News & Comment

Our genomes are highly organized spatially in three-dimensions (3D). In interphase nuclei, the genome is anchored and regulated by various nuclear scaffolds and structures, including the nuclear lamina at the nuclear edge, and nucleoli located more internally within the nucleoplasm. Recently, great effort has been made to understand the intricacies of 3D genome organization and its relevance to genomic and nuclear function. Over the years, many concepts, mathematical models, visual and biochemical methods, and analysis pipelines have been presented to study various aspects of this organization in a multidisciplinary manner, such as is also reflected within this collection.

More than a century after the first description of amyloids by Alois Alzheimer, and despite the enormous research efforts since then, the field is still full of surprises. While searching for answers to questions for example on the driving force, mechanism, and regulation of amyloidogenesis, or on the structure, physiological and pathological roles of different amyloid aggregates, unexpected properties are regularly revealed, broadening their application possibilities. This Collection aims to focus on the beneficial sides of amyloid formation, primarily exploring the potential use of amyloids in material science, bioengineering, and synthetic chemistry.

High-throughput transcriptomics has revolutionised the field of transcriptome research by offering a cost-effective and powerful screening tool. Standard bulk RNA sequencing (RNA-Seq) enables characterisation of the average expression profiles for individual samples and facilitates identification of the molecular functions associated with genes differentially expressed across conditions. RNA-Seq can also be applied to disentangle splicing variants and discover novel transcripts, thus contributing to a comprehensive understanding of the transcriptome landscape. A closely related technique, single-cell RNA-Seq, has enabled the study of cell-type-specific gene expressions in hundreds to thousands of cells, aiding the exploration of cell heterogeneity. Nowadays, bulk RNA-Seq and single-cell RNA-Seq serve as complementary tools to advance and accelerate the development of transcriptome-based resources. This Collection illustrates how the current global research community makes use of these techniques to address a broad range of questions in life sciences. It demonstrates the usefulness and popularity of high-throughput transcriptomics and presents the best practices and potential issues for the benefit of future end-users.

Recent advances in genome editing technologies have redefined our ability to probe and precisely edit the human genome and epigenome in vitro and in vivo. More specifically, RNA-guided CRISPR/Cas systems have revolutionized the field due to their simplicity in design and adaptability across biological systems. This Collection highlights results in CRISPR/Cas technology that increase the efficiency of precision genome editing, and allow genetic manipulation in model systems traditionally intractable to site-directed gene modification.

The tumor microenvironment (TME) comprises of components that exist within the immediate vicinity of tumor cells, including fibroblasts, immune cells, the extracellular matrix, and more. Significant advances have been made in recent years in our understanding of the components of TME and their mutual interactions. Part of the focus of this research has been on epigenetic events, which are increasingly being recognized for their importance in gene regulation and cancer progression. The Collection represents the gradual growth in our understanding of the overall process of how cancer progresses, along with the factors that play a decisive role in this progression. It features studies conducted on models representing many different cancers, and includes mechanistic reports conducted using appropriate in vitro models, studies that analyzed human cancer patients-derived specimens, clinical trials and, additionally, studies involving bioinformatics, metabolomics, chemical libraries screening, next-generation sequencing, and single-cell analysis approaches.

Membrane transporters are an important group of proteins in physiology and disease. Their functions make them common drug targets, but their location in the lipid bilayers poses a tremendous challenge to researchers. The current stage of development of structural biology, in addition to new research tools, has largely facilitated the acquisition of knowledge about transporters and mechanisms. This Collection presents recent studies, covering bioenergetics, structure and functional characterization of various transporters, lipids-protein interactions, and novel research tool development.

Optical coherence tomography (OCT) is a three-dimensional optical imaging technique, frequently (but not exclusively) used for retinal imaging, that was first reported in the early 1990s. Since this time the technological development of OCT has been strongly influenced by its potential as a medical imaging technique. The first clinical prototype for use in ophthalmology was completed in 1994, paving the way for the first commercially available ophthalmic OCT system to be released to the market in 1996. Since then, OCT has become a mainstay of ophthalmology. OCT is also widely used in research, in an array of biomedical applications, and increasingly in industrial settings. Although there is still much activity in advancing OCT technology, there has been an increased emphasis in applying OCT to translational research. One direction of this research is in the development of quantitative and computational techniques to aid in the retrieval of clinically useful information from OCT images. This Collection brings together original research articles, which exploit realistic mathematical models of OCT image formation and machine learning approaches to obtain insight not otherwise available from raw OCT images. This includes research for measuring clinically relevant parameters such as retinal nerve fibre layer thickness, fractional flow reserve, and corneal biomechanics, and for performing feature identification and image process tasks.

The COVID-19 pandemic has encouraged scientists and the general population to think more than ever before about how we interact with microbes in our indoor spaces. Research investigating transmission of SARS-CoV-2 has advanced our knowledge significantly in the last two years. However, indoor and built environment microbiomes are extremely complex polymicrobial systems. We have barely scratched the surface in our understanding of the microbial inhabitants of our indoor and urban spaces. The Microbes in the Built Environment Collection showcases recent research in this important topic around the globe.

Taphonomical analysis allows us to understand the processes that underlie site formation, as well as provide insights into the modification and composition of studied fossil materials. Taphonomy has become crucial to many scientific fields, providing conceptual advances through a renewal of models, protocols, and paradigms. In these studies, trans-disciplinary approaches (geology, palaeontology, biology, ecology, archaeology) have been developed using a wide array of methodologies. In addition, experimental work on modern assemblages, focusing on specific geological and biological processes (‘actualism’), are used to make referential data and proxies. This Collection contributes to the field’s methodological development, while gathering research articles investigating Quaternary period bone assemblages, with special interest in the Pleistocene.