lab work snap shot: past, present, future

Past: I got a paper published, which is very nice to put in the  “past work” category. Writing a scientific manuscript for publication is painful and tedious and stressful and hair wrenching for me. I normally agonize over every sentence when I write; rearranging, retyping, and taking long pauses to formulate  thoughts and structure. Writing any thing takes me a long time. In fact these last 5 sentences have already taken quite a bit of time for me to pound out. Then, when I’m all done with writing what I want to bestow, I have to edit. I am a horrible speller and normally just guess at punctuation. I have to edit and edit and edit. And edit. I can’t tell you how may drafts of my manuscript I made.  It may actually be easier to figure out at what rate I produced drafts rather than the actual number. But, in the end, when it was all done, there was reward. The reward: not having to work on it anymore. It was a good experience though, and it’s nice to have my name published on something for future resumes. You can read the abstract and download my full article here. Have a good nap!

Present: For the first time in the history of my lab we are doing some in vivo cattle experiments with the parasites we study. This is to test whether the parasites that we modify are able to clinically infect the cattle (I have wrote about this before). This experiment has direct consequences on my project. If the cows get sick then it is a good sign that my my work will…work. It is eight days after inoculation and some of the calves are getting a fever ( a very good sign). In the picture are James and Ralph. They are very good at what they do, and care very much for their animals.

Future: I’m in the process of developing my own “mutant” parasite to inoculate into cattle. My parasite line will advance us one step closer to develop a dual vaccine system that will not only protect against the symptoms of the disease but also attack the tick vectors of the disease. Do you see GFP, BSD, and more importantly Bm86 expression from my transfected parasites in these contrast pictures? Well, it is my job to find out.

in loving memory

three years ago today

“Echoes Of Mercy, Whispers Of Love.”

from the begining of expecting

Lately we have been telling lots of people that we are expecting, and those people are always excited to hear the news. However, I  yearn to share with them how we became to be expecting from when we first found out, because I know they do not understand what it has become to mean to us. So, we would like to elaborate on our experience into parenthood thus far. We want to share because, well, parents always want share about their children, but mostly because we want to give public credit to our God, the God of Jacob, and how he has graced us with this child.

Not long before the news, my wife and I decided to just let the chromosomes fall where they may. Then, with womanly inclination and two negative home pregnancy tests one week apart, my wife went to the clinic to see what could be going on. After some tests, a nurse that was very excited to find that my wife was “trying”, and not “oops” like perhaps most patients, gave her the blessed news that she was pregnant. Although I visited my wife at her lab that day, and noticed a certain sparkle, she didn’t tell me the news until we settled at home that evening. We were shocked, we said “wow”, we hugged and kissed, we smiled, we had a little tear of joy, and we prayed thanksgiving to God. More tests were done and we found out Marian’s hCG (the hormone that indicates pregnancy) levels were rising normally and everything looked normal.

Truth be told, when you find out that you will be a father for the first time it does something to you; there is an instant shift of focus.  I felt myself become less selfish, ready to love and know my child. That little baby was conceived by me, a part of me, and was already my family. It was wonderful.

We went to see an official doctor because that is what you do when you find out you’re pregnant and also there was a certain concern. He met us, and we really liked him. The doctor saw that the last hCG levels were normal and gave us possible causes for our concern, telling us to respond quickly if it got worse. He sent us with a positive yet cautious report, and told us to go to the hospital for our first ultrasound. Looking at the monitor with the black and gray picture, the ultrasound technician showed us the parts of early pregnancy formation and kept referring how small, and hard to measure the baby was. We could neither hear nor see a heartbeat. Later, the doctor called with the latest hCG results which had dropped.  hCG levels are never supposed to drop in a viable pregnancy.  They’re not even supposed to level out until significantly later on.  All data indicated that a miscarriage would occur at any time.  Finally it happened, or my wife thought it happened.  The hope that we had been grasping on to that maybe the Lord would spare this little life was all but gone.

Heartache. We had gained something so lovely that was now going to be gone. New emotions of loss and grief were experienced. Though we had not seen our baby we mourned as if we had lost a family member. Our conversations had pain in them, food was no good, and light tears often turned to deep crying. We spent time praying for comfort. The next week went by slow while we waited for healing.  Some original complications were still unresolved and the doctor wondered if there might be a chance that Marian was additionally experiencing an ectopic pregnancy. Thus, to confirm the miscarriage and determine if an imminent surgery would be necessary, we were advised to have another ultrasound.  Now my concern was not just of the loss, but also for the health of my wife. The mood was solemn as the technician asked why were back as she prepared to put the black and gray picture on the monitor. She flashed up the picture and it was very unexpected when she said, “oh, there’s something, can you see the heartbeat?”. Joy, joy, and rejoice! Grace abounded that very moment (and had before although we didn’t know it).

Praise the Lord, O my soul; all my inmost being, praise his holy name. Praise the Lord, O my soul, and forget not all his benefits-who forgives all your sins and heals all your diseases, who redeems your life from the pit and crowns you with love and compassion, who satisfies your desires with good things so that your youth is renewed like the eagle’s. The Lord works righteousness and justice for all the oppressed. He made known his ways to Moses, his deeds to the people of Israel: The Lord is compassionate and gracious, slow to anger, abounding in love. He will not always accuse, nor will he harbor his anger forever; he does not treat us as our sins deserve or repay us according to our iniquities. For as high as the heavens are above the earth, so great is his love for those who fear him; as far as the east is from the west, far has he removed our transgressions from us. As a father has compassion on his children, so the Lord has compassion on those who fear him; for he knows how we are formed, he remembers that we are dust. As for man, his days are like grass, he flourishes like a flower of the field; the wind blows over it and it is gone, and its place remembers it no more. But from everlasting to everlasting the Lord’s love is with those who fear him, and his righteousness with their children’s children- with those who keep his covenant and remember to obey his precepts. The Lord has established his throne in heaven, and his kingdom rules over all. Praise the Lord, you his angels, you mighty ones who do his bidding, who obey his word. Praise the Lord, all his heavenly hosts, you his servants who do his will. Praise the Lord, all his works everywhere in his dominion. Praise the Lord, O my soul.

Since then it has been some weeks, but during that time our emotions found new highs, new lows, and higher highs. We had another ultrasound, and everything looked normal. We had had another checkup and could hear the baby’s heartbeat on the Doppler.  It would have been much to bear alone. Select few of our family and church knew what we were going through during that time. One person in particular beared through with us in the most appropriate manner. She grieved along side and prayed for us, she was able to know when to check in or give us space when we needed it, she went to great lengths to keep from revealing our vulnerable situation to others, and she was one of the first to rejoice with us after the heartbeat.  Mrs. Murdock gave me new appreciation for the church body that God designed, and while I consider it no chance, I am very fortunate to be apart of it. God knows what He is doing.

Recently Marian and I went in for another checkup. Again the doctor checked the normal things and brought out the Doppler that he used before to monitor the baby’s heartrate. Our hearts sank when he could not find the heartbeat. “Maybe I just cant find it behind the sound of your pulse” the doctor said to Marian, and sent us for an unscheduled ultrasound at the hospital for conformation. Our thoughts turned to what we had been through already, and we prayed again. The answer to our prayer was clear in the room with the black and gray screen.We saw that the baby had grown, had a strong heartbeat, and that the baby is our son.

This child, out of our control, is a gift of grace. We would love to introduce him to you after he is born in December.

Happy Fathers day by the way.

heartbeats

Where there was only two, our family now has a third.

The doctor told us we have a “miracle baby”. We find this diagnosis very acceptable.

back yard catch

Three feet from where we mow the lawn

Ten feet from where we mow the lawn

Kamiak Butte BBQ

Family, friends, grilled meat, picnic tables, tall trees, green grass, flip flops, watermelon, sock golf, smiles and laughs. Could it be summer?

definitions

The research leader of my department is always quick to remind colleagues that definitions are the bottom line in science.  This is one of those statements that can easily roll through the mind with out breaching its massive implications. As a  scientist I observe occurrences in nature, ones that are guided by certain laws, inputs and outputs.  It is then my responsibility to define my observations as accurately as possible, with the tools I have available, in attempt to explain what is truly happening.  This is done by creating a hypothesized definition which is then put to test for it’s validity. Often times, based on my tests,  my hypothesized definition is not supported and I  have to either adjust it or create a new one. This is one aspect that I love about my work in science. That, even though I will never come close to revealing the whole truth of the matter, the definitions I create are an attempt to describe truth as best I can. It is sincere.

It is good to reflect that, in the end, the truth of our life will be  manifested through what we have thought and what we have done; and no mater what definitions we use in attempt to describe our selves, whether sincere or not, the truth will still be there,  full and unchanged. 

a yard day in may

. .. …. …….. ……………. …………………………..

I’m going to make an effort to steer this blog back to science related issues.

If you have had access to any type of media source lately you will probably be able to guess the inspiration of this post.  It comes in three parts: (A) flu overview, (B) the medics of our pandemics, and (C) the little bird that is spreading “swine flu” to millions and millions every minute of every day!!!!!!!11!1!!

Flu overview-  Flu stands for influenza which is an infectious disease caused by the influenza viron. Symptoms of this disease was described as far back as 400 BC by the Greek physician Hippocrates of C(K)os.  It belongs to a family of  RNA viruses called Orthomyxoviridae. As a side note, a biological system that relies on RNA for genomic storage is very prone to mutation because it lacks DNA polymerases which fixes genomic mess-ups during and after transcription (when the genome is copied). The influenza virus will normally invade the epithilial (outer) cells of your respiratory systems (nose, throat, lungs). You can think of your cells as factories with machines which produce products that benefit the overall economy of your body. The influenza virus breaks into these cell factory and hacks into the nucleus of the cell by plugging in it’s RNA code. The RNA reprograms the mainframe of your cell factory to stop producing products for your body and start producing the materials needed to make more influenza virus. These virus materials will then congregate at the inside surface of the infected cell and bud out using a piece of your cell membrane to contain the parts needed to hack into another one of your cells (fhe functions of viruses are incredibly fascinating).As this happens, your body is reacting by producing cytokines and chemokines in attempt to launch an immune response against the influenza hackers. Although there is some cell damage, the brunt of the symptoms you feel (aches, fever, chills, fatigue, vomiting, pneumonia, death, ect) are the result of inflammatory responses caused by your own immune system. There are three types of influenza: A, B, and C.  Let’s just talk about A because currently it is the relevant one. It is the villain of the Spanish flue of 1918, Asian flue 1957, Hong Kong flu 1968 pandemics, and the current North American 2009 pandemic. Wild aquatic birds are the natural reservoir for type A, but all viruses will jump ship given an opportunity. When it does “jump ship” it will often swap components with other influenza viruses it finds in the new host. This “swapping” leads to antigenic shift which can possibly lead to new highly pathogenic strains that our immune system has never seen before.  Type A can be broken down to several serotypes which are used to categorize particular outbreak. The most well known and devastating influenza pandemic was the Spanish flue of 1918 (estimated to have affected one half of the worlds population at that time with a body count of up to 100 million) which had the H1N1 ser0type. While this recent “swine flu” out break also has the H1N1 serotype it is a very different strain than the one found in 1918. This strain is actually a mongalized combination of strains found in North American pigs, Eurasian pigs, birds, and humans and has an  outer protein that has only been seen in pigs and never in humans. Interestingly, this new strain has never been found in swine and thus can not be contracted by being near, eating, or french kissing pigs. You might start a new pandemic with somthing else but you will not contract the 2009 N1H1 virus.

The medics of our pandemics – Who is in charge here? Who is. What? WHO!! (sorry, had to do it). The World Health Organization is, and I quote directly from their website, “the directing and coordinating authority for health within the United Nations system.” These guys compile what the world knows about health, organizes it, and then tells the world what it needs to know…about health. You can think of WHO as the “head” of the health body. The rest of the health body includes the Centers for Disease Control and Prevention (CDC) who are all over the world doing most of the arm and leg work of health, and then there are national agencies like the United States Food and Drug Association that point here and there with the fingers of health. These organizations do lots of good work in different areas. One of the things they do is determine what influenza vaccine should be produced. This vaccine is actually a cocktail of three different influenza strains that have been killed or attenuated. What some people don’t realize is that there are many many influenza strains in the world and these strains are changing all the time. It is the job of WHO to try to predict what three strains out of the whole bunch poses a the highest risk for the upcoming flu season. Thus, there are many strains that people are not vaccinated for, so getting a flu shot does not totally eliminate the possibility of getting influenza. In fact, just in the U.S. there are around 30,000-40,000 (~100/day) influenza related deaths each year. So why does this new “swine flu” have the WHO worried? If you read or watch what the CDC has to say about it you will notice that they always mention that the symptoms of the ”swine flu” are no different than seasonal flu, and that you probably won’t need to go to the emergency room. What has WHO worried is that there are just a couple orange flags. One is that this virus has never been seen before and it contains animal components. Like I said before, influenza is constantly mutating making it a moving target, but when a new target appears people get a little worried. Second yellow flag is the rate of geographical spread. This is why we are in pandemic 5 alert; it is just protocol when a single strain is detected in two or more countries.  That is it. What we know is that this “swine flu” has some characteristics of previous devastating strains but so far is no more deadly than other influenza virus, and it is spreading to different countries because people move around alot. What has the WHO excited is that they have an excuse run their preventative strategies on a relatively new strain of influenza and watch how it impacts the spread.  I think the WHO and CDC have done a very good job so far in implementing sound instruction, but to tell you the truth, I think they are kinda indulging in the media/public spot light. Just look at the smirk on Dr. Joe Bresee when he says “swine flu”.

The little bird that is spreading “swine flu” to millions and millions every minute of every day!!!!!!!11!1!! – Oh news media, why do you sell us so much fear? Oh that’s right, because we love to buy it. News coverages always tend to embellish emphasize the catchy aspects of their stories so they can keep people watching and boost their ratings above the competition. Then people start to talk, and where do people talk now a days? The internet. Specifically in online social networks. Facebook is one of those social networks, but it is a thing of the past now. You actually need a computer to check it. The new hot thing is a micro-bloging site called twitter. If you’re unfamiliar, twitter asks the question “what are you doing” and lets you give an answer in 140 characters or less that all your friends can see. What makes this popular is the simplicity and ability to use your phone to update it on the go. A hot topic can spread very fast on this site and “swine flu” was no exception. Trendrr is graphing the  ”swine flu” tags on twitter at ~10,000 per hour and ~140,000 per day. We all know that bad news travels first and that a person is smart but people are stupid, so that is a lot of people blurting out their “swine flu” fears in 140 characters or less. Well, not all are fears, some are pretty funny “swine flu” jokes. The interesting thing is that the news of this outbreak, though in misinformed hysteria,  spread faster than ever before. The WHO and CDC probably dropped their jaws. Getting the word out quickly is one of the best preventive actions you can take concerning health issues, and they realized that  this technology could be used to inform and connect with people very quickly. The CDC is now tweeting reliable information about the “swine flu” pandemic every 2-5 hours. In fact, the last tweet I got from CDC was this link telling me about new social media they are using.

Now I’m going to go tweet that I just made a blog post about “swine flu”