised due to the comodification of various biochemical agents and instances of functional interference. It is imperative to provide implant surfaces with satisfactory antibacterial and anti-inflammatory properties. Here, a dual-effect nanostructured polyetheretherketone (PEEK) surface (NP@PDA/Zn) with bionic mechano-bactericidal nanopillars and immobilized immunomodulatory Zn2+ is designed. The constructed hybrid nanopillars display remarkable antibacterial performance against Gram-negative and Gram-positive strains through the synergy of physical and chemical bactericidal effects imposed by nanopillars and Zn2+. Meanwhile, the immunoregulatory property is evaluated through the investigation of macrophage polarization both in vitro and in vivo, and the results reveal that NP@PDA/Zn could downregulate the expression of M1-related cytokines and decrease the M1 macrophage recruitment to lower the inflammatory response. Notably, the surface exhibited exceptional biocompatibility with discerning biocidal activity between bacterial and mammalian cells and antioxidant performance that effectively scavenges ROS, minimizing potential cytotoxicity. Taken together, NP@PDA/Zn presents a convenient and promising strategy of combining synergistic bactericidal activity and inflammatory regulation without any mutual interference, which can support the development of multifunctional implant-associated materials.

Advances and Challenges for GWAS Analysis in Cardiac Diseases: A Focus on Coronary Artery Disease (CAD)

The achievement of genome-wide association studies (GWAS) has rapidly progressed our understanding of the etiology of coronary artery disease (CAD). It unlocks new strategies to strengthen the stalling of CAD drug development. In this review, we highlighted the recent drawbacks, mainly pointing out those involved in identifying causal genes and interpreting the connections between disease pathology and risk variants. We also benchmark the novel insights into the biological mechanism behind the disease primarily based on outcomes of GWAS. Furthermore, we also shed light on the successful discovery of novel treatment targets by introducing various layers of "omics" data and applying systems genetics strategies. Lastly, we discuss in-depth the significance of precision medicine that is helpful to improve through GWAS analysis in cardiovascular research.

Biotechnological Perspectives of Omics and Genetic Engineering Methods in Alfalfa

For several decades, researchers are working to develop improved major crops with better adaptability and tolerance to environmental stresses. Forage legumes have been widely spread in the world due to their great ecological and economic values. Abiotic and biotic stresses are main factors limiting legume production, however, alfalfa (Medicago sativa L.) shows relatively high level of tolerance to drought and salt stress. Efforts focused on alfalfa improvements have led to the release of cultivars with new traits of agronomic importance such as high yield, better stress tolerance or forage quality. Alfalfa has very high nutritional value due to its efficient symbiotic association with nitrogen-fixing bacteria, while deep root system can help to prevent soil water loss in dry lands. The use of modern biotechnology tools is challenging in alfalfa since full genome, unlike to its close relative barrel medic (Medicago truncatula Gaertn.), was not released yet. Identification, isolation, and improvement of genes involved in abiotic or biotic stress response significantly contributed to the progress of our understanding how crop plants cope with these environmental challenges. In this review, we provide an overview of the progress that has been made in high-throughput sequencing, characterization of genes for abiotic or biotic stress tolerance, gene editing, as well as proteomic and metabolomics techniques bearing biotechnological potential for alfalfa improvement.

Laniakea: an open solution to provide Galaxy "on-demand" instances over heterogeneous cloud infrastructures

BACKGROUND

While the popular workflow manager Galaxy is currently made available through several publicly accessible servers, there are scenarios where users can be better served by full administrative control over a private Galaxy instance, including, but not limited to, concerns about data privacy, customisation needs, prioritisation of particular job types, tools development, and training activities. In such cases, a cloud-based Galaxy virtual instance represents an alternative that equips the user with complete control over the Galaxy instance itself without the burden of the hardware and software infrastructure involved in running and maintaining a Galaxy server.

RESULTS

We present Laniakea, a complete software solution to set up a "Galaxy on-demand" platform as a service. Building on the INDIGO-DataCloud software stack, Laniakea can be deployed over common cloud architectures usually supported both by public and private e-infrastructures. The user interacts with a Laniakea-based service through a simple front-end that allows a general setup of a Galaxy instance, and then Laniakea takes care of the automatic deployment of the virtual hardware and the software components. At the end of the process, the user gains access with full administrative privileges to a private, production-grade, fully customisable, Galaxy virtual instance and to the underlying virtual machine (VM). Laniakea features deployment of single-server or cluster-backed Galaxy instances, sharing of reference data across multiple instances, data volume encryption, and support for VM image-based, Docker-based, and Ansible recipe-based Galaxy deployments. A Laniakea-based Galaxy on-demand service, named Laniakea@ReCaS, is currently hosted at the ELIXIR-IT ReCaS cloud facility.

CONCLUSIONS

Laniakea offers to scientific e-infrastructures a complete and easy-to-use software solution to provide a Galaxy on-demand service to their users. Laniakea-based cloud services will help in making Galaxy more accessible to a broader user base by removing most of the burdens involved in deploying and running a Galaxy service. In turn, this will facilitate the adoption of Galaxy in scenarios where classic public instances do not represent an optimal solution. Finally, the implementation of Laniakea can be easily adapted and expanded to support different services and platforms beyond Galaxy.

A decade of genome-wide association studies for coronary artery disease: the challenges ahead

In this review, we summarize current knowledge on the genetics of coronary artery disease, based on 10 years of genome-wide association studies. The discoveries began with individual studies using 200K single nucleotide polymorphism arrays and progressed to large-scale collaborative efforts, involving more than a 100 000 people and up to 40 Mio genetic variants. We discuss the challenges ahead, including those involved in identifying causal genes and deciphering the links between risk variants and disease pathology. We also describe novel insights into disease biology based on the findings of genome-wide association studies. Moreover, we discuss the potential for discovery of novel treatment targets through the integration of different layers of 'omics' data and the application of systems genetics approaches. Finally, we provide a brief outlook on the potential for precision medicine to be enhanced by genome-wide association study findings in the cardiovascular field.

Legume genetic resources and transcriptome dynamics under abiotic stress conditions

Grain legumes are an important source of nutrition and income for billions of consumers and farmers around the world. However, the low productivity of new legume varieties, due to the limited genetic diversity available for legume breeding programmes and poor policymaker support, combined with an increasingly unpredictable global climate is resulting in a large gap between current yields and the increasing demand for legumes as food. Hence, there is a need for novel approaches to develop new high-yielding legume cultivars that are able to cope with a range of environmental stressors. Next-generation technologies are providing the tools that could enable the more rapid and cost-effective genomic and transcriptomic studies for most major crops, allowing the identification of key functional and regulatory genes involved in abiotic stress resistance. In this review, we provide an overview of the recent achievements regarding abiotic stress resistance in a wide range of legume crops and highlight the transcriptomic and miRNA approaches that have been used. In addition, we critically evaluate the availability and importance of legume genetic resources with desirable abiotic stress resistance traits.

Integrated Omics: Tools, Advances, and Future Approaches

With the rapid adoption of high-throughput omic approaches to analyze biological samples such as genomics, transcriptomics, proteomics, and metabolomics, each analysis can generate tera- to peta-byte sized data files on a daily basis. These data file sizes, together with differences in nomenclature among these data types, make the integration of these multi-dimensional omics data into biologically meaningful context challenging. Variously named as integrated omics, multi-omics, poly-omics, trans-omics, pan-omics, or shortened to just 'omics', the challenges include differences in data cleaning, normalization, biomolecule identification, data dimensionality reduction, biological contextualization, statistical validation, data storage and handling, sharing, and data archiving. The ultimate goal is towards the holistic realization of a 'systems biology' understanding of the biological question in hand. Commonly used approaches in these efforts are currently limited by the 3 i's - integration, interpretation, and insights. Post integration, these very large datasets aim to yield unprecedented views of cellular systems at exquisite resolution for transformative insights into processes, events, and diseases through various computational and informatics frameworks. With the continued reduction in costs and processing time for sample analyses, and increasing types of omics datasets generated such as glycomics, lipidomics, microbiomics, and phenomics, an increasing number of scientists in this interdisciplinary domain of bioinformatics face these challenges. We discuss recent approaches, existing tools, and potential caveats in the integration of omics datasets for development of standardized analytical pipelines that could be adopted by the global omics research community.