The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics.

ABSTRACT: A global genome database of all of Earth’s species diversity could be a treasure trove of scientific discoveries. However, regardless of the major advances in genome sequencing technologies, only a tiny fraction of species have genomic information available. To contribute to a more complete planetary genomic database, scientists and institutions across the world have united under the Earth BioGenome Project (EBP), which plans to sequence and assemble high-quality reference genomes for all ∼1.5 million recognized eukaryotic species through a stepwise phased approach. As the initiative transitions into Phase II, where 150,000 species are to be sequenced in just four years, worldwide participation in the project will be fundamental to success. As the European node of the EBP, the European Reference Genome Atlas (ERGA) seeks to implement a new decentralised, accessible, equitable and inclusive model for producing high-quality reference genomes, which will inform EBP as it scales. To embark on this mission, ERGA launched a Pilot Project to establish a network across Europe to develop and test the first infrastructure of its kind for the coordinated and distributed reference genome production on 98 European eukaryotic species from sample providers across 33 European countries. Here we outline the process and challenges faced during the development of a pilot infrastructure for the production of reference genome resources, and explore the effectiveness of this approach in terms of high-quality reference genome production, considering also equity and inclusion. The outcomes and lessons learned during this pilot provide a solid foundation for ERGA while offering key learnings to other transnational and national genomic resource projects.info:eu-repo/semantics/publishedVersio

The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.info:eu-repo/semantics/publishedVersio

Vibrational Spectroscopy of Self-Forming Synthetic PEGylated Lipids and Nanovesicles

Vibrational spectroscopy has been used to elucidate the structure and conformation of lipids and nanovesicles. In this study, three different vibrational spectroscopic techniques, namely near-infrared (NIR), Fourier transform infrared (FTIR) and Raman spectroscopies, have been employed for the comprehensive investigation of newly developed self-forming synthetic PEGylated lipids, trademarked as QuSomes. In contrast to conventional phospholipids, these new kind of lipids spontaneously form liposomes or nanovesicles upon hydration, without the supply of external activation energy. The amphiphiles considered in this study differ in their hydrophobic hydrocarbon chain length and contain different units of polyethylene glycol (PEG) hydrophilic headgroups. Such lipids are composed of 1,2-dimyristoyl-rac-glycerol-3-dodecaethylene glycol (GDM-12), 1,2-dioleoyl-rac-glycerol-3-dodecaethylene glycol (GDO-12) and 1,2-distearoyl-rac-glycerol-3-triicosaethylene glycol (GDS-23). The NIR absorption spectra of these new artificial lipids have been recorded by using a novel miniaturized dual-detector micro-mirror spectrometer based on micro-opto-electro-mechanical systems (MOEMS) technology. Similarly, FTIR and Raman spectroscopic techniques have been used to establish the "molecular fingerprint" of these lipids. In addition, laser tweezers Raman spectroscopy (LTRS) has been utilized to optically trap and manipulate single lipid nanoparticles and nanovesicles. Likewise, fluorescence correlation spectroscopy (FCS) has been employed to determine the size distribution of those nanovesicles in suspension. This work focused on the study of thermotropic phase behaviors and associated changes in the conformational order/disorder of such lipids and nanovesicles in suspensions. For this purpose, variable-temperature sample holders have been designed and were employed to acquire the temperature-dependence infrared and Raman spectra of these lipids and nanovesicles in the temperature range of -4 to 110 oC. Phase transition temperature profiles have been deduced by either monitoring the shifts in the vibrational peak positions or plotting vibrational peak intensity ratios in the C–H stretching region as a function of temperature. Furthermore, several spectral indicators have been deduced and correlated with various aspects of molecular structure as well as intramolecular motion and intermolecular interactions. Finally, to supplement our observations of phase transformations, a thermodynamic approach known as differential scanning calorimetry (DSC) has been applied and revealed a good agreement with the infrared and Raman spectroscopic results

Tomographic imaging via spectral encoding of spatial frequency

Three-dimensional optical tomographic imaging plays an important role in biomedical research and clinical applications. We introduce spectral tomographic imaging (STI) via spectral encoding of spatial frequency principle that not only has the capability for visualizing the three-dimensional object at sub-micron resolution but also providing spatially-resolved quantitative characterization of its structure with nanoscale accuracy for any volume of interest within the object. The theoretical basis and the proof-of-concept numerical simulations are presented to demonstrate the feasibility of spectral tomographic imaging

Investigation of nanoscale structural alterations of cell nucleus as an early sign of cancer

Background: The cell and tissue structural properties assessed with a conventional bright-field light microscope play a key role in cancer diagnosis, but they sometimes have limited accuracy in detecting early-stage cancers or predicting future risk of cancer progression for individual patients (i.e., prognosis) if no frank cancer is found. The recent development in optical microscopy techniques now permit the nanoscale structural imaging and quantitative structural analysis of tissue and cells, which offers a new opportunity to investigate the structural properties of cell and tissue below 200-250 nm as an early sign of carcinogenesis, prior to the presence of microscale morphological abnormalities. Identification of nanoscale structural signatures is significant for earlier and more accurate cancer detection and prognosis. Results: Our group has recently developed two simple spectral-domain optical microscopy techniques for assessing 3D nanoscale structural alterations -spectral-encoding of spatial frequency microscopy and spatial-domain low-coherence quantitative phase microscopy. These two techniques use the scattered light from biological cells and tissue and share a common experimental approach of assessing the Fourier space by various wavelengths to quantify the 3D structural information of the scattering object at the nanoscale sensitivity with a simple reflectance-mode light microscopy setup without the need for high-NA optics. This review paper discusses the physical principles and validation of these two techniques to interrogate nanoscale structural properties, as well as the use of these methods to probe nanoscale nuclear architectural alterations during carcinogenesis in cancer cell lines and well-annotated human tissue during carcinogenesis. Conclusions: The analysis of nanoscale structural characteristics has shown promise in detecting cancer before the microscopically visible changes become evident and proof-of-concept studies have shown its feasibility as an earlier or more sensitive marker for cancer detection or diagnosis. Further biophysical investigation of specific 3D nanoscale structural characteristics in carcinogenesis, especially with well-annotated human cells and tissue, is much needed in cancer research

Real-time quantitative visualization of 3D structural information

We demonstrate a novel approach for the real time visualization and quantification of the 3D spatial frequencies in an image domain. Our approach is based on the spectral encoding of spatial frequency principle and permits the formation of an image as a color map in which spatially separated spectral wavelengths correspond to the dominant 3D spatial frequencies of the object. We demonstrate that our approach can visualize and analyze the dominant axial internal structure for each image point in real time and with nanoscale sensitivity to structural changes. Computer modeling and experimental results of instantaneous color visualization and quantification of 3D structures of a model system and biological samples are presented.We acknowledge the funding support from National Cancer Institute (R21CA152935, YL).peer-reviewe

Spectral encoding of spatial frequency approach for characterization of nanoscale structures

An approach to acquire axial structural information at nanoscale is demonstrated. It is based on spectral encoding of spatial frequency principle to reconstruct the structural information about the axial profile of the three-dimensional (3D) spatial frequency for each image point. This approach overcomes the fundamental limitations of current optical techniques and provides nanoscale accuracy and sensitivity in characterizing axial structures. Numerical simulation and experimental results are presented. We acknowledge the funding support from National Cancer Institute (CA152935, CA164433) and thank Donna Stolz and the staff at Center for Biologic Imaging at University of Pittsburgh for their help with TEM imaging.We acknowledge the funding support from National Cancer Institute (CA152935, CA164433) and thank Donna Stolz and the staff at Center for Biologic Imaging at University of Pittsburgh for their help with TEM imaging.peer-reviewe

Real-time quantitative visualization of 3D structural information

We demonstrate a novel approach for the real time visualization and quantification of the 3D spatial frequencies in an image domain. Our approach is based on the spectral encoding of spatial frequency principle and permits the formation of an image as a color map in which spatially separated spectral wavelengths correspond to the dominant 3D spatial frequencies of the object. We demonstrate that our approach can visualize and analyze the dominant axial internal structure for each image point in real time and with nanoscale sensitivity to structural changes. Computer modeling and experimental results of instantaneous color visualization and quantification of 3D structures of a model system and biological samples are presented.We acknowledge the funding support from National Cancer Institute (R21CA152935, YL).peer-reviewe