Effective Approaches to Study the Genetic Variability of SARS-CoV-2.

Significant efforts are being made in many countries around the world to respond to the COVID-19 pandemic by developing diagnostic reagent kits, identifying infected people, determining treatment methods, and finally producing effective vaccines. However, novel coronavirus variants may potentially reduce the effectiveness of all these efforts, demonstrating increased transmissibility and abated response to therapy or vaccines, as well as the possibility of false negative results in diagnostic procedures based on nucleic acid amplification methods. Since the end of 2020, several variants of concern have been discovered around the world. When information about a new, potentially more dangerous strain of pathogen appears, it is crucial to determine the moment of its emergence in a region. Eventually, that permits taking timely measures and minimizing new risks associated with the spreading of the virus. Therefore, numerous nations have made tremendous efforts to identify and trace these virus variants, which necessitates serious technological processes to sequence a large number of viral genomes. Here, we report on our experience as one of the primary laboratories involved in monitoring SARS-CoV-2 variants in Russia. We discuss the various approaches used, describe effective protocols, and outline a potential technique combining several methods to increase the ability to trace genetic variants while minimizing financial and labor costs.

Search and sequence analysis tools services from EMBL-EBI in 2022.

The EMBL-EBI search and sequence analysis tools frameworks provide integrated access to EMBL-EBI's data resources and core bioinformatics analytical tools. EBI Search (https://www.ebi.ac.uk/ebisearch) provides a full-text search engine across nearly 5 billion entries, while the Job Dispatcher tools framework (https://www.ebi.ac.uk/services) enables the scientific community to perform a diverse range of sequence analysis using popular bioinformatics applications. Both allow users to interact through user-friendly web applications, as well as via RESTful and SOAP-based APIs. Here, we describe recent improvements to these services and updates made to accommodate the increasing data requirements during the COVID-19 pandemic.

The influence of environmental setting on the community ecology of Ediacaran organisms.

The broad-scale environment plays a substantial role in shaping modern marine ecosystems, but the degree to which palaeocommunities were influenced by their environment is unclear. To investigate how broad-scale environment influenced the community ecology of early animal ecosystems, we employed spatial point process analyses (SPPA) to examine the community structure of seven late Ediacaran (558-550 Ma) bedding-plane assemblages drawn from a range of environmental settings and global localities. The studied palaeocommunities exhibit marked differences in the response of their component taxa to sub-metre-scale habitat heterogeneities on the seafloor. Shallow-marine (nearshore) palaeocommunities were heavily influenced by local habitat heterogeneities, in contrast to their deeper-water counterparts. The local patchiness within shallow-water communities may have been further accentuated by the presence of grazers and detritivores, whose behaviours potentially initiated a propagation of increasing habitat heterogeneity of benthic communities from shallow to deep-marine depositional environments. Higher species richness in shallow-water Ediacaran assemblages compared to deep-water counterparts across the studied time-interval could have been driven by this environmental patchiness, because habitat heterogeneities increase species richness in modern marine environments. Our results provide quantitative support for the 'Savannah' hypothesis for early animal diversification-whereby Ediacaran diversification was driven by patchiness in the local benthic environment.

Raman and IR Spectroscopy Studies on Propane at Pressures of Up to 40 GPa.

Raman and IR spectroscopy studies on propane were performed at pressures of up to 40 GPa at ambient temperatures using the diamond anvil cell technique. Propane undergoes three phase transitions at 6.4(5), 14.5(5), and 26.5(5) GPa in Raman spectroscopy and at 7.0(5), 14.0(5), and 27.0(5) GPa in IR spectroscopy. The phase transitions were identified using the Raman and IR splitting modes and the appearance or disappearance of peaks, which clearly corresponded to the changes in the frequencies of the modes as the pressure changed. Our results demonstrate the complex high-pressure behavior of solid propane.

Laser heating in diamond anvil cells: developments in pulsed and continuous techniques.

Developments in continuous and pulsed laser-heating techniques, and finite-element calculations for diamond anvil cell experiments are reported. The methods involve the use of time-resolved (5 ns gated) incandescent light temperature measurements to determine the time dependence of heat fluxes, while near-IR incandescent light temperature measurements allow temperature measurements to as low as 500 K. Further optimization of timing in pulsed laser heating together with sample engineering will provide additional improvements in data collection in very high P-T experiments.