Systems Glycobiology: Past, Present, and Future

Glycobiology is a glycan-based field of study that focuses on the structure, function, and biology of carbohydrates, and glycomics is a sub-study of the field of glycobiology that aims to define structure/function of glycans in living organisms. With the popularity of the glycobiology and glycomics, application of computational modeling expanded in the scientific area of glycobiology over the last decades. The recent availability of progressive Wet-Lab methods in the field of glycobiology and glycomics is promising for the impact of systems biology on the research area of the glycome, an emerging field that is termed “systems glycobiology.” This chapter will summarize the up-to-date leading edge in the use of bioinformatics tools in the field of glycobiology. The chapter provides basic knowledge both for glycobiologists interested in the application of bioinformatics tools and scientists of computational biology interested in studying the glycome.

Bioinformatics as a Tool for the Structural and Evolutionary Analysis of Proteins

This chapter deals with the topic of bioinformatics, computational, mathematics, and statistics tools applied to biology, essential for the analysis and characterization of biological molecules, in particular proteins, which play an important role in all cellular and evolutionary processes of the organisms. In recent decades, with the next generation sequencing technologies and bioinformatics, it has facilitated the collection and analysis of a large amount of genomic, transcriptomic, proteomic, and metabolomic data from different organisms that have allowed predictions on the regulation of expression, transcription, translation, structure, and mechanisms of action of proteins as well as homology, mutations, and evolutionary processes that generate structural and functional changes over time. Although the information in the databases is greater every day, all bioinformatics tools continue to be constantly modified to improve performance that leads to more accurate predictions regarding protein functionality, which is why bioinformatics research remains a great challenge.

Biological Evaluation and Molecular Docking Studies of Benzalkonium Ibuprofenate

The third-generation ionic liquids (ILs), which are being used to produce double active pharmaceutical ingredients (d-APIs) with tunable biological activity along with novel performance, enhancement, and delivery options, have been revolutionizing the area of drug discovery since the past few decades. Herein we report the in vitro antibacterial and anti-inflammatory activity of benzalkonium ibuprofenate (BaIb) that are being used as in-house d-API, with a particular focus on its interaction with respective protein target through molecular docking study. The evaluation of the biological activity of BaIb with the antibacterial and anti-inflammatory target at the molecular level revealed that the synthesized BaIb could be designed as a potential double active drug since it retains the antibacterial and anti-inflammatory activity of its parent drugs, benzalkonium chloride (BaCl) and sodium ibuprofenate (NaIb), respectively.

Search for Human-Specific Proteins Based on Availability Scores of Short Constituent Sequences: Identification of a WRWSH Protein in Human Testis

Little is known about protein sequences unique in humans. Here, we performed alignment-free sequence comparisons based on the availability (frequency bias) of short constituent amino acid (aa) sequences (SCSs) in proteins to search for human-specific proteins. Focusing on 5-aa SCSs (pentats), exhaustive comparisons of availability scores among the human proteome and other nine mammalian proteomes in the nonredundant (nr) database identified a candidate protein containing WRWSH, here called FAM75, as human-specific. Examination of various human genome sequences revealed that FAM75 had genomic DNA sequences for either WRWSH or WRWSR due to a single nucleotide polymorphism (SNP). FAM75 and its related protein FAM205A were found to be produced through alternative splicing. The FAM75 transcript was found only in humans, but the FAM205A transcript was also present in other mammals. In humans, both FAM75 and FAM205A were expressed specifically in testis at the mRNA level, and they were immunohistochemically located in cells in seminiferous ducts and in acrosomes in spermatids at the protein level, suggesting their possible function in sperm development and fertilization. This study highlights a practical application of SCS-based methods for protein searches and suggests possible contributions of SNP variants and alternative splicing of FAM75 to human evolution.

Hydrazone-Based Small-Molecule Chemosensors

The hydrazone functional group is widely applied in several fields. The versatility and large use of this chemotype are attributed to its easy and straightforward synthesis and unique structural characteristics which is useful for different chemical and biological purposes. Recently hydrazone scaffold has been widely adopted in the design of small-molecule fluorescent and colorimetric chemosensors for detecting metals and anions because of its corresponding non-covalent interactions. This chapter provides an overview of hydrazone-based fluorescent and colorimetric chemosensors for anions and metals of biological interest, with their representative rational designs in the last 15 years. We hope this chapter inspires the development of novel and powerful fluorescent and colorimetric chemosensors for a broad range of applications.

Scaffolding Contigs Using Multiple Reference Genomes

Scaffolding is an important step of the genome assembly and its function is to order and orient the contigs in the assembly of a draft genome into larger scaffolds. Several single reference-based scaffolders have currently been proposed. However, a single reference genome may not be sufficient alone for a scaffolder to correctly scaffold a target draft genome, especially when the target genome and the reference genome have distant evolutionary relationship or some rearrangements. This motivates researchers to develop the so-called multiple reference-based scaffolders that can utilize multiple reference genomes, which may provide different but complementary types of scaffolding information, to scaffold the target draft genome. In this chapter, we will review some of the state-of-the-art multiple reference-based scaffolders, such as Ragout, MeDuSa and Multi-CAR, and give a complete introduction to Multi-CSAR, an improved extension of Multi-CAR.