Archive for the ‘Applied Sciences’ Category

Understanding SARS-CoV-2 and COVID19

Monday, September 14th, 2020
Image Source: Ann Kiernan for “The Washington Post”, June 18, 2020

Here we go: another blog post on the coronavirus pandemia that is ongoing globally. The race to a vaccine continues (will discuss a little about that below), however this post will be focused on the virus that caused the disease COVID19 (Coronavirus Disease 2019), named SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2), its biology, complexity, how changes in its genetic material could make harder to develop vaccines against it, the latest reports on tropism to specific human cells and organs and how the outlook for the near future looks like. In addition, I will discuss cases being reported of secondary infections in the same person and people that was “cured” from a first infection developing complex syndromes (especially children) and long-term neurological problems in older people. This pandemia is ongoing for more than 6 months, and I am very happy with how the scientific community is collaborating worldwide (collaboration in science is key, totally opposite to the system we were used to before) accelerating our understanding on the invisible enemy we are dealing with. Unfortunately, it is still not enough to eliminate it yet, but we are on the right track.

Biology of the Virus

What is the best way to understand a virus and its biology? First, we need to isolate the virus from patients and sequence its genetic material. With this information, we can use the databases available to scientists to compare its sequence and even identify how it is evolving comparing different strains in different places of the globe. The second thing to do is to study how the virus “attacks” the host (yes, us, humans). The good news are that both information is getting out fast with several scientists studying both topics very deeply. There is already a catalogue of SARS-CoV-2 mutations available and comparisons to see which genetic changes facilitate the infection and how it will affect the disease course (for more information check the article describing it here). To date, more than 100,000 isolates have been sequenced and made public ( Two SARS-CoV-2 viruses collected from anywhere in the world differ by an average of just 10 genetic letters out of 30,000 (the virus genome has 30 Kilobases or 30,000 bases) that could confer evolutionary advantages. Based on these studies, it is a possibility that the virus will acquire mutations that could change its susceptibility to antibodies and immunity affecting treatment and vaccination. The second way to understand the disease is to analyze the the tropism of the virus when it enters the human body. Tropism is which cells it binds to and in which organs it affects when inside the body. A recent report just released from a group that evaluated thousands of cell types (a type of “coronavirus cell atlas”) and organs from patients infected identified that the virus enters our respiratory system, however it has tropism to several other cell types and organs – see the Figure below. The idea here is that all these cell types in different organs in the human body have a protein (lock) that binds to the virus “spike” protein (key). When the key unlocks that lock the virus enters the cell and multiply, killing it and causing all the signs and symptoms that we see in the disease. Based on this study, we can tell how complex is the spread of the virus in the human body and why each person has a different reaction to the disease.

Source: Figure from article entitled “A single-cell RNA expression map of human coronavirus entry factors” published in the journal “Cell Reports”

Re-infection Cases

Another problem that worries the research community, especially for a successful vaccine to work, is the recent reports of cases of re-infection with the virus. Most of these are probably re-infection with other strains, very similar to the common cold or flu virus that we can get it more than once in a year, for example. The first report was in Hong Kong (see article here) and now we see a lot of reports with cases of re-infection. Most people who are infected with the coronavirus produce detectable antibodies that would be expected to protect against a second infection by the virus. Even people who had only mild symptoms may also have immune “memory” that prevent symptoms on a second exposure. It is clear now that is not the case. Even though it is early to make conclusions, this could impact vaccination when a vaccine is ready.

Post-COVID19 Syndrome

The last important issue that have been reported since April of this year when the spread of the virus started and now it is much clearer is that people considered cured developed neurological problems and other signs and symptoms that persist until today. Remember (check the Figure above) that the virus infects cells from the brain and the nervous system, so neurological problems would be expected. For the sickest patients, infection with the new coronavirus is proving to be a full-body assault, causing damage well beyond the lungs. And even after patients who become severely ill have recovered and cleared the virus, physicians have begun seeing evidence of the infection’s lingering effects (check the article for more information here). Another worrying post-coronavirus effect that has been reported is a mysterious, new disease called multisystem inflammatory syndrome in children (MIS-C, and also known as pediatric multisystem inflammatory syndrome or PIMS). It has affected hundreds of children around the world since it was first discovered earlier this year. Other syndromes have been reported everywhere now and that is concerning. What is causing these post-COVID19 syndromes? Why in children? We still do not have the answers to these questions. Let’s hope the scientists can uncover this mystery.

Updates on the Vaccine Race

Finally, let me discuss a bit about the “pause” that the AstraZeneca/Oxford University vaccine had last week because of a severe side-effect in one patient that had inflammation in the central nervous system. First, that is common to happen, especially when you are dealing with a fast-track vaccine trials and with people with different genetic backgrounds. Second, the “pause” was important to show to the world that this vaccine is trustworthy since the researchers from both places coordinating it are using the best scientific guidelines with very strict rules (trust is important!). Third, side-effects will happen, the severity of them that will be key for a successful vaccine. Finally, the vaccine race continues and I just read that AstraZeneca and the University of Oxford is going forward with their trial after the “pause”.

Final remarks

All the information I just discussed here is just the tip of the iceberg on the complexity of this virus and how it infects humans. We are starting to understand several processes on how the virus infects human cells, which cells and organs have the tropism for it and how people with different genetic backgrounds from different places react to it. Post-COVID19 effects are getting clear (it happens) but we still have lots of WHYs to focus on right now. I always finalize my posts with some advices: the best thing to do now is still social isolation, take the measures to avoid getting infected and stay mentally sane. I confess that I am already having mental issues (don’t leave the house for almost 4 months!). Stay strong. We will overcome this crazy pandemia. And let’s thank the scientists and healthcare professionals everywhere that are making it possible to gather all the information we have to date on this disease. A brighter future is closer… I hope!

Big Data analytics – the future of healthcare?

Tuesday, July 2nd, 2013

With the cost of mapping an individual human genome poised to break several financial barriers, bringing personalized medicine closer to reality, the healthcare and life sciences industries are now grappling with managing the explosive growth of data and information. Big Data is a buzzword, or a catch-phrase, used to describe a massive volume of both structured and unstructured information that is so large that it’s difficult to process using traditional databases and software techniques. Life Sciences and Biomedicine have been highly affected by the generation of large data sets, specifically by overloads of genomics information. Applying downstream analytics in a volatile data environment, overseeing data storage and movement, and transforming the data to improve patient outcomes and quality of life are just some of the challenges faced today in this field. In this regard, more sophisticated, innovative and robust information technology is being developed to aggregate, manage, analyze and share Big Data. In order to deal with this overload of information in life sciences, the Obama Administration launched a U$200 million Project in 2012 named “Big Data Research and Development Initiative”, which aims to transform the use of Big Data for scientific discovery and biomedical research, among other areas. The White House claimed in a statement that in the same way that past Federal investments in Information Technology Research and Development have led to dramatic advances in supercomputing and the creation of the web, this initiative will transform our ability to use Big Data for scientific discovery, environmental and biomedical research, education, and national security. It is indeed critical to collaborate and use tools to facilitate the technology ecosystem to develop innovative solutions to seemingly intractable problems emerging in healthcare today. This is mainly because Big Data presents a challenge that is so big and so complex that no single individual, company or institution – no matter how accomplished or illustrious – can solve it alone. Importantly, biomedical infrastructure for Big Data analytics lags behind the curve and new solutions both in hardware and software will be necessary to overcome the obstacles. Big Data in Biomedicine can pave the way in healthcare to a better understanding of people’s health and disease, especially now that mobile devices such as tablets, phones, watches and others have been implemented to collect an individual’s health information. I believe that the methods used by Facebook, Twitter, Google and other big corporations (such as commodity hardware, open source software, and ubiquitous instrumentation) to deal with big chucks of information will prove just as revolutionary for healthcare as they have for communications and retail. This new revolution could mean changes in clinical care, however challenges such as privacy of the information are a big barrier. Solutions to deal with privacy and security have been developed recently but this field is in its infancy, opening up opportunities for new ideas and technological breakthroughs. It is an exciting time now that both Information Technology and Biomedicine are converging in the Big Data era. A lot of interesting developments will happen in the next five years or so and we will need several Big Data solutions to deal with health information.


Can Microbes Help Us Loose Weight?

Sunday, March 31st, 2013

Gut Microbes may be key players in the weight battle, according to new studies. In people, microbial cells outnumber the human ones in several orders of magnitude, and recent studies reflect a growing awareness of the crucial role played by trillions of bacteria and other microorganisms that live in a specific ecosystem in the gut. Perturbations in this environment can have profound and sometimes devastating effects for the host. Microbiome, which is the totality of microbes, their genetic elements (genomes), and environmental interactions in a defined environment, have been a subject of research since they may be able to explain some complex diseases opening new opportunities for drug development and therapies. Studies mainly funded by the National Institutes of Health (NIH) in the United States for the Human Microbiome Project (HMP) demonstrate important correlations between the microbiome and human health and disease. These projects will leverage advances made by the HMP’s large scale sequencing efforts, with the advancement of new tools and technology to examine the relationship between changes in the human microbiome and diseases of interest. Fifteen Projects studying the relationship of microbiomes with cancer, autoimmune diseases and other factors are ongoing (for more information see NIH Human Microbiome Project’s Webpage). In one of such studies, the results obtained suggest that the specific effects of gastric bypass surgery (generally used to decrease the size of the stomach in obese people, so they can loose weight) on the microbiota contribute to its ability to cause weight loss and that finding ways to manipulate microbial populations to mimic those effects could become a valuable new tool to address obesity (see more in the article “Gut Microbes could help us loose weight” by Emily Singer at the MIT Technology Review). Previous studies with people and mice have found that the nature of microbes in the intestines changes after gastric bypass, with some groups growing more prominent and others decreasing in number. However, nobody was able to demonstrate whether the altered microbial composition was merely a side effect of the bypass surgery, or whether shifting bacterial populations could help people lose weight. In order to address this question, Kaplan and colleagues used a diet rich in fat to feed mice and then performed either bypass or a “placebo” surgery on the animals. Mice in the bypass group lost around 30 percent of their body weight within three weeks of the procedure. But even before the mice dropped weight, those in the bypass group already had an altered mix of intestinal bacteria. In addition, the bypass mice had more of certain types of microbes called Gamma proteobacteria, particularly Escherichia species compared to the other group. Some species of Escherichia are pathogenic, but others help prevent inflammation and maintain intestinal health. Mice that did a bypass surgery also had more Akkermansia bacteria, which can feed cells in the intestines with mucus, particularly when the host is cutting calories (for more information check the scientific article “Conserved Shifts in the Gut Microbiota Due to Gastric Bypass Reduce Host Weight and Adiposity” by Liou et al). The group speculates that the microbes somehow trigger fat-burning changes in the host’s metabolism. The researchers are now testing the effects of altering levels of individual microbes, as well as some of the chemicals they produce to see the effects. For example, gastric bypass changed the ratio of molecules called short-chain fatty acids, which often serve as chemical signals. Depending on the results, scientists might be able to create a cocktail of weight-loss microbes. So the answer is yes, our little friends (the microbes), could be of some help for people that need to loose weight. Maybe specific microbiota “pills” will be produced in the future, so you could just “rebuild” your gut microbial population to avoid getting fat and sick. Who knows? Let’s wait and see… (Image Source: Science Clarified)


Welcome to the “narciss-omics” era

Saturday, April 28th, 2012

Everything started more than a decade ago, in 2001, when the first draft of a human genome was finished, published and made available for the whole scientific community through an array of bioinformatics tools. After this important milestone, a new field of study emerged named “omics”. The suffix -ome is generally used in molecular biology referring to a totality of some sort – in this case the total genome or sequence of bases of the DNA of an organism. The genomics field started before the human genome sequencing, since several organisms had their genomes sequenced; for example viruses and bacteria. Technology evolved fast since 2001 and now we are entering the “personalomics” era. The cost and time spent to sequence a human genome has dropped considerably, and today one genome can be sequenced in a few hours costing a few thousand dollars. A decade ago, the first human genome consumed millions of dollars from the government of the United States for years. These new advances in technology have enabled important studies in the “omics” field. The blog post today will discuss two recent studies that did whole genome sequencing applied to personalized medicine. Different methods can be used to generate not just whole genome sequencing of an individual but all sorts of measurements such as transcriptomics (all genes or RNAs expressed by the cells), metabolomics (all metabolites in the bloodstream of a person), imunogenomics (auto-antibodies from that individual) and so on. “Omics” studies mark the beginning of a new era of personalized medicine in which we will be able to track diseases before they are diagnosed. The first study discussed in this post was published on Science Translational Medicine and analyzed the “genometype” or the predictive capacity that a genome sequence has in detecting a disease using genome sequencing of a large number of monozygotic twins (to read more check the article “The Predictive Capacity of Personal Genome Sequencing”). In this case, just the genomes of twins were sequenced and the results of the study suggested that genetic testing will not be the determinant of patient care and will not substitute preventive medicine such as risk assessment based on family history, physical status and lifestyle. This study provides strong evidence that whole-genome sequence of individuals alone does not tell much, and a model of gene-environment interaction should be considered. For example, the future of personalized genomic medicine can be glimpsed in a second report published in the journal Cell in which Michael Snyder’s genomic sequence (who is also the lead author of the study) with the other “omics” were uncovered to give a read-out on his predisposition to disease, and his body’s response to viral infections and the onset of type 2 diabetes. As a proof-of-principle example of personalized genomic medicine, it is distinct from other studies because it applies whole-genome diagnostics to a healthy person rather than to individuals with disease, before the disease appears. Snyder, a geneticist at Stanford University School of Medicine in California, joins other researchers who have publicly aired their own genome sequence (others include J. Craig Venter, James Watson and celebrities such as Ozzy Osbourne from the rock band Black Sabbath). Snyder’s ‘Integrative Personal Omics Profile’ named iPOP, was created by merging his genomic sequence with RNA, protein, metabolic and auto-antibody profiles taken 20 times over a 2 year period (for more information see the article “Personal Omics Profiling Reveals Dynamic Molecular and Medical Phenotypes”). The results revealed Snyder to be genetically predisposed to type 2 diabetes, despite no family history or other risk factors. During the study, his blood glucose levels escalated following the second of two viral infections, and he was subsequently diagnosed with the disease. Snyder has since made drastic dietary and lifestyle changes to manage his blood sugar levels and the glucose levels went down showing the power of such study. However, there is a lot of criticism and skepticism about it. For example, Richard Gibbs of Baylor College of Medicine in Houston, Texas, has humorously dubbed it “the narciss-ome” or the beginning of the “narciss-omics” era according to a Nature magazine journalist (check the article “The rise of the narciss-ome”). The geneticist George Church of Harvard Medical School in Boston, Massachusetts says that a criticism of this paper is that it’s anecdotally about one person, but that’s also its strength since it shows an integrative “omics” in a timeframe of 2 years. Well, when comparing both studies (of course each one has its limitations) it is clear that “personalomics” should incorporate different measures with time since our bodies are constantly changing based on the environmental cues (diet, lifestyle, infections, etc…). The conclusion is that the sequence of the human genome is important; however since it is static, it is not enough to give us all answers. Genomic sequences should be integrated with other “omics” technologies to guide doctors in the new era of personalized medicine. Or should I say “narciss-omics” era? (Image credits: deviantART)

Genes, patents and arts – copyrights on our DNA?

Saturday, September 24th, 2011

This blog post is a mix of a scientific controversy with an artistic vision. There has been growing concern with the idea of patenting or “copyrighting” genes from human genomes. The debate has been on and off after the sequence of the first draft of the human genome in 2001. Recently, it came back again after the company Myriad Genetics won a case in court for the patents of both breast cancer genes BRCA1 and 2. And what does arts has to do with genes and “copyrights”? The first artist to depict the structure of the DNA was Salvador Dali, who included DNA spirals in his surreal, phantasmagoric paintings in the 1950s. Dali was ahead of his time as most artists living in Europe, especially in Paris (for more information see the article “The art of DNA – Back to bases” in The Economist). It took the publication of Dr Watson’s book, “The Double Helix”, in 1968, the emergence of biotechnology and the manipulation of genetic material or “genes” in the 1970s, to edge the DNA molecule towards the centre of the public gaze. Since then, many artists have followed in Dali’s wake. Well, paintings, masterpieces, books, images and every creation and invention is patentable. But can we say that a piece of our own self, our DNA, the molecule of life is a creation or invention? Since it is already in our cells, the answer is no. The claim that lawyers are using is that as soon as the piece of the DNA corresponding to a gene is taken out of the cells and manipulated by molecular biology it could be considered a creation. Could this be? To understand this issue better we need to define how the word patent applies to genetics. A gene patent is a patent on a specific gene sequence, its usage, and often its chemical composition. The problem is that there is a big debate over whether these patents advance technology by providing scientists with an incentive to create, or hinder research by creating a lot of barriers and licensing fees to utilize research that is patented. In the case of both BRCA1 and 2, the company that holds the patents provides genetic testing for women that has familial history of breast cancer. This helps to identify the carriers of mutations and improve preventive medicine. However, the discussion is why just one specific company can hold the rights to a specific test? Should this be opened to other companies to reach more people with lower prices? The answer is yes I believe, but the law for gene patenting went to the other direction some years ago. The comparison with arts is that the creation and invention such as paintings or machines can be patented since they were designed from “nothing”. In the case of genes, even after being manipulated, they were already in our DNA inside our cells. In a NYTimes article by Andrew Pollack some time ago (“Ruling Upholds Gene Patent in Cancer Test”), the controversy is cautiously discussed and the decision on the patentability of genes and DNA was well accepted by most of the biotechnology industry. The point is that thousands of human genes have been patented, and some biotechnology executives say such patents are essential for encouraging innovation. Is that the case? In my opinion, genes are not a creation or invention even if they were manipulated by molecular biology. On the other hand, the genetic test used to detect the mutation or the defect in the gene is an innovation and can be patented. The controversy still continues since even though the court maintained the patents of both BRCA 1 and 2 to Myriad Genetics, court appeals will probably happen. For now, it looks like genes are still patentable. But we never know what the future holds for such cases…

Genetic Tests: facts and fictions

Thursday, June 23rd, 2011

Are you more susceptible to developing cancer? Are you getting heart disease? Is obesity in your future? Your risk for many diseases and health conditions is just partly written in your genes. One day soon we will be able to visit our doctor and find out more about our health risks for the next years through genetic testing. But scientists (and I am included in this category) have many things to learn about genes before this becomes a reality. Genetic Testing regulation turned into a controversial topic after the FDA in the USA blocked some Over The Counter Predictive Tests and started paying more attention to this market. Several companies have been offering predictive genetic tests (examples are 23andme, Navigenics, Pathway Genomics, and others); however the tests they offer can be misleading in some cases. This is mainly because the environment plays a role in complex conditions. Genetic Tests for monogenic disorders such as Cystic Fibrosis, Huntington’s disease, etc are well established and reliable in most of the cases. In monogenic disorders, the affected individual will have a mutation or a genetic defect in a single gene or just a few making it easier to detect the underlying problem. In the case of predictive tests for complex diseases such as diabetes, cancer, arthritis, and others, several genes and the environment can affect the condition making it more difficult to get conclusions. I am not saying the consumer should avoid doing these tests; they just need to be careful and if some defect is detected they need to verify the veracity of it. Predictive Tests in some cases have a lot of support in the literature for the analyses, but in most of the cases there is no scientific evidence. Some say these tests are “recreational”. I think this is a start for an area that is not very explored yet. The companies offering these services have to mature and the beginning is always difficult. I believe that what needs to be done is a better explanation to the consumer on how these tests work, what they are really paying for and a better support after they get the results. Whole Genome sequencing companies such as Knome offer the sequencing of a person’s genome with a follow-up to explain the findings. In my opinion this is good; however there are a lot of regions in the genome that we do not understand yet. In fact, these companies are offering services coupled to research. The person that pays for whole genome sequencing will sign a consent form if he/she wants that the sequenced genome become public and available for research. Maybe that is a good way to better understand human genomes. In the case of genetic tests, the results could be a “Yes” or “No” answer but for most of them it will be a “Maybe”. This happens mainly because we are realizing that the environment has a big role in interacting with genes. In conclusion, the increasing need for regulation is a fact and there is still a lot of fiction in several of these tests that companies are offering (one example is the Genetic Tests for Sports Performance; well, genes are important, but the environment that can be exemplified by nutrition and training are also important factors). I believe we need to start somewhere and that is what is happening right now. Let’s see how the regulation will shape the genetic tests’ market from now on. I am curious…