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Antigen binding by antibodies requires precise orientation of the complementarity- determining region (CDR) loops in the variable domain to establish the correct contact surface. Members of the family Camelidae have a modified form of immunoglobulin gamma (IgG) with only heavy chains, called Heavy Chain only Antibodies (HCAb). Antigen binding in HCAbs is mediated by only three CDR loops from the single variable domain (V H H) at the N-terminus of each heavy chain. This feature of the V H H, along with their other important features, e.g., easy expression, small size, thermo-stability and hydrophilicity, made them promising candidates for therapeutics and diagnostics. Thus, to design better V H H domains, it is important to thoroughly understand their sequence and structure characteristics and relationship. In this study, sequence characteristics of V H H domains have been analysed in depth, along with their structural features using innovative approaches, namely a structural alphabet. An elaborate summary of various studies proposing structural models of V H H domains showed diversity in the algorithms used. Finally, a case study to elucidate the differences in structural models from single and multiple templates is presented. In this case study, along with the above-mentioned aspects of V H H, an exciting view of various factors in structure prediction of V H H, like template framework selection, is also discussed., Competing Interests: Frederic Cadet is associated with PEACCEL, Paris, France. Jean-Christophe Gelly and Alexandre G. de Brevern are associated with IBL, Paris, France. Jean-Philippe Meyneil is employed by ISoft, Paris, France. Alain Malpertuy is employed by Atragene, Paris, France. Nicolas K. Shinada is sponsored by Discngine, Paris, France and ANRT, France. All other authors declare no competing interests., (©2020 Melarkode Vattekatte et al.)

The VHHs are antigen-binding region/domain of camelid heavy chain antibodies (HCAb). They have many interesting biotechnological and biomedical properties due to their small size, high solubility and stability, and high affinity and specificity for their antigens. HCAb and classical IgGs are evolutionary related and share a common fold. VHHs are composed of regions considered as constant, called the frameworks (FRs) connected by Complementarity Determining Regions (CDRs), a highly variable region that provide interaction with the epitope. Actually, no systematic structural analyses had been performed on VHH structures despite a significant number of structures. This work is the first study to analyse the structural diversity of FRs of VHHs. Using a structural alphabet that allows approximating the local conformation, we show that each of the four FRs do not have a unique structure but exhibit many structural variant patterns. Moreover, no direct simple link between the local conformational change and amino acid composition can be detected. These results indicate that long-range interactions affect the local conformation of FRs and impact the building of structural models., (Copyright © 2016 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.)

Sequencing the human genome began in 1994, and 10 years of work were necessary in order to provide a nearly complete sequence. Nowadays, NGS technologies allow sequencing of a whole human genome in a few days. This deluge of data challenges scientists in many ways, as they are faced with data management issues and analysis and visualization drawbacks due to the limitations of current bioinformatics tools. In this paper, we describe how the NGS Big Data revolution changes the way of managing and analysing data. We present how biologists are confronted with abundance of methods, tools, and data formats. To overcome these problems, focus on Big Data Information Technology innovations from web and business intelligence. We underline the interest of NoSQL databases, which are much more efficient than relational databases. Since Big Data leads to the loss of interactivity with data during analysis due to high processing time, we describe solutions from the Business Intelligence that allow one to regain interactivity whatever the volume of data is. We illustrate this point with a focus on the Amadea platform. Finally, we discuss visualization challenges posed by Big Data and present the latest innovations with JavaScript graphic libraries.

Gene regulation networks control differentiation and function of hundreds of cell types. Dysfunctions of transcription factors, which are key elements in the regulation pathways, are involved in numerous pathologies. The recent development of genomics technologies allows the study of gene regulation mechanisms and help us understand their impact on the cells. Bioinformatic tools are needed to fully exploit data obtained by genomics approaches. Thus, bioinformatics play an essential role in the characterisation of the transcription factors binding sites and their target genes. In this review we will introduce the main breakthroughs in bioinformatics area for the comprehension of regulation mechanisms. We will insist on i) the approaches "with a priori" for the genome annotation based on known transcription factors binding sites, ii) the approaches "without a priori" for the discovery of new binding sites and iii) the functional annotation of the target genes of those transcription factors. Finally, we will present recent examples of the fruitful use of in silico studies for the comprehension of regulation mechanisms and of the consequences of their dysfunction.

Artemisinin is a natural product used as an alternative drug in the treatment of severe and multidrug-resistant malaria. In the present work we show that artemisinin shares with other sesquiterpene lactones the ability to inhibit the activation of the nuclear factor NF-kB: by this mechanism, artemisinin, as well as parthenolide, inhibits nitric oxide synthesis in cytokine-stimulated human astrocytoma T67 cells. These results suggest that artemisinin, in addition to its antiparasitic properties, could also exert a therapeutic effect on neurological complications of malaria.