Category Archives: Genome

An important milestone in the fight against Covid-19 came in early January, when the entire viral genome of the novel coronavirus that causes the disease was sequenced for the first time. Since then, the full coronavirus genome, taken from thousands of infected patients around the globe, has been sequenced.

This vast bank of genome sequences is an important resource. Particularly as viruses such as coronavirus have a high mutation rate, with the genome sequence varying up to 0.02%. This may sound low, but considering the human genome varies by only 0.001% between individuals, its clear the virus mutates much faster than we do and can quickly evolve.

Sequencing the coronavirus at different points in time can tell us how it is adapting and can indicate the direction it is likely to take.

In a recent study, the London School of Hygiene and Tropical Medicine analysed the viral genome sequences isolated from over 5,000 Covid-19 patients around the world. So what does this analysis of genome variations tell us? What implications does it have for vaccines, treatments and testing? And what does it tell us about the future direction of this destructive pathogen?

All viral vaccines contain material that resembles the virus they are trying to protect against. This fools the immune system into mounting a response and producing antibodies ready to be used should it ever encounter the real thing. In the case of the coronavirus, the immune system produces antibodies that target the spike protein the part of the virus that is used to invade our cells.

One concern is that the virus will mutate to form escape mutants. These are mutated versions of the virus that the vaccine-induced antibodies wont recognise. We see this with other viruses, such as influenza. The flu vaccine has to be altered each year to counter changes to circulating strains.

Luckily, the novel coronavirus has a lower mutation rate than influenza. And while the London School of Hygiene and Tropical Medicine study identified changes in the S gene the gene that makes the spike of the various virus strains, mutations in this gene were comparatively rare. Mutations in the epitope regions the sites in the spike protein the antibodies attach to were also infrequent.

Initial searches for an effective treatment have focussed on existing drugs, as seen in recent reports of the success of dexamethasone. While this drug prevents a hyperactive immune reaction to the virus, other promising drugs, such as remdesivir, directly target the virus itself. Remdesivir specifically targets the enzyme the virus needs to replicate.

Previous studies found two mutations in the enzyme gene that confer resistance to remdesivir, but the London School of Hygiene and Tropical Medicine study didnt find many instances of these mutations. Wide use of the drug, however, will put selective pressure on the virus environmental factors that contribute to evolutionary change so monitoring these mutations will be important.

To diagnose a current infection, diagnostic tests look for certain genes from the virus. The accuracy of these tests depends on the target areas of the genome being as expected.

The first published diagnostic method, released shortly after the first viral genome was sequenced, screened for more than one viral gene considered to be well conserved across viral strains. Well-conserved genes are important for the virus to function and so tend not to change as the organism evolves. Most diagnostic tests since have continued to screen for two or more coronavirus genes, although the genes they test for often vary.

The authors of the LSHTM study looked for variations in regions of the genome screened for in common diagnostic tests and found several mutations that could result in false negatives, where a person has the disease but the test says they dont. These mutations had a strong geographical distribution, so clinical scientists need to be aware of locally circulating strains when considering which tests to use.

Similarly, once restrictions on international travel are relaxed, scientists will need to be wary of possible false negatives among imported cases of the disease.

Some viruses that cross the species barrier into humans are ill-equipped to replicate in their human host and fail to sustain a presence in the human population. However, the coronavirus has already achieved sustained human-to-human transmission, but will this presence be maintained? And if so, will the virus evolve to become more or less lethal?

Like mutations in any organism, for a viral mutation to prevail, it must provide an evolutionary advantage. There is no evolutionary advantage to a virus if it kills its host, particularly if it kills the host before transmitting to a new one. But evoking symptoms in the infected person, such as coughing and sneezing, can help the virus transmit to a new host and this does offer an evolutionary advantage.

To identify which mutations may help the virus survive, the authors of the study set out to identify convergent mutations mutations that occurred in different parts of the world and at a higher than random rate, suggesting that these mutations benefit the survival of the virus.

Although scientists have analysed many genomes, the study of the genome-disease relationship is still a work in progress. Unfortunately, there is a bias in the database of genome sequences because samples from patients with more severe symptoms are more likely to be sequenced, making it difficult to associate particular mutations to how severe the disease is.

Of course, disease outcomes are affected by other factors, too, such as how old or sick the host is. The effect of interventions also has to be considered. Until a large dataset of genome data from mild or non-symptomatic patients from a diverse population is available, it will be difficult to deduce how the convergent mutations identified translate to severity of disease.

Claire Crossan, Research Fellow, Virology, Glasgow Caledonian University.

This article first appeared on The Conversation.

View original post here:
What coronavirus mutations mean for its vaccine, treatment and testing - Scroll.in

[98 pages report] This market research report includes a detailed segmentation of the global genome editing market by technology (CRISPR, TALEN, ZFN, and Others), by application (Cell Line Engineering, Genetic Engineering, and Others), By end-user (Research Institutes, Biotechnology and Pharmaceutical Companies, and Contract Research Organizations), by regions (North America, Europe, Asia Pacific, and Rest of the World).

Request For Report[emailprotected]https://www.trendsmarketresearch.com/report/sample/9845

Overview of the Global Genome Editing Market

Infoholics market research report predicts that the Global Genome Editing Market will grow at a CAGR of 14.4% during the forecast period. The market has witnessed steady growth in the past few years with the development in technology and the introduction of highly sensitive, robust, and reliable systems in the market. The market is fueled due to increase in genetic disorders, increasing investment and funds, and technological advancements in genome editing.

The market continues to grow and is one of the increasingly accepted market in many countries worldwide. Vendors are focusing towards obtaining funds and collaborating with universities to enlarge their research and development capabilities. The majority of the revenue is generated from the leading players in the market with dominating sales of ThermoFisher Scientific, GenScript Corp., Sangamo Therapeutics, Lonza Group, and Horizon Discovery Group plc.

According to Infoholic Research analysis, North America accounted for the largest share of the global genome editing market in 2018. US dominates the market with majority of genome editing companies being located in this region. However, China has not been too far behind and has great government support for the research in genome editing field.

Genome Editing Market by Technology:

In 2018, the CRISPR segment occupied the largest share due to specific, effective, and cost-effective nature of the technology. Many companies are focusing on providing genome editing services. For instance, in January 2019, Horizon Discovery extended CRISPR screening service to primary human T cells.

Get Complete TOC with Tables and[emailprotected]https://www.trendsmarketresearch.com/report/discount/9845

Genome Editing Market by Applications:

In 2018, the cell line engineering accounted the maximum share followed by genetic engineering. Increase in the number of people suffering with genetic disorders has driven the growth of the genome editing market.

Genome Editing Market by End Users:

In 2018, the biotechnology and pharmaceutical companies gained the highest market share for genome editing market due to increased pervasiveness of cancer and infectious diseases are driving research goings-on in biotechnology & pharmaceutical companies segment.

Genome Editing Market by Regions:

The market is dominated by North America, followed by Asia Pacific and Europe. The major share of the North America market is from the US due to quick adoption of new and advanced technologies.

Genome Editing Market Research Competitive Analysis The market is extremely fragmented with several smaller companies struggling for market share. Big pharmaceutical establishments have also united with venture capitalists to provide funding to the start-ups. In 2015, Bayer financed $335 million and in the very same year, Celgene combined with Abingworth invested $64 million in CRISPR Therapeutics. The NIH recently granted 21 somatic cell genome editing grants of almost $86 million over the next half a decade. These endowments are the foremost to be granted through the Somatic Cell Genome Editing (SCGE) program that was initiated in January 2018 with NIH Common Fund.

The companies are collaborating and licensing to increase their capabilities in the market. CRISPR, TALEN, ZFN, Meganuclease, ARCUS, and RTDS are some of the key technology areas concentrated by key players in the market. Since 2015, the deals on the CRISPR technology has drastically increased.

Key vendors:

Key competitive facts

Benefits The report provides complete details about the usage and adoption rate of genome editing market. Thus, the key stakeholders can know about the major trends, drivers, investments, vertical players initiatives, and government initiatives towards the healthcare segment in the upcoming years along with details of the pureplay companies entering the market. Moreover, the report provides details about the major challenges that are going to impact the market growth. Additionally, the report gives complete details about the key business opportunities to key stakeholders in order to expand their business and capture the revenue in specific verticals, and to analyze before investing or expanding the business in this market.

<<< Get COVID-19 Report Analysis >>>https://www.trendsmarketresearch.com/report/covid-19-analysis/9845

Key Takeaways:

Read more:
Genome Editing Market to Exhibit Rapid Surge in Consumption in the COVID-19 Crisis 2025 - 3rd Watch News

As of the end of June, there were more than 10.4 million confirmed cases of COVID-19 worldwide. The real number, of course, is much higher, though unknown, because of limited tests and because of how many people who are infected never have symptoms and so never think to get a test. At the nonprofit Chan Zuckerberg Biohub, researchers are using changes in the virus genome to estimate the number of undetected infectionsand found that in some areas, more than 90% of cases werent discovered.

In a new paper, not yet peer-reviewed, the researchers estimated the numbers of infected people in 12 locations in Europe, China, and the U.S., along with the probability of case detection over time and how long it took to detect an outbreak in a given area. As the virus began to spread in each location, the majority of infectionsmore than 98%were undetected in the first few weeks. While that number went down as testing increased, the researchers estimated that in Shanghai, for instance, 92% of infectionsor 3,900 caseswere never detected over a nearly two-month period.

By studying the virus genome, its possible to estimate infections across a population even when large-scale testing isnt happening. The virus genome mutates at a fairly constant rate as it spreads through the population, says Lucy Li, the data scientist at the Chan Zuckerberg Biohub who led the study. For example, if we know that one mutation occurs every three transmissions, and we see that on average, there are two mutations between confirmed cases, then that suggests around one in six infections are detected. The studys methods, she says, were more complex, looking at factors like randomness in mutation and variations in how infectious people are. Using genetic data that labs share in a global database, the researchers used a mathematical model to run an analysis of the mutations.

Looking at data ending in early April, the researchers found that Shanghai had the largest number of undetected cases. In other locations, the estimate was lower, but that may have been because of what stage the outbreak was in at the time the data was collected. They estimated that New York, for example, had only 13% undetected infections (that analysis might change with more data).

There are many factors that could explain the differences between locations: different demographics of people who have different rates of becoming symptomatic, sub-populations who have less access to testing facilities, availability of testing, Li says. Furthermore, as this analysis was carried out during the early stages of the epidemic in the U.S., New York, like other U.S. states, had relatively few available viral genomes. This means the relatively low estimate of undetected infections in New York could be due to a delay in available genomes.

Other studies have also suggested that large numbers of people arent being diagnosed. A recent study published in Science Translational Medicine looked at the number of Americans who went to the doctor with flu-like illnesses in March but werent diagnosed with the fluand werent tested for the new coronavirus because testing was so limited. There was a spike in doctor visits at the time. Based on the data, along with extrapolations about people who were likely sick but never went to the doctor, the study estimated that as many as 8.7 million Americans were infected with COVID-19 at the time, but fewer than 20% were diagnosed.

Although COVID-19 testing rates are growing in the U.S.with around half a million tests a day nowthe country still isnt testing at the level that many epidemiologists recommend (and much less than the 5 million a day Trump promised in April). Li says that though more tests are needed, its also critical to test strategically to find people who arent experiencing symptoms. Given that the majority of the population still has not been infected, random testing is not the most efficient at finding asymptomatic infections because most tests would still return negative, she says. More intensive test-and-trace efforts would help focus testing efforts to those who have known exposures and increase the likelihood of finding previously undetected infections.

Link:
Studying COVID-19 mutations may reveal how many infections are undetec - Fast Company

Written by Kabir Firaque, Mehr Gill | New Delhi | Updated: July 5, 2020 10:02:10 am There exists a very simple thumb rule, used frequently over the years. The new research, however, has described it as a myth

Dogs live shorter lives than humans, and so a six-year-old dog is at a far later stage of its life than a six-year-old child. A dog can even be a grandparent at age six. What, then, is its age in human years? New research, published in the journal Cell Systems has come up with a formula and a graph to determine that.

Was there not a formula already?

There exists a very simple thumb rule, used frequently over the years. The new research, however, has described it as a myth. According to the popular rule, you multiply a dogs age by 7, and you supposedly get its equivalent age in human years: For example, a four-year-old dog is 28 in human years. Only, its not so simple.

Why not?

The new research, which is based on epigenetics, has found the comparison between human years and dog years is not perfectly linear which would have been the case had the 1:7 thumb rule been reliable. The relationship, in fact, follows the red curve shown in the figure.

How can I use this curve to determine my dogs age in human years?

First, find your dogs age along the horizontal (X) axis. Suppose your dog is four years old. Locate 4 on the horizontal axis, then trace your finger upwards until you reach the red curve. From that point, move left towards the vertical (Y) axis, where you have human years (illustrated with Tom Hanks at various ages). Your finger will touch the vertical axis at, in this case, 52 years.

So, a four-year-old dog is equivalent in physiological age to a 52-year-old Tom Hanks (or any 52-year-old human). This is almost twice as much the age you would get (28) if you followed the 1:7 thumb rule.

What is the basis of this new calculation?

It is based on molecular changes in the human genome and dog genome over time. Researchers at the University of California at San Diego analysed patterns over time in methylation a term that refers to specific chemical changes in the genome.

This is the field that is known as epigenetics, which studies chemical modifications that influence which genes are off or on, without altering the original genetic sequence itself. The new formula, the researchers said, provides a new epigenetic clock for determining the age of a cell, tissue or organism.

How did the researchers derive the formula?

The UC San Diego team had previously published epigenetic clocks for humans. For the new study, they collaborated with dog genetics experts at UC Davis and the US National Human Genome Research Institute. They analysed blood samples from 105 Labrador retrievers for changes with age.

Only Labradors?

Indeed, that is one limitation of the new epigenetic clock, acknowledged by senior author Trey Ideker himself. (The first author is Tina Wang, Idekers former graduate student, who first suggested the idea for such a study.) In a statement, Ideker acknowledged that the new epigenetic clock was developed using a single breed of dog, and some dog breeds are known to live longer than others. More research will be needed, he said.

Will it work for my dog if it is not a Labrador?

Ideker said it is accurate for humans and mice, as well as Labrador retrievers. He predicts that the clock will apply to all dog breeds. As such, it may provide a useful tool for veterinarians and even for evaluating anti-ageing interventions, the researchers suggest.

How so?

There are a variety of anti-ageing interventions in the market, with some of these standing on a more solid scientific foundation than others. But, as Ideker noted in the statement, how do you know if a product will truly extend your life without waiting 40 years or so?

If you refer to the new epigenetic clock, you need not wait, he suggested. What if you could measure your age-associated methylation patterns before, during and after the intervention to see if its doing anything?

The Indian Express is now on Telegram. Click here to join our channel (@indianexpress) and stay updated with the latest headlines

For all the latest Explained News, download Indian Express App.

See more here:
Explained: How old is your dog in human years? Here is a new calculation to find out - The Indian Express

INTRODUCTION

The three-dimensional organization of the eukaryotic genome plays a central role in gene regulation (1). Its spatial organization has been prominently characterized by molecular and cellular approaches including high-throughput chromosome conformation capture (Hi-C) (2) and fluorescent in situ hybridization (3). Topologically associated domains (TADs), genomic regions that display a high degree of interaction, were revealed and found to be a key architectural feature (4). Direct three-dimensional localization microscopy of the chromatin fiber at the nanoscale (5) confirmed the presence of TADs in single cells but also, among others, revealed great structural variation of chromatin architecture (3). To comprehensively resolve the spatial heterogeneity of chromatin, super-resolution microscopy must be used. Previous work showed that nucleosomes are distributed as segregated, nanometer-sized accumulations throughout the nucleus (68) and that the epigenetic state of a locus has a large impact on its folding (9, 10). However, to resolve the fine structure of chromatin, high labeling densities, long acquisition times, and, often, cell fixation are required. This precludes capturing dynamic processes of chromatin in single live cells, yet chromatin moves at different spatial and temporal scales.

The first efforts to relate chromatin organization and its dynamics were made using a combination of photoactivated localization microscopy (PALM) and tracking of single nucleosomes (11). It could be shown that nucleosomes mostly move coherently with their underlying domains, in accordance with conventional microscopy data (12); however, a quantitative link between the observed dynamics and the surrounding chromatin structure could not yet be established in real time. Although it is becoming increasingly clear that chromatin motion and long-range interactions are key to genome organization and gene regulation (13), tools to detect and to define bulk chromatin motion simultaneously at divergent spatiotemporal scales and high resolution are still missing.

Here, we apply deep learningbased PALM (Deep-PALM) for temporally resolved super-resolution imaging of chromatin in vivo. Deep-PALM acquires a single resolved image in a few hundred milliseconds with a spatial resolution of ~60 nm. We observed elongated ~45- to 90-nm-wide chromatin domain blobs. Using a computational chromosome model, we inferred that blobs are highly dynamic entities, which dynamically assemble and disassemble. Consisting of chromatin in close physical and genomic proximity, our chromosome model indicates that blobs, nevertheless, adopt TAD-like interaction patterns when chromatin configurations are averaged over time. Using a combination of Deep-PALM and high-resolution dense motion reconstruction (14), we simultaneously analyzed both structural and dynamic properties of chromatin. Our analysis emphasizes the presence of spatiotemporal cross-correlations between chromatin structure and dynamics, extending several micrometers in space and tens of seconds in time. Furthermore, extraction and statistical mapping of multiple parameters from the dynamic behavior of chromatin blobs show that chromatin density regulates local chromatin dynamics.

Super-resolution imaging of complex and compact macromolecules such as chromatin requires dense labeling of the chromatin fiber to resolve fine features. We use Deep-STORM, a method that uses a deep convolutional neural network (CNN) to predict super-resolution images from stochastically blinking emitters (Fig. 1A; see Materials and Methods) (15). The CNN was trained to specific labeling densities for live-cell chromatin imaging using a photoactivated fluorophore (PATagRFP); we therefore refer to the method as Deep-PALM. We chose three labeling densities 4, 6, and 9 emitters/m2 per frame in the ON-state to test on the basis of the comparison of simulated and experimental wide-field images (fig. S1A). The CNN trained with 9 emitters/m2 performed significantly worse than the other CNNs and was thus excluded from further analysis (fig. S1B; see Materials and Methods). We applied Deep-PALM to reconstruct an image set of labeled histone protein (H2B-PATagRFP) in human bone osteosarcoma (U2OS) cells using the networks trained on 4 and 6 emitters/m2 per frame (see Materials and Methods). A varying number of predictions by the CNN of each frame of the input series were summed to reconstruct a temporal series of super-resolved images (fig. S1C). The predictions made by the CNN trained with 4 emitters/m2 show large spaces devoid of signal intensity, especially at the nuclear periphery, making this CNN inadequate for live-cell super-resolution imaging of chromatin. While collecting photons from long acquisitions for super-resolution imaging is desirable in fixed cells, Deep-PALM is a live imaging approach. Summing over many individual predictions leads to considerable motion blur and thus loss in resolution. Quantitatively, the Nyquist criterion states that the image resolution R=2/ depends on , the localization density per second, and the time resolution (16). In contrast, motion blur strictly depends on the diffusion constant D of the underlying structure R=4D. There is thus an optimum resolution due to the trade-off between increased emitter sampling and the avoidance of motion blur, which was at a time resolution of 360 ms for our experiments (Fig. 1B and fig. S1D).

(A) Wide-field images of U2OS nuclei expressing H2B-PATagRFP are input to a trained CNN, and predictions from multiple input frames are summed to construct a super-resolved image of chromatin in vivo. (B) The resolution trade-off between the prolonged acquisition of emitter localizations (green line) and motion blur due to diffusion of the underlying diffusion processes (purple line). For our experimental data, the localization density per second is = (2.4 0.1) m2s1, the diffusion constant is D = (3.4 0.8) 103 m2s1 (see fig. S8B), and the acquisition time per frame is = 30 ms. The spatial resolution assumes a minimum (69 5 nm) at a time resolution of 360 ms. (C) Super-resolution images of a single nucleus at time intervals of about 10 s. Scale bars, 2 m. (D) Magnification of segregated accumulations of H2B within a chromatin-rich region. Scale bar, 200 nm. (E) Magnification of a stable but dynamic structure (arrows) over three consecutive images. Scale bars, 500 nm. (F) Fourier ring correlation (FRC) for super-resolved images resulting in a spatial resolution of 63 2 nm. FRC was conducted on the basis of 332 consecutive super-resolved images from two cells. a.u. arbitrary units.

Super-resolution imaging of H2B-PATagRFP in live cells at this temporal resolution shows a pronounced nuclear periphery, while fluorescent signals in the interior vary in intensity (Fig. 1C). This likely corresponds to chromatin-rich and chromatin-poor regions (8). These regions rearrange over time, reflecting the dynamic behavior of bulk chromatin. Chromatin-rich and chromatin-poor regions were visible not only at the scale of the whole nucleus but also at the resolution of a few hundred nanometers (Fig. 1D). Within chromatin-rich regions, the intensity distribution was not uniform but exhibited spatially segregated accumulations of labeled histones of variable shape and size, reminiscent of nucleosome clutches (6), nanodomains (9, 11), or TADs (17). At the nuclear periphery, prominent structures arise. Certain chromatin structures could be observed for ~1 s, which underwent conformational changes during this period (Fig. 1E). The spatial resolution at which structural elements can be observed (see Materials and Methods) in time-resolved super-resolution data of chromatin was 63 2 nm (Fig. 1E), slightly more optimistic than the theoretical prediction (Fig. 1B) (18).

We compared images of H2B reconstructed from 12 frames (super-resolved images) by Deep-PALM in living cells to super-resolution images reconstructed by 8000 frames of H2B in fixed cells (fig. S2, A and B). Overall, the contrast in the fixed sample appears higher, and the nuclear periphery appears more prominent than in images from living cells. However, in accordance with the previous super-resolution images of chromatin in fixed cells (6, 8, 9, 11, 17) and Deep-PALM images, we observe segregated accumulations of signal throughout the nucleus. Thus, Deep-PALM identifies spatially heterogeneous coverage of chromatin, as previously reported (6, 8, 9, 11, 17). We further monitor chromatin temporally at the nanometer scale in living cells.

To quantitatively assess the spatial distribution of H2B, we developed an image segmentation scheme (see Materials and Methods; fig. S3), which allowed us to segment spatially separated accumulations of H2B signal with high fidelity (note S1 and figs. S4 and S5). Applying our segmentation scheme, ~10,000 separable elements, blob-like structures were observed for each super-resolved image (166 resolved images per movie; Fig. 2A). The experimental resolution does not enable us to elucidate their origin and formation because tracking of blobs in three dimensions would be necessary to do so (see Discussion). We therefore turned to a transferable computational model introduced by Qi and Zhang (19), which is based on one-dimensional genomics and epigenomics data, including histone modification profiles and binding sites of CTCF (CCCTC-binding factor). To compare our data to the simulations, super-resolution images were generated from the modeled chromosomes. Within these images, we could identify and characterize chromatin blobs analogously to those derived from experimental data (see Materials and Methods; Fig. 2B).

(A) Super-resolved images show blobs of chromatin (left). These blobs are segmented (see Materials and Methods and note S1) and individually labeled by random color (right). Magnifications of the boxed regions are shown. Scale bars, 2 m (whole nucleus); magnifications, 200 nm. (B) Generation of super-resolution images and blob identification and characterization for a 25million base pair (Mbp) segment of chromosome 1 from GM12878 cells, as simulated in Qi and Zhang (19). Beads (5-kb genomic length) of a simulated polymer configuration within a 200-nm-thick slab are projected to the imaging plane, resembling experimental super-resolved images of live chromatin. Blobs are identified as on experimental data. (C) From the centroid positions, the NND distributions are computed for up to 40 nearest neighbors (blue to red). The envelope of the k-NND distributions (black line) shows peaks at approximately 95, 235, 335, and 450 nm (red dots). (D) k-NND distributions as in (B) for simulated data. (E) Area distribution of experimental and simulated blobs. The distribution is, in both cases, well described by a lognormal distribution with parameters (3.3 2.8) 103 m2 for experimental blobs and (3.1 3.2) 103 m2 for simulated blobs (means SD). PDF, probability density function. (F) Eccentricity distribution for experimental and simulated chromatin blobs. Selected eccentricity values are illustrated by ellipses with the corresponding eccentricity. Eccentricity values range from 0, describing a circle, to 1, describing a line. Prominent peaks arise because of the discretization of chromatin blobs in pixels. The data are based on 332 consecutive super-resolved images from two cells, in each of with ~10,000 blobs were identified.

For imaged (in living and fixed cells) and modeled chromatin, we first computed the kth nearest-neighbor distance (NND; centroid-to-centroid) distributions, taking into account the nearest 1st to 40th neighbors (Fig. 2C and fig. S2, C and D, blue to red). Centroids of the nearest neighbors are (95 30) nm (means SD) apart, consistent with previous and our own super-resolution images of chromatin in fixed cells (9) and slightly further than what was found for clutches of nucleosomes (6). The envelope of all NND distributions (Fig. 2C, black line) shows several weak maxima at ~95, 235, 335, and 450 nm, which roughly coincide with the peaks of the 1st, 7th, 14th, and 25th nearest neighbors, respectively (Fig. 2C, red dots). In contrast, simulated data exhibit a prominent first nearest-neighbor peak at a slightly smaller distance, and higher-order NND distribution decay quickly and appear washed out (Fig. 2D). This hints toward greater levels of spatial organization of chromatin in vivo, which is not readily recapitulated in the used state-of-the-art chromosome model.

Next, we were interested in the typical size of chromatin blobs. Their area distribution (Fig. 2E) fit a log-normal distribution with parameters (3.3 2.8) 103 m2 (means SD), which is in line with the area distribution derived from fixed samples (fig. S2E) and modeled chromosomes. Notably, blob areas vary considerably, as indicated by the high SD and the prominent tail of the area distribution toward large values. Following this, we calculated the eccentricity of each blob to resolve their shape (Fig. 2F and fig. S2F). The eccentricity is a measure of the elongation of a region reflecting the ratio of the longest chord of the shape and the shortest chord perpendicular to it (Fig. 2F; illustrated shapes at selected eccentricity values). The distribution of eccentricity values shows an accumulation of values close to 1, with a peak value of ~0.9, which shows that most blobs have an elongated, fiber-like shape and are not circular. In particular, the eccentricity value of 0.9 corresponds to a ratio between the short and long axes of the ellipse of 1:2 (see Materials and Methods), which results, considering the typical area of blobs in experimental and simulated data, in roughly 92-nm-long and 46-nm-wide blobs on average. A highly similar value was found in fixed cells (fig. S2F). The length coincides with the value found for the typical NND [Fig. 2C; (95 30) nm]. However, because of the segregation of chromatin into blobs, their elongated shape, and their random orientation (Fig. 2A), the blobs cannot be closely packed throughout the nucleus. We find that chromatin has a spatially heterogeneous density, occupying 5 to 60% of the nuclear area (fig. S6, A and B), which is supported by a previous electron microscopy study (20).

Blob dimensions derived from live-cell super-resolution imaging using Deep-PALM are consistent with those found in fixed cells, thereby further validating our method, and in agreement with previously determined size ranges (6, 9). A previously published chromosome model based on Hi-C data (and thus not tuned to display blob-like structures per se) also displays blobs with dimensions comparable to those found here, in living cells. Together, these data strongly suggest the existence of spatially segregated chromatin structures in the sub100-nm range.

The simulations offer to track each monomer (chromatin locus) unambiguously, which is currently not possible to do from experimental data. Since the simulations show blobs comparable to those found in experiment (Fig. 2), simulations help to indicate possible mechanisms leading to the observation of chromatin blobs. For instance, because of the projection of the nuclear volume onto the imaging plane, the observed blobs could simply be overlays of distant, along the one-dimensional genome, noninteracting genomic loci. To examine this possibility, we analyzed the gap length between beads belonging to the same blob along the simulated chromosome. Beads constitute the monomers of the simulated chromosome, and each bead represents roughly 5 kb (19).

The analysis showed that the blobs are mostly made of consecutive beads along the genome, thus implying an underlying domain-like structure, similar to TADs (Fig. 3A). Using the affiliation of each bead to an intrinsic chromatin state of the model (Fig. 3B), it became apparent that blobs along the simulated chromosome consisting mostly of active chromatin are significantly larger than those formed by inactive and repressive chromatin (Fig. 3C). These findings are in line with experimental results (10) and results from the simulations directly (19), thereby validating the projection and segmentation process.

(A) Gap length between beads belonging to the same blob. An exemplary blob with small gap length is shown. The blob is mostly made of consecutive beads being in close spatial proximity. (B) A representative polymer configuration is colored according to chromatin states (red, active; green, inactive; and blue, repressive). (C) The cumulative distribution function (CDF) of clusters within active, inactive, and repressive chromatin. Inset: Mean area of clusters within the three types of chromatin. The distributions are all significantly different from each other, as determined by a two-sample Kolmogorov-Smirnov test (P < 1050). (D) Distribution of the continuous residence time of any monomer within a cluster (0.5 0.3 s; means SD). Inset: Continuous residence time of any monomer within a slab of 200-nm thickness (1.5 1.6 s; means SD). (E) The blob association strength between any two beads is measured as the frequency at which any two beads are found in one blob. The association map is averaged over all simulated configurations (upper triangular matrix; from simulations), and experimental Hi-C counts are shown for the same chromosome segment [lower triangular matrix; from Rao et al. (40)]. The association and Hi-C maps are strongly correlated [Pearsons correlation coefficient (PCC) = 0.76]. (F) Close-up views around the diagonal of Hi-Clike matrices. The association strength is shown together with the inverse distance between beads (top; PCC = 0.85) and with experimental Hi-C counts [bottom; as in (E)]. The data are based on 20,000 polymer configurations.

Since chromatin is dynamic in vivo and in computer simulations, each bead can diffuse in and out of the imaging volume from frame to frame. We estimated that, on average, each bead spent approximately 1.5 s continuously within a slab of 200-nm thickness (Fig. 3D). Furthermore, a bead is, on average, found only 0.55 0.33 s continuously within a blob, which corresponds to one to two experimental super-resolved images (Fig. 3D). These results suggest that chromatin blobs are highly dynamic entities, which usually form and dissemble within less than 1 s. We thus constructed a time-averaged association map for the modeled chromosomes, quantifying the frequency at which each locus is found with any other locus within one blob. The association map is comparable to interaction maps derived from Hi-C (Fig. 3E). Notably, interlocus association and Hi-C maps are strongly correlated, and the association map shows similar patterns as those identified as TADs in Hi-C maps, even for relatively distant genomic loci [>1 million base pairs (Mbp)]. A similar TAD-like organization is also apparent when the average inverse distance between loci is considered (Fig. 3F, top), suggesting that blobs could be identified in super-resolved images because of the proximity of loci within blobs in physical space. The computational chromosome model indicates that chromatin blobs identified by Deep-PALM are mostly made of continuous regions along the genome and cannot be attributed to artifacts originating from the projection of the three-dimensional genome structure to the imaging plane. The simulations further indicate that the blobs associate and dissociate within less than 1 s, but loci within blobs are likely to belong to the same TAD. Their average genomic content is 75 kb, only a fraction of typical TAD lengths in mammalian cells (average size, 880 kb) (4), suggesting that blobs likely correspond to sub-TADs or TAD nanocompartments (17).

To quantify the experimentally observed chromatin dynamics at the nanoscale, down to the size of one pixel (13.5 nm), we used a dense reconstruction of flow fields, optical flow (Fig. 4A; see Materials and Methods), which was previously used to analyze images taken on confocal (12, 14), and structured illumination microscopes (8). We examined the suitability of optical flow for super-resolution on the basis of single-molecule localization images using simulations. We find that the accuracy of optical flow is slightly enhanced on super-resolved images compared to conventional fluorescence microscopy images (note S2 and fig. S7, A to C). Experimental super-resolution flow fields are illustrated on the basis of two subsequent images, between which the dynamics of structural features are apparent to the eye (fig. S7, D and E). On the nuclear periphery, connected regions spanning up to ~500 nm can be observed [fig. S7D (i and ii), marked by arrows]. These structures are stable for at least 360 ms but move from frame to frame. The flow field is shown on top of an overlay of the two super-resolved images and color-coded [fig. S7D (iii); the intensity in frame 1 is shown in green, the intensity in frame 2 is shown in purple, and colocalization of both is white]. Displacement vectors closely follow the redistribution of intensity from frame to frame (roughly from green to purple). Similarly, structures within the nuclear interior (fig. S7E) can be followed by eye, thus further validating and justifying the use of a dense motion reconstruction as a quantification tool of super-resolved chromatin motion.

(A) A time series of super-resolution images (left) is subject to optical flow (right). (B) Blobs of a representative nucleus (see movie S1) are labeled by their NND (left), area (middle), and flow magnitude (right). Colors denote the corresponding parameter magnitude. (C) The average blob area, (D) NND, (E) density, and (F) flow magnitude are shown versus the normalized distance from the nuclear periphery (lower x axis; 0 is on the periphery and 1 is at the center of the nucleus) and versus the absolute distance (upper x axis). Line and shaded area denote the means SE from 322 super-resolved images of two cells. Scale bar, (A) and (B): 3 m.

Using optical flow fields, we linked the spatial appearance of chromatin to their dynamics. Effectively, the blobs were characterized with two structural parameters (NND and area) and their flow magnitude (Fig. 4B). Movie S1 shows the time evolution of those parameters for an exemplary nucleus. Blobs at the nuclear periphery showed a distinct behavior from those in the nuclear interior. In particular, the periphery exhibits a lower density of blobs, but those appear slightly larger and are less mobile than in the nuclear interior (Fig. 4, C to F), in line with previous findings using conventional microscopy (14). The peripheral blobs are reminiscent of dense and relatively immobile heterochromatin and lamina-associated domains (21), which extend only up to 0.5 m inside the nuclear interior. In contrast, blob dynamics increase gradually within 1 to 2 m from the nuclear rim.

To further elucidate the relationship between chromatin structure and dynamics, we analyzed the correlation between each pair of parameters in space and time. Therefore, we computed the auto- and cross-correlation of parameter maps with a given time lag across the entire nucleus (in space) (Fig. 5A). In general, a positive correlation denotes a low-low or a high-high relationship (a variable de-/increases when another variable de-/increases), while, analogously, a negative correlation denotes a high-low relationship. The autocorrelation of NND maps [Fig. 5A (i)] shows a positive correlation; thus, regions exist spanning 2 to 4 m, in which chromatin is either closely packed (low-low) or widely dispersed (high-high). Likewise, blobs of similar size tend to be in spatial proximity [Fig. 5A (iii)]. These regions are not stable over time but rearrange continuously, an observation bolstered by the fact that the autocorrelation diminishes with increasing time lag. The cross-correlation between NND and area [Fig. 5A (ii)] shows a negative correlation for short time lags, suggesting that large blobs appear with a high local density while small ones are more isolated. The correlation becomes slightly positive for time lags 20 s, indicating that big blobs are present in regions that were sparsely populated before and small blobs tend to accumulate in previously densely populated regions. This is in line with dynamic reorganization and reshaping of chromatin domains on a global scale, as observed in snapshots of the Deep-PALM image series (Fig. 1A).

(A) The spatial auto- and cross-correlation between parameters were computed for different time lags. The graphs depict the correlation over space lag for each parameter pair, and different colors denote the time lag (increasing from blue to red). (B) Illustration of the instantaneous relationship between local chromatin density and dynamics. The blob density is shown in blue; the magnitude of chromatin dynamics is shown by red arrows. The consistent negative correlation between NND and flow magnitude is expressed by increased dynamics in regions of high local blob density. Data represent the average over two cells. The cells behave similarly such that error bars are omitted for the sake of clarity.

The flow magnitude is positively correlated for all time lags, while the correlation displays a slight increase for time lags 20 s [Fig. 5A (vi)], which has also been observed previously (8, 12, 22). The spatial autocorrelation of dynamic and structural properties of chromatin are in stark contrast. While structural parameters are highly correlated at short but not at long time scales, chromatin motion is still correlated at a time scale exceeding 30 s. At very short time scales (<100 ms), stochastic fluctuations determine the local motion of the chromatin fiber, while coherent motion becomes apparent at longer times (22). However, there exists a strong cross-correlation between structural and dynamic parameters: The cross-correlation between the NND and flow magnitude shows notable negative correlation at all time lags [Fig. 5A (iv)], strongly suggesting that sparsely distributed blobs appear less mobile than densely packed ones. The area seems to play a negligible role for short time lags, but there is a modest tendency that regions with large blobs tend to exhibit increased dynamics at later time points [10 s; Fig. 5A (v)], likely due to the strong relationship between area and NND.

In general, parameter pairs involving chromatin dynamics exhibit an extended spatial auto- or cross-correlation (up to ~6 m; the lower row of Fig. 5A) compared to correlation curves including solely structural parameters (up to 3 to 4 m). Furthermore, the cross-correlation of flow magnitude and NND does not considerably change for increasing time lag, suggesting that the coupling between those parameters is characterized by an unexpectedly resilient memory, lasting for at least tens of seconds (23). Concomitantly, the spatial correlation of time-averaged NND maps and maps of the local diffusion constant of chromatin for the entire acquisition time enforces their negative correlation at the time scale of ~1 min (fig. S8). Such resilient memory was also proposed by a computational study that observed that interphase nuclei behave similar to concentrated solutions of unentangled ring polymers (24). Our data support the view that chromatin is mostly unentangled since entanglement would influence the anomalous exponent of genomic loci in regions of varying chromatin density (24). However, our data do not reveal a correlation between the anomalous exponent and the time-averaged chromatin density (fig. S8), in line with our previous results using conventional microscopy (14).

Overall, the spatial cross-correlation between chromatin structure and dynamics indicates that the NND between blobs and their mobility stand in a strong mutual, negative relationship. This relationship, however, concerns chromatin density variations at the nanoscale, but not global spatial density variations such as in euchromatin or heterochromatin (14). These results support a model in which regions with high local chromatin density, i.e., larger blobs are more prevalent and are mobile, while small blobs are sparsely distributed and less mobile (Fig. 5B). Blob density and dynamics in the long-time limit are, to an unexpectedly large extent, influenced by preceding chromatin conformations.

The spatial correlations above were only evaluated pairwise, while the behavior of every blob is likely determined by a multitude of factors in the complex energy landscape of chromatin (19, 22). Here, we aim to take a wider range of available information into account to reveal the principle parameters, driving the observed chromatin structure and dynamics. Using a microscopy-based approach, we have access to a total of six relevant structural, dynamic, and global parameters, which potentially shape the chromatin landscape in space and time (Fig. 6A). In addition to the parameters used above, we included the confinement level as a relative measure, allowing the quantification of transient confinement (see Materials and Methods). We further included the bare signal intensity of super-resolved images and, as the only static parameter, the distance from the periphery since it was shown that dynamic and structural parameters show some dependence on this parameter (Fig. 4). We then used t-distributed stochastic neighbor embedding (t-SNE) (25), a state-of-the-art dimensionality reduction technique, to map the six-dimensional chromatin features (the six input parameters) into two dimensions (Fig. 6A and see note S3). The t-SNE algorithm projects data points such that neighbors in high-dimensional space likely stay neighbors in two-dimensional space (25). Visually apparent grouping of points (Fig. 6B) implies that grouped points exhibit great similarity with respect to all input features, and it is of interest to reveal which subset of the input features can explain the similarity among chromatin blobs best. It is likely that points appear grouped because their value of a certain input feature is considerably higher or lower than the corresponding value of other data points. We hence labeled points in t-SNE maps which are smaller than the first quartile point or larger than the third quartile point. Data points falling in either of the low/high partition of one input feature are colored accordingly for visualization (Fig. 6D; blue/red points, respectively). We then assigned a rank to each of the input features according to their nearest-neighbor fraction (n-n fraction): Since the t-SNE algorithm conserves nearest neighbors, we described the extent of grouping in t-SNE maps by the fraction of nearest neighbors, which fall in either one of the subpopulations of low or high points (illustrated in fig. S9). A high n-n fraction (Fig. 6C) therefore indicates that many points marked as low/high are indeed grouped by t-SNE and are therefore similar. The ranking (from low to high n-n fraction) reflects the potency of a given parameter to induce similar behavior between chromatin blobs with respect to all input features.

(A) The six-dimensional parameter space is input to the t-SNE algorithm and projected to two dimensions. (B) The two-dimensional embedding of an exemplary dataset is shown and colored according to the magnitude of each input feature (blue to red; the parameter average is shown in beige). (C) Points below the first (blue) and above the third (red) quartile points of the corresponding parameter are marked, and the parameters are ranked according to the fraction of nearest neighbors that fall in one of the marked regions. (D) Data points marked below the first or above the third quartile points are labeled according to the feature in which they were marked. Priority is given to the feature with the higher n-n fraction if necessary. (E) t-SNE analysis is carried out for each nucleus over the whole time series, and it is counted how often a parameter ranked first. The results are visualized as a pie chart. The NND predominantly ranks first in about two-thirds of all cases. (F) Marked points in (C) and (D) are mapped back onto the corresponding nuclei, and the CDF over space is shown (means SE). Pie chart and CDF computations are based on 322 super-resolved images from two cells.

The relative frequency at which each parameter ranked first provides an intuitive feeling for the most influential parameters in the dataset (Fig. 6E). The signal intensity plays a negligible role, suggesting that our data are free of potential artifacts related to the bare signal intensity. Furthermore, the blob area and the distance from the periphery likewise do not considerably shape chromatin blobs. In contrast, the NND between blobs was found to be the main factor inducing the observed characteristics in 67% of all-time frames across all nuclei. The flow magnitude and confinement level together rank first in 26% of all cases (11 and 17%, respectively). These numbers suggest that the local chromatin density is a universal key regulator of instantaneous chromatin dynamics. Note that no temporal dependency is included in the t-SNE analysis and, thus, the feature extraction concerns only short-term (360 ms) relationships. The characteristics of roughly one-fourth of all blobs at each time point are mainly determined by similar dynamical features. Mapping chromatin blobs as marked in Fig. 6 (C and D) back to their respective positions inside the nucleus (Fig. 6F) shows that blobs with low/high flow magnitude or confinement level markedly also grouped in physical space, which is highly reminiscent of coherent motion of chromatin (12). In contrast, blobs with extraordinary low or high NND were found interspersed throughout the nucleus, in line with spatial correlation analysis between structural and dynamic features (Fig. 5). Our results point toward a large influence of the local chromatin density on the dynamics of chromatin at the scale of a few hundred nanometers and within a few hundred milliseconds. At longer time and length scales, however, previous results suggest that this relationship is lost (14).

With Deep-PALM, we present temporally resolved super-resolution images of chromatin in living cells. Our technique identified chromatin nanodomains, named blobs, which mostly have an elongated shape, consistent with the curvilinear arrangement of chromatin, as revealed by structured illumination microscopy (8) with typical axes lengths of 45 to 90 nm. A previous study reported ~30-nm-wide clutches of nucleosomes in fixed mammalian cells using STORM nanoscopy (6), while the larger value obtained using Deep-PALM may be attributed to the motion blurring effect in live-cell imaging. However, histone acetylation and methylation marks were shown to form nanodomains of diameter 60 to 140 nm, respectively (9), which includes the computed dimensions for histone H2B using Deep-PALM.

To elucidate the origin of chromatin blobs, we turned to a simulated chromosome model, which displays chromatin blobs similar to our experimental data when seen in a super-resolution reconstruction. The simulations suggest that chromatin blobs consist of continuous genomic regions with an average length of 75 kb, assembling and disassembling dynamically within less than 1 s. Monomers within blobs display a distinct TAD-like association pattern in the long-time limit, suggesting that the identified blobs represent sub-TADs. Transient formation is consistent with recent findings that TADs are not stable structural elements but exhibit extensive heterogeneity and dynamics (3, 5). To experimentally probe the transient assembly of chromatin blobs, it would be interesting to track individual blobs over time. However, this is a nontrivial task. While the size (area/volume) or shape of blobs could be used to establish correspondences between blobs in subsequent frames, the framework needs to be flexible enough to allow for blob deformations since blobs likely arise stochastically and are not rigid bodies. Achieving an even shorter acquisition time per frame in the future could help minimize the influence of blob deformations and make tracking feasible. The second challenge is to distinguish between disassembly and out-of-focus diffusion of a blob. The three-dimensional imaging at sufficient spatial and temporal resolution will be helpful in the future to overcome this hurdle.

Using an optical flow approach to determine the blob dynamics instead, we found that structural and dynamic parameters exhibit extended spatial and temporal (cross-) correlations. Structural parameters such as the local chromatin density (expressed as the NND between blobs) and area lose their correlation after 3 to 4 m and roughly 40 s in the spatial and temporal dimension, respectively. In contrast, chromatin mobility correlations extend over ~6 m and persist during the whole acquisition period (40 s). Extensive spatiotemporal correlation of chromatin dynamics has been presented previously, both experimentally (12) and in simulations (22), but was not linked to the spatiotemporal behavior of the underlying chromatin structure until now. We found that the chromatin dynamics are closely linked to the instantaneous but also to past local structural characterization of chromatin. In other words, the instantaneous local chromatin density influences chromatin dynamics in the future and vice versa. On the basis of these findings, we suggest that chromatin dynamics exhibit an extraordinary long memory. This strong temporal relationship might be established by the fact that stress propagation is affected by the folded chromosome organization (26). Fiber displacements cause structural reconfiguration, ultimately leading to a local amplification of chromatin motion in local high-density environments. This observation is also supported by the fact that increased nucleosome mobility grants chromatin accessibility even within regions of high nucleosome density (27).

Given the persistence at which correlations of chromatin structure and, foremost, dynamics occur in a spatiotemporal manner, we speculate that the interplay of chromatin structure and dynamics could involve a functional relationship (28): Transcriptional activity is closely linked to chromatin accessibility and the epigenomic state (29). Because chromatin structure and dynamics are related, dynamics could also correlate with transcriptional activity (14, 30, 31). However, it is currently unknown whether the structure-dynamics relationship revealed here is strictly mutual or whether it may be causal. Simulations hint that chromatin dynamics follows from structure (22, 23); this question will be exciting to answer experimentally and in the light of active chromatin remodelers to elucidate a potential functional relationship to transcription. Chromatin regions that are switched from inactive to actively transcribing, for instance, undergo a structural reorganization accompanied by epigenetic modifications (32). The mechanisms driving recruitment of enzymes inducing histone modifications such as histone acetyltransferases, deacetylases, or methyltransferases are largely unknown but often involve the association to proteins (33). Their accessibility to the chromatin fiber is inter alia determined by local dynamics (27). Such a structure-dynamics feedback loop would constitute a quick and flexible way to transiently alter gene expression patterns upon reaction to external stimuli or to coregulate distant genes (1). Future work will study how structure-dynamics correlations differ in regions of different transcriptional activity and/or epigenomic states. Furthermore, probing the interactions between key transcriptional machines such as RNA polymerases with the local chromatin structure and recording their (possibly collective) dynamics could shed light into the target search and binding mechanisms of RNA polymerases with respect to the local chromatin structure. Deep-PALM in combination with optical flow paves the way to answer these questions by enabling the analysis of time-resolved super-resolution images of chromatin in living cells.

Human osteosarcoma U2OS expressing H2B-PATagRFP cells were a gift from S. Huet (CNRS, UMR 6290, Institut Gntique et Dveloppement de Rennes, Rennes, France); the histone H2B was cloned, as described previously (34). U2OS cells were cultured in Dulbeccos modified Eagles medium [with glucose (4.5 g/liter)] supplemented with 10% fetal bovine serum (FBS), 2 mM glutamine, penicillin (100 g/ml), and streptomycin (100 U/ml) in 5% CO2 at 37C. Cells were plated 24 hours before imaging on 35-mm petri dishes with a no. 1.5 coverslip-like bottom (ibidi, Biovalley) with a density of 2 105 cells per dish. Just before imaging, the growth medium was replaced by Leibovitzs L-15 medium (Life Technologies) supplemented with 20% FBS, 2 mM glutamine, penicillin (100 g/ml), and streptomycin (100 U/ml).

Imaging of H2B-PAtagRFP in living U2OS cells was carried out on a fully automated Nikon Ti-E/B PALM (Nikon Instruments) microscope. The microscope is equipped with a full incubator enclosure with gas regulation to maintain a temperature of ~37C for normal cell growth during live-cell imaging. Image sequences of 2000 frames were recorded with an exposure time of 30 ms per frame (33.3 frames/s). For Deep-PALM imaging, a relatively low power (~50 W/cm2 at the sample) was applied for H2B-PATagRFP excitation at 561 nm and then combined with the 405 nm (~2 W/cm2 at the sample) to photoactivate the molecules between the states. Note that for Deep-PALM imaging, switched fluorophores are not required to stay as long in the dark state as for conventional PALM imaging. We used oblique illumination microscopy (11) combined with total internal reflection fluorescence (TIRF) mode to illuminate a thin layer of 200 nm (axial resolution) across the nucleus. The reconstruction of super-resolved images improves the axial resolution only marginally (fig. S1, E and F). Laser beam powers were controlled by acoustic optic-modulators (AA Opto-Electronic). Both wavelengths were united into an oil immersion 1.49-NA (numerical aperture) TIRF objective (100; Nikon). An oblique illumination was applied to acquire image series with a high signal-to-noise ratio. The fluorescence emission signal was collected by using the same objective and spectrally filtered by a Quad-Band beam splitter (ZT405/488/561/647rpc-UF2, Chroma Technology) with a Quad-Band emission filter (ZET405/488/561/647m-TRF, Chroma Technology). The signal was recorded on an electron-multiplying charge-coupled device camera (Andor iXon X3 DU-897, Andor Technology) with a pixel size of 108 nm. For axial correction, Perfect Focus System was applied to correct for defocusing. NIS-Elements software was used for acquiring the images.

The same cell line (U2OS expressing H2B-PAtagRFP), as in live-cell imaging, was used for conventional PALM imaging. Before fixation, cells were washed with phosphate-buffered saline (PBS) (three times for 5 min each) and then fixed with 4% paraformaldehyde (Sigma-Aldrich) diluted in PBS for 15 min at room temperature. A movie of 8000 frames was acquired with an exposure time of 30 ms per frame (33.3 frames/s). In comparison to Deep-PALM imaging, a relatively higher excitation laser of 561 nm (~60 W/cm2 at the sample) was applied to photobleach H2B-PATagRFP and then combined with the 405 nm (~2.5 W/cm2 at the sample) for photoactivating the molecules. We used the same oblique illumination microscopy combined with TIRF system, as applied in live-cell imaging.

PALM images from fixed cells were analyzed using ThunderSTORM (35). Super-resolution images were constructed by binning emitter localizations into 13.5 13.5 nm pixels and blurred by a Gaussian to match Deep-PALM images. The image segmentation was carried out as on images from living cells (see below).

The CNN was trained using simulated data following Nehme et al. (15) for three labeling densities (4, 6, and 9 emitters/m2 per frame). Raw imaging data were checked for drift, as previously described (12). The detected drift in raw images is in the range of <10 nm and therefore negligible. The accuracy of the trained net was evaluated by constructing ground truth images from the simulated emitter positions. The structural similarity index is computed to assess the similarity between reconstructed and ground truth images (36)SSIM=x,y(2xx+C1)(2xy+C2)(x2+y2+C1)(x2+y2+C2)(1)where x and y are windows of the predicted and ground truth images, respectively, and denote their local means and SD, respectively, and xy denotes their cross-variance. C1 = (0.01L)2 and C2 = (0.03L)2 are regularization constants, where L is the dynamic range of the input images. The second quantity to assess CNN accuracy is the root mean square error between the ground truth G and reconstructed image RRMSE=1NN(RG)2(2)where N is the number of pixels in the images. After training, sequences of all experimental images were compared to the trained network, and predictions of single Deep-PALM images were summed to obtain a final super-resolved image. An up-sampling factor of 8 was used, resulting in an effective pixel size of 108 nm/8 = 13.5 nm. A blind/referenceless image spatial quality evaluator (37) was used to determine the optimal number of predictions to be summed. For visualization, super-resolved images were convolved with a Gaussian kernel ( = 1 pixel) and represented using a false red, green, and blue colormap. The parameters of the three trained networks are available at https://github.com/romanbarth/DeepPALM-trained-models.

Fourier ring correlation (FRC) is an unbiased method to estimate the spatial resolution in microscopy images. We follow an approach similar to the one described by Nieuwenhuizen et al. (38). For localization-based super-resolution techniques, the set of localizations is divided into two statistically independent subsets, and two images from these subsets are generated. The FRC is computed as the statistical correlation of the Fourier transforms of both subimages over the perimeter of circles of constant frequency in the frequency domain. Deep-PALM, however, does not result in a list of localizations, but in predicted images directly. The set of 12 predictions from Deep-PALM were thus split into two statistically independent subsets, and the method described by Nieuwenhuizen et al. (38) was applied.

The super-resolved images displayed isolated regions of accumulated emitter density. To quantitatively assess the structural information implied by this accumulation of emitters in the focal plane, we developed a segmentation scheme that aims to identify individual blobs (fig. S3). A marker-assisted watershed segmentation was adapted to accurately determine blob boundaries. For this purpose, we use the raw predictions from the deep CNN without convolution (fig. S3A). The foreground in this image is marked by regional maxima and pixels with very high density (i.e., those with I > 0.99 Imax; fig. S3B). Since blobs are characterized by surrounding pixels of considerably less density, the Euclidian distance transform is computed on the binary foreground markers. Background pixels (i.e., those pixels not belonging to any blobs) are expected to lie far away from any blob center, and thus, a good estimate for background markers are those pixels being furthest from any foreground pixel. We hence compute the watershed transform on the distance transform of foreground markers, and the resulting watershed lines depict background pixels (fig. S3C). Equipped with fore- and background markers (fig. S3D), we apply a marker-controlled watershed transform on the gradient of the input image (fig. S3E). The marker-controlled watershed imposes minima on marker pixels, preventing the formation of watershed lines across marker pixels. Therefore, the marker-controlled watershed accurately detects boundaries and blobs that might not have been previously marked as foreground (fig. S3F). Last, spurious blobs whose median- or mean intensity is below 10% of the maximum intensity are discarded, and each blob is assigned a unique label for further correspondence (fig. S3G). The area and centroid position are computed for each identified blob for further analysis. This automated segmentation scheme performs considerably better than other state-of-the-art algorithms for image segmentation because of the reliable identification of fore- and background markers accompanied by the watershed transform (note S1).

Centroid position, area, and eccentricity were computed. The eccentricity is computed by describing the blobs as an ellipseE=1a2/b2(3)where a and b are the short and long axes of the ellipse, respectively.

We chose to use a computational chromatin model, recently introduced by Qi and Zhang (19), to elucidate the origin of experimentally determined chromatin blobs. Each bead of the model covers a sequence length of 5 kb and is assigned 1 of 15 chromatin states to distinguish promoters, enhancers, quiescent chromatin, etc. Starting from the simulated polymer configurations, we consider monomers within a 200-nm-thick slab through the center of the simulated chromosome. To generate super-resolved images as those from Deep-PALM analysis, fluorescence intensity is ascribed to each monomer. Monomer positions are subsequently discretized on a grid with 13.5-nm spacing and convolved with a narrow point-spread function, which results in images closely resembling experimental Deep-PALM images of chromatin. Chromatin blobs were then be identified and characterized as on experimental data (Fig. 2, A and B). Mapping back the association of each bead to a blob (if any) allows us to analyze principles of blob formation and maintenance using the distance and the association strength between each pair of monomers, averaged over all 20,000 simulated polymer configurations.

The radial distribution function g(r) (also pair correlation function) is calculated (in two dimensions) by counting the number of blobs in an annulus of radius r and thickness dr. The result is normalized by the bulk density = n/A, with the total number of blobs n and, A, the area of the nucleus, and the area of the annulus, 2r drdn(r)=g(r)2rdr(4)

Super-resolved images of chromatin showed spatially distributed blobs of varying size, but the resolved structure is too dense for state-of-the-art single-particle tracking methods to track. Furthermore are highly dynamic structures, assembling and dissembling within one to two super-resolved frames (Fig. 3D), which makes a single-particle tracking approach unsuitable. Instead, we used a method for dynamics reconstruction of bulk macromolecules with dense labeling, optical flow. Optical flow builds on the computation of flow fields between two successive frames of an image series. The integration of these flow fields from super-resolution images results in trajectories displaying the local motion of bulk chromatin with temporal and high spatial resolution. Further, the trajectories are classified into various diffusion models, and parameters describing the underlying motion are computed (14). Here, we use the effective diffusion coefficient D (in units of m2/s), which reflects the magnitude of displacements between successive frames (the velocity of particles or monomers in the continuous limit) and the anomalous exponent (14). The anomalous exponent reflects whether the diffusion is free ( = 1, e.g., for noninteracting particles in solution), directed ( > 1, e.g., as the result from active processes), or hindered ( < 1, e.g., because of obstacles or an effective back-driving force). Furthermore, we compute the length of constraint Lc, which is defined as the SD of the trajectory positions with respect to its time-averaged position. Denoting R(t; R0), the trajectory at time t originating from R0, the expression reads Lc(R0) = var(R(t; R0))1/2, where var denotes the variance. The length of constraint is a measure of the length scale explored of the monomer during the observation period. A complementary measure is the confinement level (39), which computes the inverse of the variance of displacements within a sliding window of length : C / var(R(t; R0)), where the sliding window length is set to four frames (1.44 s). Larger values of C denote a more confined state than small ones.

The NND and the area, as well as the flow magnitude, were calculated and assigned to the blobs centroid position. To calculate the spatial correlation between parameters, the parameters were interpolated from the scattered centroid positions onto a regular grid spanning the entire nucleus. Because not every pixel in the original super-resolved images is assigned a parameter value, we chose an effective grid spacing of five pixels (67.5 nm) for the interpolated parameter maps. After interpolation, the spatial correlation was computed between parameter pairs: Let r = (x, y)T denote a position on a regular two-dimensional grid and f(r, t) and g(r, t) two scalar fields with mean zero and variance one, at time t on that grid. The time series of parameter fields consist of N time points. The spatial cross-correlation between the fields f and g, which lie a lag time apart, is then calculated asC(,)=1Ntx,yf(r,t)g(r+,t+)x,yf(r,t)g(r,t+)(5)where the space lag is a two-dimensional vector = (x, y)T. The sums in the numerator and denominator are taken over the spatial dimensions; the first sum is taken over time. The average is thus taken over all time points that are compliant with time lag . Subsequently, the radial average in space is taken over the correlation, thus effectively calculating the spatial correlation C(, ) over the space lag =x2+y2. If f = g, then the spatial autocorrelation is computed.

We denote as global parameters those that reflect the structural and dynamic behavior of chromatin spatially resolved in a time-averaged manner. Examples involve the diffusion constant, the anomalous exponent, the length of constraint, but also time-averaged NND maps, etc. (fig. S8). Those parameters are useful to determine time-universal characteristics. The spatial correlation between those parameters is equivalent to the expression given for temporally varying parameters when the temporal dimension is omitted, effectively resulting in a correlation curve C().

The distance from the periphery, intensity, their NND, area, flow magnitude, and confinement level of each identified blob form the six-dimensionalinput feature space for t-SNE analysis. The parameters for each blob (n = 3,260,232; divided into subsets of approximately 10,000) were z-transformed before the t-SNE analysis. The t-SNE analysis was performed using MATLAB and the Statistics and Machine Learning Toolbox (Release 2017b; The MathWorks Inc., Natick, MA, USA) with the Barnes-Hut approximation. The algorithm was tested using different distance metrics and perplexity values and showed robust results within the examined ranges (note S3 and fig. S10).

Acknowledgments: We acknowledge support from the Ple Scientifique de Modlisation Numrique, ENS de Lyon for providing computational resources. We thank B. Zhang (Massachusetts Institute of Technology) for providing data of simulated chromosomes and S. Kocanova (LBME, CBI-CNRS; University of Toulouse) for providing PALM videos for fixed cells. We thank H. Babcock (Harvard University), A. Seeber (Harvard University), and M. Tamm (Moscow State University) for valuable feedback on the manuscript. Funding: This publication is based upon work from COST Action CA18127, supported by COST (European Cooperation in Science and Technology). This work is supported by Agence Nationale de la Recherche (ANR) ANDY and Sinfonie grants. Author contributions: H.A.S. designed and supervised the project. R.B. designed the data analysis and wrote the code. H.A.S. carried out experimental work. R.B. carried out the data analysis. H.A.S. and R.B. interpreted results. H.A.S., R.B., and K.B. wrote the manuscript. Competing interests: The authors declare that they have no competing interests. Data and materials availability: All data needed to evaluate the conclusions in the paper are present in the paper and/or the Supplementary Materials. Additional data related to this paper may be requested from the authors.

View original post here:
Coupling chromatin structure and dynamics by live super-resolution imaging - Science Advances

The antiviral drug remdesivir has been approved for emergency use among hospitalized COVID-19 patients, and in recent studies, has shown promise as a treatment for the pandemic disease.

How exactly does remdesivir counter SARS-CoV-2 -- the coronavirus strain responsible for COVID-19?

With hat tips to virologist Jan Carette, PhD, geneticist Judith Frydman, PhD, and infectious-disease expert Bob Shafer, MD, let's follow the coronavirus downstream as it courses through its agenda within the infected cell.

Toward the end, we'll zero in on one of the virus's several Achilles heels, and we'll see how remdesivir could help -- and alas, why it may not be able to save the day on its own.

Previously, I tracked the novel coronavirus's invasion of a susceptible cell. When we left off, SARS-CoV-2 had come riding into the cell like a Lilliputian aquanaut, stealthily stowed inside a little membrane-bound bubble called an endosome.

Within that endosome, the virus remains clad in its own membrane coat, or envelope, which (when things go right for the virus) fuses with the membrane of the surrounding endosome. The viral envelope's contents spill into the (relatively) vast surrounding cellular ocean, or cytosol, that occupies the space between the cell's nucleus and its outer membrane.

Chief among those contents is the virus's genome, which wriggles out of its self-imposed prison to pursue its destiny: It aspires to generate thousands of identical progeny that will eventually burst out through the cell's enclosing membrane and fan out to infect more cells.

That lonely single strand of RNA that is the virus's genome has a big job to do -- two, in fact, Frydman and Carette told me -- in order to bootstrap itself into parenting a pack of progeny. For one thing, it must replicate itself in entirety and in bulk, with each copy the potential seed of a new viral particle. For another, it must generate multiple partial copies of itself -- sawed-off snippets that serve as instruction guides telling the cell's protein-making machines, called ribosomes, how to manufacture the virus's more than two dozen proteins.

To do both of those things, the virus needs its own special kind of polymerase: a protein that acts as a copy machine for genetic material. Every living cell uses polymerases to copy its DNA-based genome, as well as to transcribe the resident genes along that genome into RNA-based instructions that ribosomes can read.

The SARS-CoV-2 genome, unlike ours, is made of RNA, so it's already ribosome-friendly; but replicating itself means making RNA copies of RNA. Our cells never need to do this, and they lack polymerases that can.

SARS-CoV-2's genome, though, does carry a gene coding for an RNA-to-RNA polymerase. If that lone RNA strand can find and latch onto a ribosome, the latter can translate the viral polymerase's genetic blueprint into a working polymerase. Fortunately for the virus, there can be as many as 10 million ribosomes in a single cell.

Once made, the viral polymerase whirls into action, cranking out not only multiple copies of the full-length viral genome -- replication -- but also smaller sections, representing individual viral genes or groups of them. These smaller sections can clamber aboard ribosomes and command that they produce all of the proteins needed to assemble numerous new viral offspring.

This repertoire of newly created proteins includes, notably, more polymerase molecules. Each copy of the SARS-CoV-2 genome can be fed repeatedly through prolific polymerase molecules, generating myriad faithful reproductions of the initial RNA strand.

Well, mostly faithful. We all make mistakes, and the viral polymerase is no exception; actually it's pretty sloppy as polymerases go -- much more so than our own cells' polymerases, Carette and Frydman told me. So the copies of the initial viral genome -- and their copies -- are at risk of being riddled with copying errors, aka mutations.

However, coronavirus polymerases, including SARS-CoV-2's, come uniquely equipped with a sidekick "proofreader protein" that catches most of those errors. It chops out the wrongly inserted chemical component and gives the polymerase another, generally successful, stab at inserting the proper chemical unit into the growing RNA sequence.

Here's where remdesivir could become important. It belongs to a class of antiviral drugs that work by posing as legitimate chemical building blocks of a DNA or RNA sequence. These poseurs get themselves stitched into the nascent strand and gum things up so badly that the polymerase stalls out or produces a defective product. Remdesivir has the virtue of not messing up our cells' own polymerases, said Shafer, who maintains a continuously updated database of results from trials of drugs targeting SARS-CoV-2.

"Now the virus is making a lot of rotten genomes that poison the viral replication process," Frydman told me. If its progeny are defective and unable to bust out and invade other cells throughout the body, the virus's mission is defeated -- and the patient gets better.

But while remdesivir is pretty good -- better than many other antivirals, anyway -- at faking out the viral polymerase's companion proofreader protein, it's far from perfect, Shafer said. Some intact viral-genome copies may still manage to get made, escape from the cell, and infect other cells -- mission accomplished.

Using remdesivir in combination with some still-sought, as-yet-undiscovered drug that could block the proofreader could turn out to be a more surefire strategy than remdesivir alone.

Barring that, it may well be that the most lethal aspect of SARS-CoV-2 is our own immune response to it.

Stay tuned.

Image of SARS-CoV-2 emerging from the surface of cells cultured in the lab, courtesy of National Institute of Allergy and Infectious Diseases-Rocky Mountain Laboratories, NIH

Link:
How remdesivir works, and why it's not the ultimate coronavirus killer - Scope

The first reported case of COVID-19 was 13 March 2020 in Kenya and 10 weeks later, not a single genome is available publicly from any of the East African Community countries (Kenya, Tanzania, Burundi, Uganda, Rwanda, South Sudan). Why is it so? And why does it matter? Globally the main focus during this outbreak has been rapid COVID testing and not whole-genome sequencing. The team at Nextstrain has highlighted the utility of whole-genome sequencing in addition to rapid testing. We have presented below some of the challenges to obtaining whole genomes in East Africa and most importantly we have suggested a way forward.

If you would like to keep up to date with our content on coronavirus, you cansign up for our site here,where you can subscribe to our newsletters for free!

REGISTER NOW!

As a diagnostic, whole genomes are critical. Sequences confirm the identity of the disease-causing pathogen and can be further used for studying diversity, tracing movement of virus strains, designing models that can predict the disease spread and to better understand the enemy. A recent French study in bioRxiv has claimed the SARS-CoV-2 strain in France was not imported from China. This highlights the importance of a sequencing initiative to be able to properly trace the progress of the pandemic in every setting the Icelandic approach.

Real-time data are very important because they serve as a diagnostic test that guides quick patient management and decision-making from an epidemiological standpoint; and genomics would provide further tools in designing therapeutic approaches.

Over the years, millions of USD have been spent building genomic sequencing facilities in East Africa. In Kenya, Biosciences for east and central Africa (plant and animal) and KEMRIWellcome Trust (both Nairobi, Kenya) (human health) are partnerships with national governments and international funders but to date neither have delivered a genome.

In Uganda, the Uganda Virus Research Institute (UVRI; Entebbe, Uganda), is a centre of excellence in virus research with the human and infrastructural capacity and international support for genome sequencing. However, UVRI has also not yet delivered a single SARS-CoV-2 genome.

Tanzania has a different landscape. There are no large international sequencing facilities, but the national research organizations, universities and hospitals like Muhimbili National Hospital (Dar es Salaam, Tanzania) and the Sokoine University of Agriculture (SUA; Morogoro, Tanzania) have various platforms such as the Illumina (CA, USA) MiSeq, HiSeq and the Oxford Nanopore MinION. They too have not yet generated any SARS-CoV-2 genomes.

So why have none of these institutions with the sequencing infrastructure and support in Kenya, Tanzania and Uganda not delivered the much-needed SARS-CoV-2 genomes yet?

Taking the highest tech genomics tools to the farmers in East Africa

DNA sequencing in Africa is currently a laborious task requiring researchers to send data to a centralized sequencing lab in Kenya or to await results from overseas. Here, Laura Boykin tells her story of working with the Tanzanian Agricultural Research Institute.

For Kenya, the biggest hurdle is a lack of partnerships. So far, all the work on COVID-19 is handled solely by the Ministry of Health (MoH; Nairobi, Kenya). Accordingly, there has been no access to samples considering also that this disease is highly infectious and these samples need to be handled in biosafety level 4 labs. Due to poor partnerships (aka poor coordination), the work is largely being done in KEMRI and private medical labs such as Lancet. The other limitations are:

Power, computers, internet and PCR machines are not a challenge.

The sequencing capacity is there especially in research and academic institutes; the SUA has the Thermo Fisher Scientific (MA, USA) Ion Torrent that they use for foot and mouth disease and other animal research, the Kilimanjaro Clinical research Institute (KCRI, Moshi, Tanzania) has the Illumina MiSEQ (I have seen this personally) which they use for their tuberculosis research; the Government Chemist Laboratory Authority (Dar es Salaam, Tanzania) has a genetic analyzer and was able to acquire the Illumina HiSEQ, which they use for their forensic studies; the National Health Laboratory (Dar es Salaam, Tanzania) also has a genetic analyzer. There are two laboratories which are capable of sequencing using Oxford Nanopore Technologies (Oxford, UK). These are Muhimbili national hospital and the SUA in collaboration with the NHL. There were no funds to do the sequencing at the beginning of the outbreak but now the SUA has secured some funds to sequence, Muhimbili might get a donation to do so too. Another laboratory that is capable of sequencing but does not have the funds to do so is the KCRI. Capacity and skills are not a problem. However, in a government setting and in most institutes, employees are given specific tasks as per institute mandate. Its true that we have many people trained in sequencing, but some are outside government settings/employment and some of those who are in government employment are not in clinical research. For example, the cassava disease diagnostic team was focused on agricultural research. Some of the trained people are not trained to handle clinical samples. So clearly there is a disconnect between clinical and agricultural disease diagnostic techniques.

Another challenge is lack of local partnerships (internal collaborations among different institutes in Tanzania). There are no good networks that connect healthcare facilities with research and academic institutes. Most healthcare facilities do not have the critical mass of trained experts in sequencing and due to their mandates and the sheer heaviness of their routine workload, they rarely have the bandwidth to pursue research regularly. Herein comes the need to forge strong links between the two that would have been in prime position to address this pandemic. Unfortunately it has not been easy; from my personal experience there are a lot of territorial issues at play that are hard to overcome. Perhaps this pandemic might bring a change in mindset.

Another challenge is global but is felt more in countries like Tanzania; inadequate funding for R&D. While the government, through the Tanzania Commission for Science and Technology (COSTECH) and other institutes, provides for R&D funding, it is still limited especially when compared to the costs of running genomics experiments. External funding is always difficult especially for researchers who are not part of a consortium led by PIs from Europe and/or North America. This has helped establish centers but has meant that the moment funding runs out the lab is less active, the reagents and consumables run out and equipment ends up in disuse.

There appears to be a lack of awareness among policy makers and/or not enough initiative from the local scientists working in this field to inform our policy makers about the importance of whole genome sequencing for management of COVID-19. Since most sequencing initiatives in the country are led by foreign consortia (which we feel needs to change) led from either Europe or North America it is possible that the benefits from such projects are rarely seen by policy makers in Tanzania. We see there needs to be a clear link between the governments and local scientists to work on the same matters from different perspectives. We hope the donated research reagents to the African CDC will reach the institutes as soon as they arrive the airport without customs delays.

There is both human and infrastructural capacity in sequencing at UVRI and the Medical Research Council all based at Entebbe, Uganda. However, the COVID-19 genomes are not yet out in the public arena.

There are computers, access to internet, power and the supplies required to carry out PCR testing and analysis of coronavirus/COVID-19 infections, which were initially provided by the UVRI through its running projects and currently with the support of the government. However, more supplies would be needed to monitor the entry and spread of the virus in the communities.

As of today, it is the sole responsibility of the Ministry of Health (Kampala, Uganda) as the mandated institution of government to lead all COVID-19 pandemic-related issues. This includes checking for possible cases with suspected symptoms, isolation/quarantine, collecting samples, sample analysis and announcement of outcomes of testing and treatment. In addition, task forces were established to coordinate COVID-19-related issues at national, regional and district level. The laboratory analysis of the suspected COVID-19 samples is carried out by UVRI. Although there are other institutions with both human and infrastructural capacity in molecular biology and disease diagnostics, there are limited partnerships on widening the testing for COVID-19 in the country to involve the private sector. This may be partly due to the highly infectious nature of the disease and the requirement to carry out the laboratory testing and analysis in a biosafety level 4 containment facility such as UVRI. However, there are some partnerships within the private sector in management of the disease.

Insight into SARS-CoV-2 genome spells good news for vaccine development

Infectious disease researchers have identified just five SARS-CoV-2 gene variants, suggesting a vaccine for COVID-19 could be highly effective.

This article is written by East African Scientists and international partners who have been working for years on collaborative research projects, including The Cassava Virus Action Project, around managing emerging plant virus disease pandemics using novel molecular diagnostics and genomics. The team was disheartened to watch COVID-19 arrive and spread in East African countries, where they have successfully partnered to build capacity in rapid plant virus diagnostics and genome sequencing using novel portable technologies such as the Oxford Nanopore MinION, which have not been put to good use in the fight against the pandemic.

Professor Elijah Ateka Molecular Biologist

Dr. Joseph Ndunguru Molecular Plant Pathologist

Dr. Daniel Maeda Molecular and Cellular Biologist (Health Focus)

Mr. Charles Kayuki Molecular Biologist

Dr. Peter Sseruwagi Molecular disease epidemiologist

Dr. Laura M. Boykin Computational Biologist

Here is the original post:
Where Are The SARS-CoV-2 Genomes From East Africa? - BioTechniques.com

Viruses may seem like cunning villains, purposefully mutating to increasingly deadlier forms to outwit their human hosts. In reality, a lot of what happens with a virus is completely random. This randomness can make figuring out where a virus came from, how it spreads and what makes it tick especially tricky. For SARS-CoV-2, the new virus that causes COVID-19, scientists are looking to its genome for answers to some of these questions.

Researchers were recently able to determine that New York City may have been the original epicenter of the U.S. epidemic and that those initial cases were likely imported from Europe. They can tell this by looking at the genome and its sequence and seeing how they are similar or different, explains Adam Lauring, M.D., Ph.D., associate professor of microbiology and immunology and infectious disease.

Armed with virus samples taken from people with COVID-19, virologists and epidemiologists create what is known as a phylogenetic tree. This viral family tree lines up the genetic codes from each sample of virus to see whos related to whom.

Based on the genetic sequences and time of collection, you can start to paint a picture of how the virus moves through a population. The earliest [virus samples] in New York were more similar to the ones from people in Europe who were infected. You start with the dates, then look at the sequences and figure thats the most likely scenario, says Lauring. Its not foolproof, though. Theres always uncertainty.

A real world example of this uncertainty came to light with a study posted online in April, which described the deaths of two people from COVID-19 in Santa Clara, California weeks earlier than the virus was thought to be in California. What this tells us is that theres definitely missing data, says Lauring. This begs the question, he says, of where did those cases came from and how long the virus was spreading before the outbreak was recognized.

SEE ALSO: Seeking Medical Care During COVID-19

Researchers are also looking at the SARS-CoV-2 genome for clues about its true origin: the animal that infected the first person. So far, bats appear to be the most likely suspect. Looking at the phylogenetic tree, we see that a bat coronavirus is the closest relative to SARS-CoV-2, sharing around 96% of their genomes, says Lauring. But that too, is not the full story. Another animal, a small, scaly-skinned mammal called a pangolin, has been implicated as well.

The spike protein in SARS-CoV-2, the main protein on the surface that binds to the cells receptor and how the virus gets into the cell, is similar to a pangolin coronavirus spike protein, says Lauring. Its almost like, when you tell a person he has his fathers nose. That feature is similar, but across features the father and child may not look very similar. Coronaviruses, like a lot of other viruses, swap genes around.

These swaps are examples of mutations, which are common in RNA viruses like SARS-CoV-2. Laurings lab focuses on mutations in influenza, the RNA virus behind the infamous 1918 Spanish flu pandemic. Understanding how influenza mutates is critical for making decisions about the annual influenza vaccine. RNA viruses mutate relatively quickly because they lack a proofreading mechanism to look for and repair errors during replication.

MORE FROM THE LAB: Subscribe to our weekly newsletter

However, SARS-CoV-2 and its coronavirus cousins are unique among RNA viruses, because they have a proofreading enzyme. The coronavirus genomes are three times longer than youd expect them to be, and the presence of the proofreading enzyme explains that nicely, says Katherine Spindler, Ph.D., professor in the department of microbiology and immunology. Spindler is a host for the podcast This Week in Virology, which examines the latest science around SARS-CoV-2 and other viruses.

With this enzyme, the virus can make a few more errors and not have it be lethal for the virus. As a result, SARS-CoV-2 mutates more slowly than other RNA viruses. Spindler notes that only about 20 mutations have been retained in the genome so far since the beginning of 2020, despite the billions of times the virus has replicated.

SEE ALSO: Keeping Our Patients Safe During COVID-19

Even with its relatively slow mutation rate, mutations present in each persons SARS-CoV-2 genome allows researchers to do genetic tracing in real time, says Lauring. His lab hopes to study the virus genome more closely to look at how the virus is transmitted in healthcare settings and communities.

He stresses that just because a virus mutates doesnt mean the mutations are making it stronger, more likely to be transmitted, or that it will be tougher to develop a vaccine. My hunch is evolution wont be the biggest challenge in developing a vaccine. There are viruses that evolve relatively quickly for which we do have vaccines, for example polio, measles, mumps, Ebola, hepatitis A, notes Lauring.

Spindler adds that the fact that were seeing a variety of COVID-19 symptoms doesnt mean there are different mutant strains. Every new symptom that comes along, from COVID toes and skin rashes to blood clots, are likely just additional manifestations of the virus as it infects so many different people, she says. Figuring out the mysteries of SARS-CoV-2 will take years of experimental work, she says.

Like Podcasts? Add the Michigan Medicine News Breakto your Alexa-enabled device orsubscribe for updates oniTunes,Google PlayandStitcher.

More:
What the SARS-CoV-2 Genome Reveals - Michigan Medicine

The discovery of a huge number of long non-protein coding RNAs, aka lncRNAs, inthe mammalian genome was a major surprise of the recent large-scale genomics projects. Aninternational team including a bioinformatician from the Research Center of Biotechnology of the Russian Academy of Sciences, and the Moscow Institute of Physics and Technology has developed areliablemethodfor assessing therole of such RNAs. Thenew technique and the data obtained with it allow generating important hypotheses on how chromatin is composed and regulated, aswell as identifying the specific functions of lncRNAs.

Presented inNature Communications, the technology is called RADICL-seq and enables comprehensive mapping of each RNA, captured while interacting with all thegenomic regions that it targets, where many RNAs are likely to be important forgenome regulation and structure maintenance.RNA and gene regulationIt was previously believed that RNA functions mostly as an intermediary in building proteins based on a DNA template, with very rare exceptions such as ribosomal RNAs. However, with the development of genomic analysis, it turned out that not all DNA regions encode RNA, and not all transcribed RNA encodes proteins.

Although the number of noncoding RNAs and those that encode proteins is about the same, the function of most noncoding RNA is still not entirely clear.

Every type of cell has its own set of active genes, resulting in the production ofspecific proteins. This makes a brain cell different from a blood cell of the same organism despite both sharing the same DNA. Scientists are now coming to theconclusion that RNA is one of the factors that determine which genes are expressed, or active.

Long noncoding RNAs are known to interact with chromatin DNA tightly packaged with proteins. Chromatin has the ability to change its conformation, or shape, so that certain genes are either exposed for transcription or concealed. Long noncoding RNAs contribute to this conformation change and the resulting change in gene activity by interacting with certain chromatin regions. To understand the regulatory potential of RNA in addition to it being a template for protein synthesis it is important to know which chromatin region any given RNA interacts with.

How it works

RNAs interact with chromatin inside the cell nucleus by binding tochromatin-associated proteins that fold a DNA molecule. There are several technologies that can map such RNA-chromatin interactions. However, all of them have significant limitations. They tend to miss interactions, or require a lot of input material, or disrupt the nuclear structure.

Toaddress these shortcomings, a RIKEN-led team has presented a new method: RNA and DNA Interacting Complexes Ligated and Sequenced, or RADICL-seq for short. The technique produces more accurate results and keeps the cells intact upuntil theRNA-chromatin contacts are ligated.

The main idea of the RADICL-seq method is the following. First, the RNA is crosslinked to proteins located close to it in the nucleus of cells with formaldehyde. Then, DNA is cut into pieces by digesting it with a special protein. After that, thetechnology employs RNaseH treatment to reduce ribosomal RNA content, thus increasing the accuracy of the result. Then, by using a bridge adapter (amolecule with single-stranded and double-stranded ends) the proximal DNA and RNA are ligated. After the reversal of crosslinks, the RNA-adapter-DNA chimera is converted to double-stranded DNA for sequencing, revealing the sequence of the ligated RNA and DNA.

Decoding the noncoding

Incomparison with other existing methods, RADICL-seq mapped RNA-chromatin interactions with a higher accuracy. Moreover, the superior resolution ofthetechnology allowed the team to detect chromatin interactions not only with thenoncoding but also with the coding RNAs, including those found far from their transcription locus. The research confirmed that long noncoding RNAs play animportant role in the regulation of gene expression occurring at a considerable distance from the regulated gene.

This technology can also be used to study cell type-specific RNA-chromatin interactions. The scientists proved it by looking at two noncoding RNAs in a mouse cell, one of them possibly associated with schizophrenia. They found that aninteraction pattern between chromatin and those RNAs in two different cells theembryonic stem cell and the oligodendrocyte progenitor cell correlated with preferential gene expression in those cell types.

The new methods flexibility means scientists can gather additional biological information by modifying the experiment. In particular, this technology can make it possible to identify direct RNA-DNA interactions not mediated by chromatin proteins. The analysis performed by bioinformaticians from the Research Center ofBiotechnology and MIPT showed that not only the standard double helix interactions between DNA and RNA but also those involving RNA-DNA triplexes could participate in gene regulation. Also, such interactions highlight the significance of noncoding RNA in protein targeting to particular gene loci.

We are planning to conduct further research on the role of RNA in the regulation ofgene expression, chromatin remodeling, and ultimately, cell identity. Hopefully, we will be able to regulate genes by using these noncoding RNAs in the near future. This can be especially helpful for treating diseases, saysYulia Medvedeva, who leads the Regulatory Transcriptomics and Epigenomics group at the Research Center of Biotechnology, RAS, and heads the Lab of Bioinformatics for Cell Technologies at MIPT. She also manages the grant project supported by the Russian Science Foundation, which co-funded the study.

Reference:Bonetti, A., Agostini, F., Suzuki, A.M. et al. RADICL-seq identifies general and cell typespecific principles of genome-wide RNA-chromatin interactions. Nat Commun 11, 1018 (2020). https://doi.org/10.1038/s41467-020-14337-6.

This article has been republished from the following materials. Note: material may have been edited for length and content. For further information, please contact the cited source.

Read more:
A Method for Assessing the Role of Long Non-protein Coding RNAs - Technology Networks

The 15th Annual Endangered Species Day sees more than 31,000 species around the world threatened with extinction, according to the IUCN Red List. That is almost one third of the groups of animals listed on their website.

Researchers are now using a vast remote database to help protect endangered species. This genomic library allows the team to access vital datasets more efficiently than ever before, thanks to a collaboration between the University of Sydney and Amazon Web Services (AWS).

Were often working with more than a billion pieces of jigsaw puzzle and no guide, says senior research manager Dr Carolyn Hogg. The software now helps condense the scientists work enormously, enabling them to analyse massive amounts of data in minutes rather than hours - regardless of where they are in the world.

In the long term, the researchers aim to share this genome data publicly. The ultimate goal would be to create a universal genomic library and tools that other researchers and conservation managers can access in order to make science-based decisions, adds Dr Hogg.

Go here to see the original:
Endangered species could be saved with this tech-based solution - Euronews