Compare your culture to one of the cultures discussed in this unit. On a sheet of paper, list the cultures you are comparing and make one column titled “similarities,” and a second column titled “differences.” Now, list as many similarities and differences between the two as you can think of. Are there more similarities or differences between the two cultures you selected? Have you ever met anyone from this culture? How can you use this information to build greater respect between cultures?

Similarities and Differences

SARS-CoV-2 is a betacoronavirus with a linear single-stranded, positive-sense RNA genome, whose outbreak caused the ongoing COVID-19 pandemic. The ability of coronaviruses to rapidly evolve, adapt, and cross species barriers makes the development of effective and durable therapeutic strategies a challenging and urgent need. As for other RNA viruses, genomic RNA structures are expected to play crucial roles in several steps of the coronavirus replication cycle. Despite this, only a handful of functionally-conserved coronavirus structural RNA elements have been identified to date. Here, we performed RNA structure probing to obtain single-base resolution secondary structure maps of the full SARS-CoV-2 coronavirus genome both in vitro and in living infected cells. Probing data recapitulate the previously described coronavirus RNA elements (5' UTR and s2m), and reveal new structures. Of these, ∼10.2% show significant covariation among SARS-CoV-2 and other coronaviruses, hinting at their functionally-conserved role. Secondary structure-restrained 3D modeling of these segments further allowed for the identification of putative druggable pockets. In addition, we identify a set of single-stranded segments in vivo, showing high sequence conservation, suitable for the development of antisense oligonucleotide therapeutics. Collectively, our work lays the foundation for the development of innovative RNA-targeted therapeutic strategies to fight SARS-related infections.

/pdf/genome-wide-mapping-of-sars-cov-2-rna-structures-identifies-4z5o3tufgm.pdf

Genome-wide mapping of SARS-CoV-2 RNA structures identifies therapeutically-relevant elements.

Fluorescence imaging technology has gradually become a new and promising tool for in vivo visualization detection. Because it can provide real-time sub-cellular resolution imaging results, it can be widely used in the field of biological detection and medical detection and treatment. However, due to the limited imaging depth (1-2 mm) and self-fluorescence background of tissue emitted in the visible region (400-700 nm), it fails to reveal biological complexity in deep tissues. The traditional near infrared wavelength (NIR-I, 650-950 nm) is considered as the first biological window, because it reduces the NIR absorption and scattering from blood and water in organisms. NIR fluorescence bioimaging's penetration is larger than that of visible light. In fact, NIR-I fluorescence bioimaging is still interfered by tissue autofluorescence (background noise), and the existence of photon scattering, which limits the depth of tissue penetration. Recent experimental and simulation results show that the signal-to-noise ratio (SNR) of bioimaging can be significantly improved at the second region near infrared (NIR-II, 1,000-1,700 nm), also known as the second biological window. NIR-II bioimaging is able to explore deep-tissues information in the range of centimeter, and to obtain micron-level resolution at the millimeter depth, which surpass the performance of NIR-I fluorescence imaging. The key of fluorescence bioimaging is to achieve highly selective imaging thanks to the functional/targeting contrast agent (probe). However, the progress of NIR-II probes is very limited. To date, there are a few reports about NIR-II fluorescence probes, such as carbon nanotubes, Ag2S quantum dots, and organic small molecular dyes. In this paper, we surveyed the development of NIR-II imaging contrast agents and their application in cancer imaging, medical detection, vascular bioimaging, and cancer diagnosis. In addition, the hotspots and challenges of NIR-II bioimaging are discussed. It is expected that our findings will lay a foundation for further theoretical research and practical application of NIR-II bioimaging, as well as the inspiration of new ideas in this field.

Recent Progress in NIR-II Contrast Agent for Biological Imaging.

The Short- and Long-Range RNA-RNA Interactome of SARS-CoV-2.

SARS-CoV-2 carries the largest single-stranded RNA genome and is the causal pathogen of the ongoing COVID-19 pandemic. How the SARS-CoV-2 RNA genome is folded in the virion remains unknown. To fill the knowledge gap and facilitate structure-based drug development, we develop a virion RNA in situ conformation sequencing technology, named vRIC-seq, for probing viral RNA genome structure unbiasedly. Using vRIC-seq data, we reconstruct the tertiary structure of the SARS-CoV-2 genome and reveal a surprisingly "unentangled globule" conformation. We uncover many long-range duplexes and higher-order junctions, both of which are under purifying selections and contribute to the sequential package of the SARS-CoV-2 genome. Unexpectedly, the D614G and the other two accompanying mutations may remodel duplexes into more stable forms. Lastly, the structure-guided design of potent small interfering RNAs can obliterate the SARS-CoV-2 in Vero cells. Overall, our work provides a framework for studying the genome structure, function, and dynamics of emerging deadly RNA viruses.

/pdf/the-architecture-of-the-sars-cov-2-rna-genome-inside-virion-2fgvok7hk4.pdf

The architecture of the SARS-CoV-2 RNA genome inside virion.

Dengue (DENV) and Zika (ZIKV) viruses are clinically important members of the Flaviviridae family with an 11 kb positive strand RNA genome that folds to enable virus function. Here, we perform structure and interaction mapping on four DENV and ZIKV strains inside virions and in infected cells. Comparative analysis of SHAPE reactivities across serotypes nominates potentially functional regions that are highly structured, conserved, and contain low synonymous mutation rates. Interaction mapping by SPLASH identifies many pair-wise interactions, 40% of which form alternative structures, suggesting extensive structural heterogeneity. Analysis of shared interactions between serotypes reveals a conserved macro-organization whereby interactions can be preserved at physical locations beyond sequence identities. We further observe that longer-range interactions are preferentially disrupted inside cells, and show the importance of new interactions in virus fitness. These findings deepen our understanding of Flavivirus genome organization and serve as a resource for designing therapeutics in targeting RNA viruses.

/pdf/structure-mapping-of-dengue-and-zika-viruses-reveals-3hqmk19xni.pdf

Structure mapping of dengue and Zika viruses reveals functional long-range interactions

Dengue and Zika are clinically important members of the Flaviviridae family that utilizes an 11kb positive strand RNA for genome regulation. While structures have been mapped primarily in the UTRs, much remains to be learnt about how the rest of the genome folds to enable function. Here, we performed secondary structure and pair-wise interaction mapping on four dengue serotypes and four Zika strains in their native virus particles and infected cells. Comparative analysis of SHAPE reactivities across serotypes nominated potentially functional regions that are highly structured, show structure conservation, and low synonymous mutation rates, including a structure associated with ribosome pausing. Pair-wise interaction mapping by SPLASH further reveals new pair-wise interactions, in addition to the known circularization sequence. 40% of pair-wise interactions form alternative structures, suggesting extensive structural heterogeneity. Analysis of shared pair-wise interactions between serotypes revealed macro-organization whereby interactions are preserved at their physical locations, beyond their sequence identities. In addition, structure mapping of virus genomes released in solution - as well as inside host cells - showed that other helicases, in addition to the ribosome, play a role in unwinding viral structures inside cells. Mutational experiments that disrupt in cell and in virion pair-wise interactions result in virus attenuation, demonstrating their importance during the virus life-cycle.

/pdf/structure-mapping-of-dengue-and-zika-viruses-reveals-new-169vlxgbad.pdf

Xuyang Sun

Papers

Structure mapping of dengue and Zika viruses reveals functional long-range interactions

Structure mapping of dengue and Zika viruses reveals new functional long-range interactions