Tag: science

The ‘microscopic’ edition: recapping Genetic Engineering & Biotechnology News

So I mentioned earlier that a good portion of January became hectic, to the point that I didn’t get quite as much finished as originally planned.

This meant I was behind on my science news round-ups. I’m hoping that my schedule is back on track, and that it will become a weekly post (but definitely a biweekly post) starting again this week.

Since I missed a week, this week’s post is a combination of recaps of articles I’ve read over the past two weeks (I decided I would only recap 3 articles this week).

Currently I’ve just been reading and sharing articles from Genetic Engineering & Biotechnology News, though I may start at least reading news from other sites to share here as well. As I mentioned in my first post, their site is updated Monday-Friday with new articles, and if you subscribe to their site you can get their daily newsletter (which is what I do).

So again–this is going to be a fairly long post, probably somewhere between a ten and fifteen minute read.

The first article I want to recap is “Tomoplasma gondii linked to brain tumor”.

The protozoan, Toxoplasma gondii, is one of the world’s most common parasites and is the causative agent of Toxoplasmosis. It has been estimated that approximately 11% of the US population over the age of six has been infected at one point with Toxoplasma gondii.

Colored image of the Toxoplasma gondii protozoan (c)istockphotos credit: Dr_Microbe

We come into contact with Toxoplasma gondii, through either under cooked infected meats, infected cat feces (as cats are a host for the protozoan), or it is passed from mother to child during pregnancy.

After entering the human body, the protozoan forms cysts within various tissues including the skeletal tissue, the heart, brain, and eyes. Depending on how old a person is when they come into contact with Toxoplasma and the strength of their immune system, the cysts may remain throughout the individual’s lifetime.

Toxoplasma now been linked with Alzheimer’s and Parkinson’s diseases, epilepsy, and various cancers. One group of researchers decided to look to see if there could be a linnk between parasite infection/cyst formation and the possible risk of developing glioma brain tumors.

The researchers published their paper “Toxoplasma gondii infection and the risk of adult glioma in two prospective studies” in the International Journal of Cancer. I have not read teh paper–because it is behind a pay wall (hopefully it will be freely available at some point over the next year).

Their reasoning to look at brain cancer, is that the brain tissue is one of the tissues that hte parasite tends to favor in terms of cyst formation. Glioma, is a rare (but fatal) neurological cancer. It is the most common primary brain tumor, though it can occur at any age and part of the central nervous system where the glial cells are found.

Approximately 80% of malignant brain tumors are gliomas, with a very low five-year survival rate of only five percent.

The scientists were wanting to see if there was any correlation between having been exposed to the Toxoplasma parasite at some point in life and development of glioma tumors later in life.

The two groups that they looked at showed that there could be a possible correlation between infection with the parasite and development of glioma tumors. They stated though that a larger and more diverse number of cases were needed to to see if the findings (presence of antibodies against the surface antigens of the parasite) are reproducible.

If the findings are reproducible looking at larger and more diverse groups, then reducing exposure to the parasite could be an easy way to help prevent the development of these highly aggressive and lethal brain tumors. Though it does need to be stressed that exposure to Toxoplasma gondii isn’t the only possible cause for the development of the tumors.

The second article I read was “Dengue virus blocking antibody indentified”

Dengue fever is caused by a flavivirus, carried by mosquitoes, and infects somewhere between 50 and 100 million people per year. Therefore finding a treatment(s) or a vaccine is needed, and is something that scientists have been working on for some time.

3-D image of Dengue Virus. (c) Image created by Kateryna Kon stock.adobe.com

One of the major problems is that there are four different strains of the virus, and being infected with one strain (and building an immunity to it) doesn’t mean you’re protected from the other strains. In fact, it is just the opposite–building the immunity against one, actually makes you more vulnerable to infection from one of the other three strains.

The research group published their paper “Structural basis for antibody inhibition of flavivirus NS1-triggered endothelial dysfunction” in Science. Since I don’t remember if I have a password for the journal or not, I haven’t read the paper yet (it isn’t behind a pay wall per say, but you do need an account with the journal to read it).

It has been shown that the dengue virus has a specific protein (NS1 or non-structural protein 1) that it uses to attach to endothelial cells around organs. This protein helps weaken cellular membranes and allows the virus to enter the cells. The weakening of cellular membranes and movement of the virus may also lead to the rupture of blood vessels.

The research group found that an antibody that would physically block NS1 from being able to attach to other cells. Therefore helping to slow the spread of the virus. This is an important discovery, due to the fact the antibody is against the protein and not the coding sequence. This means that it should be effective against all four strains of the dengue virus (the physical structure of the NS1 protein should be similar enough for the antibody to recognize it).

If shown to be effective against all four strains of the dengue virus, and if it gets into (and through) clinical trials, it would mean that there is at least one possible treatment for dengue fever. It would also open the door to looking at other flavivirus diseases (such as Zika or West Niles) to see if an antibody against their surface binding proteins would also be effective or not.

The final article I want to recap is “Taurine enhances the microbiome’s resistance to future pathogens”

There has been a wealth of research done over the years that show our microbiome in our gut plays a role in just about every part of our day-to-day lives, and can be connected to numerous different diseases and conditions (though more research still needs to be done to show that the microbiome is playing a significant role whatever the disease or condition is).

So one of the problems when we develop a bacterial infection, is that the antibiotic treatment doesn’t just get rid of the bad bacteria, it also gets rid of some of the good bacteria in our gut. This is one reason, why now doctors suggest that you eat yogurt that is fortified with the ‘good’ bacteria to help recolonize your gut as you’re taking your antibiotics.

Therefore, a key area of research now in infectious disease is to find alternatives to antibiotics for treating bacterial infections–but hopefully not harm our native gut microbiome.

It has recently been shown that taurine (an amino sulfonic acid, it is derived from cysteine), which is found in foods such as meats, fish, and eggs could help enhance the protection of the gut by the native microbiome.

Taurine biosynthesis. Image (c) www.chm.bris.ac.uk/motm/taurine/taurineh.htm

Taurine is also a molecule that we can make ourselves from the amino acid cysteine (see above image). Taurine can be found in the brain, retina, muscle tissues, and in bile acids. The presence of taurine in the bile acids helps up digest fats and oils in our gut.

The group published their paper “Infection trains the host for microbiota-enhanced resistance to pathogens” in the journal Cell. Hopefully it will be freely available to read within a year.

When present in high enough concentration in the gut, it helps the microbes produce excess amounts of sulfides to prevent any cellular respiration from occurring in the gut. By helping to prevent cellular respiration, it helps to then prevent the colonization of invasive bacterial pathogens that rely on cellular respiration to replicate and invade neighboring cells/tissues.

Their research showed that even an small initial infection can be enough to induce taurine production (bile acids), which then led to the increase in population of certain bacterial species in the gut. If a second infection (same or similar bacteria) occurred, the microbiome was quicker to react. But treating the animal with an over the counter medication (one to say soothe an upset stomach, deal with diarrhea or even indigestion), was enough to actually allow the pathogenic bacteria to colonize the gut by removing sulfide producing bacteria in the gut.

This also shows that we should take into consideration our own microflora when taking over the counter medications–because you never know when you could possibly come down with food poisoning or some other bacterial infection.

So that wraps up this week’s Science News Round-Up. I could have covered quite a few more articles, but decided that three to four articles is a good number, especially if I can get a good variety in the articles. I think that going from protozoan parasites, to viruses, to bacteria was a good choice this week–it kept everything at the microscopic level (more or less).

Again, let me know what you think of the post–too much scientific jargon still? Is there something that you would like me to cover in more detail? Do you have a specific site you go to read science news on?

Image References:

Image of Toxoplasma gondii again is from istockphoto.com; image credit: Dr_microbe

Image of Dengue virus again is from stock.adobe.com; image credit: Kateryna Kon

Image of taurine biosynthesis is from the following site: www.chm.bris.ac.uk/motm/taurine/taurineh.htm

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Fishy Friday: Another pick from the New England Aquarium & Photography Challenge Day 40

Well this is probably going to be a shortish post mainly because while I have more photos of fish from the New England Aquarium that I will be sharing–the identification of the fish is taking quite a while (it’s hard when you type in a color and hope to see your fish within the first twenty or thirty photos).

Anyway today’s photo winner(s) are the garden eels.

Garden Eels

Garden eels are members of the subfamily Heterocongrinae within the conger eel family Congridae. These eels are found in the warmer oceans (mostly in the Indo-Pacific area, but also in the Caribbean & eastern Pacific).

They are small eels that live burrowed in on the sea floor. Since they live in groups, when they all poke their heads out—they look like plants in a garden—hence the common name: Garden eels. Their coloring varies between species, and the average length is about two feet (twenty four inches). There are also about thirty five different species in two different genera.

Unfortunately it is difficult to tell from the picture what color the garden eels were—but I’m pretty sure that they are the yellow garden eel (Heteroconger luteolus). But when they’re all out and bobbing at the same time—they do look like a garden of eels.



One goal is going to try to figure out what the different fish are in most of the photographs. This is for several reasons: 1–so that I can share them as more than just a pretty picture of a fish, and 2–so that I can also learn something new and share that as well.

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National Learn About Butterflies Day and Photography Challenge Day 25

So with these different random holidays, I’ve decided that I can also work them into the photography challenge either with newly taken pictures or newly shared pictures. The butterflies are falling into the second category–newly shared pictures.

One of the many butterflies at the Butterfly Garden in the Science Museum in Boston

So besides being π day, it is also National Learn About Butterflies Day (and since it is a random unofficial holiday—no one knows exactly who to credit with the day). Since spring and summer are (hopefully) right around the corner, mid-March seems like a good time to investigate the wonder and beauty that are butterflies.

Blue Butterfly at the Butterfly Garden.

One place that people can go to learn about butterflies are butterfly gardens. Most large cities have at least one major butterfly garden (and they’re usually associated with zoos or museums). I enjoyed the one at the Science Museum in Boston, and that is actually now a new goal—to see how many other butterfly gardens I can visit in different cities.

A couple of more butterflies…..

So what are some cool facts about butterflies?

  • There are over than 20,000 types of butterflies worldwide.
  • Their wingspans can range from 1/2 inch to 11 inches. So they range from fairly small to fairly large.
  • Some butterflies mimic the coloring of others to avoid being eaten (Viceroy butterflies mimic the monarch butterfly)
  • Adult butterflies can live from a week to nearly a year, depending on the species.
  • Many butterflies migrate over long distances.  The most well-known butterfly migration is the monarch butterfly. It winters in Mexico, and then heads to the northern US and southern Canada.

To help butterflies (and bees) out, one can plant different flowers in their garden, and even different herbs as well. To help the monarch butterfly out one can plant milkweed (it gives them their off taste that keeps predators from eating them). The best thing to do is to ensure that the garden has flowers throughout the seasons (spring, summer and fall). I’m going to be trying to get more flowers out into the yard this spring and summer to see what type of butterflies I can attract.

References: https://nationaldaycalendar.com/national-learn-about-butterflies-day-march-14/

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Photography Challenge Day 4: Looking at the machine

So I decided that the photography for today’s challenge was actually taken at work earlier today. We had our yearly maintenance done on the DNA sequencer and there was one little issue that was discovered:

There seems to be some crystallized polymer on the array

So we knew that the array was having some issues, but they were issues that we could (and will continue) working around. When the door to the array was opened, it turns out that two of the little capillaries are broke and are leaking polymer every time I run the machine. This blob is about a year’s build up of polymer.

The 3730 Sequencer

This is what the machine looks like. This is the toy that I get to play with on a daily basis, running Sanger DNA sequencing for the university and off campus customers.

If I’m still in the position next year, I will get to see the array get replaced, and I may even check on the stage of the polymer blob formation over the next couple of months as well.

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National Watermelon Day (A Day Late)

So yesterday was National Watermelon Day. When I think of summer—eating watermelon is one thing that pops into my mind. Eating it on the Fourth of July, fruit salads in the summer, and munching on it during the fall. These days I usually only eat it every so often (and only when I notice that one of the small cafes on campus is carrying it). I’m never sure how it would store frozen, and it always seemed silly trying to find a very small platter of it just for myself, when I wasn’t sure how often that week I’d be eating it.


Watermelons originated (and are still found) in southern and western Africa, and the domestication of the watermelon probably started between 5,000 and 6,000 years ago. As people started to travel in the area (merchant ships and then over land), the watermelon was introduced to areas such as Italy, Greece, and other countries around the Mediterranean Sea, then to China, and then further inland to Europe, and then as sea exploration grew more watermelon was introduced into other areas of the world: the Americas and Australia.

Did you know that there are three main subspecies of watermelon? The wild (which is still harvested today), the semi-wild, and then domesticated; and within the domesticated subspecies there are literately hundreds of different varieties of watermelon. Just within the Americas, we have over 300 different varieties of watermelon that are grown each year3.

The domesticated watermelons are grouped based on their characteristics, which can range from whether or not they have seeds (so seeded vs. seedless), size (petite or mini, and then normal), and then color (which is hard to distinguish in the store; but the colors can range from the normal pinkish-red to an orange or yellow color3).


Thanks to modern molecular genetics and sequencing, scientists have been investigating the nuclear1, and chlorplast2 genomes of the watermelon. It is now known that the watermelon has diploid genome and 11 chromosomes, and is predicted to have a little over 23,000 protein encoding genes1. The use of genomics will now allow for scientists to determine which disease resistant genes have been lost in different watermelon varieties and then figure out the variety to cross them to in order to regain that disease resistant gene.

Re-introduction of disease resistant genes into food crops is essential if we’re going to have enough food to feed a growing world population. Natural crossbreeding and hybridization will work, though it may be faster re-introducing the genes on plasmids and doing it through genetic modification.

So, I will probably do another post on why genetically modified foods aren’t bad—but will end this post with this note: As the population grows, and climate change gets worse we’re going to need crops that can withstand the new climate extremes—and modifying them in the lab/control fields is the way we’re going to have to go.

  1. Guo, et al. 2012 “The draft genome of watermelon (Citrullus lanatus) and resequencing of 20 diverse accessions”. Nature Genetics: 45(1) 51:60
  2. Shi, et al. 2017 “Full Chloroplast Genome Assembly of 11 Diverse Watermelon Accessions”. Frontiers in Genetics: 8(46) 1-4
  3. Watermelon.org



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Science as art……Photography Challenge Day 25

Well today’s picture is brought to you by an unknown entomology student.  The main part of the department is in a different building and next door to the entomology and plant pathology department. At least one of the entomology classes has an art project as part of the overall semester grade. Their wing wonderful to walk through as there are different drawings, paintings, and sculptures–over the next few months, I’ll take some pictures to share with you.

Found someone’s art project in our tree this afternoon.

Lately their art projects have slowly found their way into the biochemistry & molecular biology wing (mainly because there are numerous plants in the area leading to the entomology and plant pathology wings. They moved a large paper-mâché caterpillar into the wing a little over a year ago.

This spider is part of the latest additions to the crowd. There are also a couple of ants crawling around on some hibiscus plants, and then there is a praying mantis hidden within the leaves and branches of another small “tree”. Its the one thing I love seeing is how art and science can be combined–there are several fields where it is easy to do so (entomology is just one of the them).

I’m slowly trying to figure out ways of doing more art/crafts with my field of study–biochemistry and molecular biology, that are also within the crafts that I know how to do (or decide to learn). Maybe the next afghan will have more scientific symbols on it????

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Settling into the job

So I’m settling into my position as a senior research specialist in charge of DNA sequencing. Right now I’m just making sure that I have my feet under me, to where I can handle doing the sequencing on a day-to-day basis without too many mishaps (loose lid……), before trying to do anything more in terms of protocol modifications/development–that will probably be after the new year.

Right now I’d say my job is 80% technical (with 75% of that being pipetting for anywhere from thirty minutes to three plus hours, depending on the number of samples for the day; and the other 5% is taking care of the machine). Of the remaining 20%, I’d say 15% is dedicated to customer service (looking at the data before the customers get it, and letting them know what happened with their samples (which ones failed/which ones gave noisy reads/and which ones ran fine). The last 5% of my job is administrative paperwork (filling out log sheets, order forms, making copies, tabulating charges, and getting the paperwork to the finance guy in the department).

While it can be tedious and repetitive, it is also interesting because if something doesn’t work–you get to work with the lab to try to figure out what when wrong, and what a possible solution to the problem could be.

I’ve also decided that while I’ve applied for academic positions over the last few months (mainly to make the weekly quota of job applications for unemployment)–that isn’t where I really want to be anymore–I don’t want to be stuck teaching 12 credits a semester and trying to get a research program up and running at the same time. I’d rather find a good position within a company that does outreach (or maybe spearhead an outreach program for a company), then try to survive in the academic rat race.

I’m starting to listen to my gut and realize that it is okay to turn down a potential job offer if it doesn’t seem like it is going to be what I want out of life. A few years ago I may have wanted to have my own lab and do my own research–now I want to work for a company that is trying to do something good in the world (say try to find a treatment for cancer, or a neuro-degenerative disease), and still be able to have a life outside of a lab.

I want to be able to work on crafts, continue working on personal development, getting into shape, spending time with my pets, friends, and remember that there is more to life than the nine-to-five rat race (that is found no matter where you get a job).

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November in review.

Okay, I’m a day or two behind on sitting down and evaluating the month. So November is over, and there are now less than thirty days left in the year. One big bright spot, is that I managed to get the DNA sequencing position at the DNA core facility at my alma mater. This is now letting me both expand my technical and transferrable skills to help me try to find that optimal job within industry.

Had to get a new fitbit this month, and therefore I’m not sure what my actual step total was (since there were a few days that I was relying on my iPhone for step tracking (and I may or may not have forgotten to put it in my back pocket once or twice). But I’m pretty sure I at least reached a little over 200,000 steps for the month. So I don’t think that I’ll be hitting 4+ million steps for the year. So I know that this is something that I need to work on next year—I do so well, and then I hit a low point and I allow the step goal to fall by the way side for a good portion of the year. I did manage to read a few more personal development books in November, these focused a little more on trying to manage money and getting out of debt. Read More

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Trying to find the routine again……

Well yesterday was the first day on the new job!!

                               Got the Job

So, the position is only for a year–which is totally fine, since I’m still bound and determine to get out of Oklahoma by next summer, since this state doesn’t really care that much for education (public or higher) or science for that matter. I’d been kinda disillusioned about a career in academia for awhile, and having to deal with being unemployed the past few months, due to the state budget crisis–though to be honest, I’d been thinking of getting out of academia for a while since I really don’t want to spend all of my time trying to write grants, get experiments done, publish, and on side do some teaching. I’d rather try to find a teaching position, or a position in industry that allows participation in outreach.

So the new job is on the technical side of things working in a core facility, where I will be in charge of doing the DNA sequencing, and also learning how to run the mass spectrometers as well. These technical skills, along with the “transferable” skills, will hopefully help me in finding my place in industry.

One thing that I didn’t realize–and I will admit that I should have–is that there are more possible positions than just R&D or sales rep for an PhD in industry.

I’m currently looking to see what other type of job other than R&D could be of interest to me–one thing I’ve realized is that while I want to travel, I don’t think I want it to be part of my job description (though I wouldn’t mind a little bit of travel), I just don’t want it to be 75-80%+ of the job description, so that has already struck a couple of jobs (besides the sales rep) from the list (though I might change my mind by this time next year).

So now, I have to start trying to find a routine again–I’m at work for 8hr/day (more or less), but right now I don’t have internet access, so some of the things I could get done when I have a little free time I can’t due to lack of internet access (which should hopefully be fixed by next week). So I am having to try to figure out how to balance–trying to workout in the evenings (the mornings are just a no-go right now) with both personal and professional development, and my mental unwinding time before trying to go to bed.

I’ve realized that there might not be enough hours in the day to do what I need, though once I can access the internet from work, there may be a few more hours that I can push a little more into. One thing I need to do, is try to convert an notebook/journal into an actual planner that I will make use of–a bullet journal of a sort. I like planners, I like lists, I like making goals—I just haven’t found the planner or journal that I think could do all of that for me–so I am going to spend a good part of December trying to create a bullet journal for 2018–I just don’t know if I can find one big enough for what I want to put in it.

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Two goals and a plane ticket……

Well this is the first entry for my series on getting ready to travel to, around, and then back from London.  This past weekend I decided that I needed to expand the horizon for job searching…….I mean I’ve put out seventy job applications since the end of March, and about half have come back as nos–either I didn’t have the entire skill set; I hadn’t been publishing that many papers (forgot to add in the handful of in-house student publications that my name is on); I had my PhD too long (yep, in today’s job market there are a large number of labs that prefer to hire scientists who have only been out of grad school less than four to five years; right now I’m not going to age myself and say how long I’ve had mine); or I didn’t have a strong background in a subject. Another quarter have also been ignored–I’ve sent a follow-up email and have yet to hear a peep back on the status of my application–I don’t mind getting rejected. At least that tells me that my application was at least considered. When I don’t get a response, I figure that my application for whatever reason ended up in the trash (or recycling) bin.

Okay lets look at these responses logically and from the opposite viewpoint–industry is about the bottom line; they don’t want to waste time training someone, if they can find the skill set in someone who may not have the terminal degree (that person may only have a masters). I understand this, and almost wish that they’d just list their preferred qualifications as the minimum qualifications.  Why?  Because I will still apply for a job even if I’m lack a skill or two–because I will honestly state that I know little (to nothing) about that skill, but I’m willing to learn; with the hopes that there will be someone who is willing to take the chance. Read More

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