Nature News Article: Machine learning spots treasure trove of elusive viruses

nature
Many viruses are difficult to study because they cannot be grown in the lab. Credit: Sebastian Kaulitzki/SPL/Getty for Nature.

An interesting news article was just published in Nature about how the emerging tool of artificial intelligence (AI) is making it easier for scientists to study viruses. The article,  written by science journalist Amy Maxmen, focuses on the difficulty of identifying the vast number of viruses within our bodies, as they are difficult to isolate or culture, and because we know so little about them that we don’t know what to even look for. To overcome this challenge, several computational scientists have applied artificial intelligence (AI) or machine learning approaches to sequencing the bulk of the microbiome (bacteria and viruses) that inhabits human tissues.  Given the complexity of this vast microbial ecosystem, AI approaches are showing great promise in decoding or identifying novel viruses among the sea of other sequences, most of which will be bacterial or host in origin. This could be an important direction in revealing important relationships or dynamics between viruses, bacteria, and human cells.

Viruses overall play a major role in human health and disease, from causing known conditions like the flu or HIV to potentially having an effect on the human microbiome and maybe even ME/CFS disease. Indeed, a recent review article in Clinical Science on the state of ME/CFS microbiome research pointed out that viruses that infect bacteria could alter the microbiome by transferring genes to these bacteria or by outright killing them, and that this could have a direct or indirect effect on human health. This makes the human virome an interesting topic in the context of ME/CFS, and an area that needs more study. Derya was quoted in the Nature article, and he speculated on the potential impact: “Biomedical researchers have long wondered whether viruses contribute to the symptoms of several elusive conditions, such as [ME/CFS] and inflammatory bowel disease. Derya Unutmaz, an immunologist at the Jackson Laboratory for Genomic Medicine in Farmington, Connecticut, speculates that viruses might trigger a destructive inflammatory reaction — or they might modify the behaviour of bacteria in a person’s microbiome, which in turn could destabilize metabolism and the immune system.”

To read the full Nature article, click here. 

ME/CFS Clinician Spotlight: Lucinda Bateman, M.D.

LB Photo
We are excited to present Dr. Lucinda (Cindy) Bateman as part of our “People in ME/CFS Research” spotlight series. Cindy is the Founder and Medical Director of the Bateman Horne Center (BHC), which is also the clinical core for the JAX ME/CFS CRC. At BHC, she cares for patients suffering from ME/CFS and Fibromyalgia, educates physicians and patients about these diseases, and develops clinical research projects with Dr. Suzanne Vernon. I recently called Cindy to ask about her journey through the ME/CFS field, and how BHC got it’s start – read on for the full interview!

Continue reading “ME/CFS Clinician Spotlight: Lucinda Bateman, M.D.”

Release of the NINDS Common Data Elements (CDEs) First Draft

ninds

The National Institute of Neurological Disorders and Stroke (NINDS) branch of the NIH has now released the first draft of the ME/CFS Common Data Elements (CDEs) to the public. The CDE Working Group recently had a public review period in January 2018, where the public could review and comment on the CDEs with their recommendations. After the review period, the Working Group reviewed all of the comments and published the final CDEs.

The purpose of reviewing and revising the ME/CFS CDEs was to standardize clinical and molecular data collection to aid in comparing the results across multiple studies. NINDS has asked that researchers who have been funded by the NIH use these CDEs in their research of ME/CFS whenever possible.

Click here to read the first draft of the Common Data Elements for ME/CFS on the NINDS website.

 

Scientist Spotlight: Julia Oh, Ph.D.

julia-oh

As part of  our “People in ME/CFS Research” spotlight series, I talked with Dr. Julia Oh, who  is an Assistant Professor in Microbiology at The Jackson Laboratory and the Associate Director of the JAX ME/CFS project, leading the microbiome project. Her lab investigates how our microbes contribute to our health by using diverse technologies like genomics, synthetic biology, and genome engineering to target and manipulate the microbiota. Here is her interesting background, and more about the very exciting research directions she focuses on involving the bacteria that we cohabit with in our bodies. Keep reading for the full interview!

Continue reading “Scientist Spotlight: Julia Oh, Ph.D.”

Site Visit by Connecticut Patients and Advocates to Jackson Laboratory

IMG_0443
Six local patients and advocates visited JAX to discuss ME/CFS. From right; Kathy Kushwara, Barbara Stillman, Pat McKenney, Cathy Jecture, Tim Hill, Diane Ryan, and program manager Courtney Gunter.

Derya and I were happy to meet with six local Connecticut representatives from the Fibromyalgia and Chronic Fatigue Syndrome Informational & Support Group on February 26, 2018. The group visited JAX so that they could learn more about the ME/CFS project and to tour the lab. They are a local group based in Litchfield, CT, and meet twice a month to provide information, support, and a sense of community to local patients who are suffering from Fibromyalgia and ME/CFS. They gave us valuable insight about the disease, plus some suggestions on how we can improve our community outreach efforts here at JAX.

Continue reading “Site Visit by Connecticut Patients and Advocates to Jackson Laboratory”

Approaches in Biomedical Research: Flow Cytometry, Part 2

Our first Flow Cytometry educational series was focused on understanding how flow cytometry works, the types of machines used, and how data is collected. In this second part in the series, we will go over some types of flow cytometry data and how that data is interpreted.

What are the different types of flow cytometry data that are collected?

In flow cytometry, there are a few types of light that are detected by the sensors during the data acquisition. The source of light (which is non-fluorescent) can create two different paths. The first is called Forward scatter (FSC), which is formed as laser light hits a cell, and is turned into a digital version that reflects the size of the cell (Figure 1). Second, this same laser light also causes Side scatter (SSC), which is a measure of the internal complexity of the cell. For example, if there are many granules in the cell, there will be a higher SSC than for a cell with little granularity. Together, this can be very informative for separating different cell types, which can be further combined with fluorescence data, discussed below.

FSC and SSC FigureFigure 1: Detecting size and granularity of the cells by using laser light.

Continue reading “Approaches in Biomedical Research: Flow Cytometry, Part 2”

Bateman Horne Center Panel Discussion of Unrest

Yesterday (February 7, 2018), the clinical core for The JAX ME/CFS CRC, Bateman Horne Center, held a screening of Unrest, followed by a panel discussion of the documentary. The panel discussion was shared via their Facebook page, and will also be posted to the BHC Youtube page.

The panel, which consisted of two married couples affected by ME/CFS, discussed the similarities they saw between Jen Brea’s portrayal of the disease and their own experiences. They talked about specific scenes that spoke the most to them, and how loved ones can remain engaged in caring for those who are suffering. They said that the film’s incredible intimacy has allowed people to relate to ME/CFS, and that the success of the documentary has started to lead to new conversations and engagement.

To watch the full BHC Facebook Live video, click here.

To watch Unrest, now available on Netflix, click here.