Monday 28 November 2011

A difficult task will be halted near completion by one tiny, previously insignificant detail (adapted from Murphy's Laws)

A few weeks back I was having lunch with some post-docs and the rest of the recently "purchased" PhD crew. The conversation was already going on when I joined them, but it was easy to pick up from where I got. They were talking about the dumbest, most horrific, terrible humorous mistakes previous students (undergrads and graduates) had done. Obviously, they had a lot of consideration for the fact that most of these mistakes were performed by people who were still learning, and to be fair with their dignity, some of these mistakes happen because technicians, professors, supervisors, bench supervisors and other colleagues are way to concerned about their belly buttons and cannot spare 2 minutes with a simple induction that will spare everyone future fuss. 

So apparently, one student was asked to autoclave some tips in a box. And because he never went through that induction he thought that that specific black or blueish oblique marks on the autoclave tape were handmade. So he grabbed a pen and he did his best by drawing them on the surface of the tape, stripe by stripe the tape was filled with oblique lines. Job done, he went to his supervisor and told him with a very satisfied expression, the same expression held by one when you did a great job so suspiciously fast, "It's done. It's autoclaved".

Well, I wasn't there to testify, but I can imagine the loud laughter. But in my opinion everyone is entitled to do mistakes, what you cannot do or should try never to, is to do something like a robot, just because you were told to. Judge what you're doing, try to understand the nature of what you are doing and most of all question it if there is something you don't understand. Whatever time it takes, if you get it then you'll never have to ask again... or hear their out loud laughter. And listen girl, it was a few years ago and people still remember, so...

Monday 21 November 2011

"A real-time, reagentless biosensor to track Bacillus subtilis helicase activity in vitro"

Title: "A real-time, reagentless biosensor to track Bacillus subtilis helicase activity in vitro"
Speaker: Matthew Greene (Centre for Biomedical Sciences, Prof. Soultanas Group, University of Nottingham)
Venue: C15 Lecture room, Pope Building, University of Nottingham.

Hot-Points:


  • He has been observing the replicase activity and trying to probe helicase activity in Bacillus subtilis.
  • There are a number of things his team can measure, such as, ssdna creation and dsdna depletion, etc. 
  • The assays he believes they can go for are listed below:
1) Single molecule assays: see Yodh et al, unknown year (sorry)
2) Bulk helicase assays: Eggleston et al., 1996
3) Internal W quenching.


  • One of his team's collaborators in Bristol produced SSB probes: see Dillingham et al., 2008. 
  • For the construction of a B. subtilis probe they performed a mutagenesis G23C based on an exposed cysteine (C51), and then a fluorescence characterisation by titration and shift assays named above:
1) F*-G23C51V
2) G23C C51V
3) Wild type SSB (wild type showed the lowest Kd)

Conclusions:


  • Results show that E. coli and B. subtilis have different sizes in what concerns binding sites. 
  • Increasing the salt (NaCl) level shifts the level of cooperativity, as it is shown next
LOW------------------------------------- HIGH
                       (NaCl)

HIGH ------------------------------------ LOW
            negative cooperativity


  • By increasing salt levels one reduces negative cooperativity


Hope you liked this second seminar posted on this brand new label. Next one is more linked to Immunology, so get your immunologist friends to visit The Toxicologist Today because there will be some dendritic cells visiting us soon! Veeeeeerrrrryyyyyyyy soon!


Sunday 20 November 2011

"The Origins and Evolution of Human Malaria"

If you're a PhD student, a Masters student, a lab technician, a responsible undergrad or a person with a keen interest in the last facts unveiled by science you are then fully aware of how important seminars are in your life. Not only important, they are also vital. Your superiors expect you to keep track on whatever is coming out, take a sneak peek, get in contact with the latest and upgrade your brains. Eventually, the day after tomorrow will take you there, to that special place where tens of people will wait for you to bring the best of your communication skills to that interface PPslides + your oral skills can offer on a late afternoon. If you succeed the audience will leave the room straight to the crisps and beverages with a smile on their face and your topic in their lips, on the other hand they will show relief in their facial expressions and yawns escaping their mouths.

To celebrate the compulsory going to seminars when the obligation luckily meets my best expectations, I decided to create yet another label in The Toxicologist Today - Seminars -, a label that will reproduce the most important facts of the very best talks I'll go to in the coming 4 years. Because of the poor light conditions and the complicated handwriting under dark environment, I must admit that I struggled to write everything I really wanted, but the core is here and the 1st talk listened to, by The Toxicologist Today, was very interesting! Note: Access the speaker's name for full CV.

***

Title: The origins and evolution of human malaria
Institute of evolutionary biology and Centre for immunity, infection and evolution
Venue: QMC, C15 seminar room, University of Nottingham

Hot-points:

  • Collected faeces from chimpanzees and Bonobos from West and Central Africa
  • Question presented - Will nucleic acids be present in faecal samples?
  • There are 5 different species of plasmodium causing malaria, mainly from
P. falciparum - Africa
P. virax - Asia
P. malariae - Africa
P. ovale - Africa
P. knowlesi - South-east Asia (macaques)

  • Gorillas are actually infected by P. falciparum
  • Bonobos are not the origin of malignant malaria
  • Analised faecal samples from wild apes and used single genome amplification (from mitochondrial DNA)
  • His team believe that there are 6 lineages and host-specific ones.
  • Human P. falciparum cluster lies within the radiation of gorilla sequences.
  • There are indeed 6 to 7 species within the subgenus Laverania.
  • Transmission dynamics is too weak for survival in hunter gatherers.
  • Transmission to humans started approximately 10000 years ago (Carter and Mendis, 2007) and this article also states that a mutation in haemoglobin C confers resistance to malaria.

Conclusions:




  • Chimpanzees and Gorillas have very high prevalence of plasmodium - mostly multiply infected (similar to humans in areas of hyper endemicity)
  • Plasmodium falciparum is originally transmitted to humans from gorillas.
Hope you've enjoyed this brand new label and the subject brought here, of interest. See you soon and try not to get bitten!







Husking Spanish Strawberries - Part 2 of 2

I've been trying to find some time to just finish a few important posts I have been postponing, some of them so important that I cannot neglect an inch of the quality level I want them to have. However, I must first complete the previous one regarding the culturing of strawberries in the south of Spain. Firstly, I don't wish to go on and on about how seriously damaged a Natural Reserve and its wildlife are being affected. People these days enjoy of some good in-depth education that does not need stressing constantly how important a role is played by both ecological balance and equilibrium of the ecosystem. Needless to say that future generations are going to suffer, just the same way we've been suffering for we are the future generation of the previous ones. Now, if environmental protection and respect for the different types of life is not that important for some parts of our societies, then let's focus on what can kill us slowly and make us really agonise in the process.

Remember when the last post said chloropicrin and bromomethane are used for means of erasing the microfauna so more space is made available for the strawberries? Well, let's very briefly know some facts then:

"Chloropicrin is a soil fumigant used for its broad biocidal and fungicidal properties, primarily in high-value crops such as strawberries, peppers, onions, tobacco, flowers, tomatoes, and nursery crops. John Stenhouse, a Scottish chemist and inventor, synthesized chloropicrin in 1848. Because chloropicrin is toxic by all routes of entry, it has the potential for widespread destruction as a chemical warfare agent." [1] 

"Chloropicrin is an irritant to all body surfaces... This liquid decomposes in the environment... Chloropicrin photodegrades, with a half-life of 20 days" [1]

Detection

The odor is a distinctive warning property of this liquid compound.
I believe these informations give you a pretty good idea of how toxic chloropicrin can be, but if by any chance you are still suspicious take a look at a garage experiment with choloripcrin shared on youtube and make up your mind the way you see fit. Embedding has been disable by request from the video creator however you can access directly by clicking here!

As for Bromomethane:
"Bromomethane is a manufactured chemical. It also occurs naturally in small amounts in the ocean where it is formed, probably by algae and kelp. It is a colorless, nonflammable gas with no distinct smell. Other names for bromomethane are methyl bromide, mono-bromomethane, and methyl fume. Trade names include Embafume and Terabol. Bromomethane is used to kill a variety of pests including rats, insects, and fungi. It is also used to make other chemicals or as a solvent to get oil out of nuts, seeds, and wool."[2]
Exposure to this chemical can affect your cardiovascular organs, your skin, your digestive system, and even cause neurological damage; although carcinogenic effects were never proven [2].

What happens to bromomethane when it enters the environment? 

o It moves very quickly into the air when released to the 
environment or when present in soil or water. 
o It breaks down slowly in air over several years. 
o It breaks down quickly in soil over a few days. 
o Small amounts can move from the soil into the 
groundwater. 
o It breaks down in groundwater over a period of several 
months. 
o It does not build up in plants or animals.

Source: [3]

If nothing else made you think twice, focus solely on the results presented by the table above and imagine how all those animals are affected by drinking water contaminated with two very strong pollutants.

[1] Medscape reference, Chloropicrin poisoning, http://emedicine.medscape.com/article/832637-overview, last visited on the 20th of November, 2011, last updated on January 2011.

[2] Agency for toxic substances and disease registry, Bromomethane, , last visited on the 20th of November 2011, last update on September 1995.

[3] Agency for toxic substances and disease registry, Bromomethane CAS# 74-83-9, http://www.atsdr.cdc.gov/toxfaqs/tfacts27.pdf, last visited on the 20th of November 2011, last updated on september 1995.

Monday 7 November 2011

Husking Spanish Strawberries - Part 1 of 2

It is not unusual to be emailed countless messages concerning different scientific, social, political or even economical topics. Some of these forwarded messages I already know them profoundly whenever they reach my mailbox. For others, I just don't care or simply refuse to waste my precious time on them. However, now and then some important issues reach my eyes, like the one I am to discuss hereby with the audience of this blog.

A few weeks back I got an email from a friend who is actually working in Spain. Because I do not know how the person would feel if I was to disclose her name in this post, I prefer to say that she is science educated and an excellent professional in her area. Nonetheless, that does not immediately trigger me to write about the numerous subjects that hit my box. The subject has got to be interesting, important to this blog's context and remarkably pertinent. By then, I thought it wasn't; not until I got the same email sent from my mother, who is not science educated, but still, is a very educated professional in areas that are not immediately science related. This made me realise that if the content of that email had been pinned up by different people, with different professional and social backgrounds, in different countries, relevance and pertinence were immediately accounted for to my standards, obviously!

The message entitled "Poison in the Spanish strawberries" had to be revealed, analysed, discussed and shared with my audience. So I will just translate to English the content of the forwarded message and expect to draw the initial deck of cards in a discussion that I hope becomes more interactive:

"When you happen to buy strawberries always mind to check their origin. If they are Spanish... be aware of the consequences they'll have on your own and your family's health status, the consequences on strawberries, on other people and the environment. 

Are the Spanish greenhouse strawberries edible?

The answer is NO!

... if the only problem of these greenhouse strawberries was just the lacking of flavour, we could consider ourselves happy... Unfortunately, these strawberries offer much more serious problems, starting with the fact that this culture covers around 6 thousand ha, where a huge part happens to be in a Protected Reserve Area - Parque Nacional de Doñana - an extraordinary sanctuary for migratory and nesting birds. Nevertheless, the local political power ignores it widely.

For these strawberries to reach their destination in the European markets, they need to be  transported by trucks and vans for thousands of kilometres. Around 16 thousand lorries complete this route every year. Considering an average of 10 tons per vehicle, these strawberries worth their weight on CO2 generated and toxic gases produced and released to the environment, thus affecting people.

But the dangers associated with these crops aren't only the ones stated before. Is the reader aware of how the Spanish strawberries are actually cultivated?

The strawberry plant is a vivacious plant capable of producing fruit for several years. However, the strawberry plants destined for this type of production are destroyed every year. For giving strawberries even when it's not their season, plants produced in vitro are put in refrigerators during the Summer's Peak, in order to simulate Winter Season, thus activating production. During the Autumn, the sandy land is cleaned and sterilised, and the microfauna destroyed by means of bromomethane (methyl bromide) and chloropicrin.

Bromomethane is a powerful poison prohibited by the Protocol of Montreal on gases that are toxic for the ozone layer. Chloropicrin, composed of chlorine and ammonia, it's not less dangerous for it blocks the pulmonary alveoli. 


The strawberry plants are grown in a soil covered by black plastic and the irrigation used includes fertilisers, pesticides and fungicides. The water comes from artesian wells from which more than half is assembled in an illegal fashion.


All these factors are responsible for transforming Andalusia into a dry savannah, causing the exodus of migratory birds and the extinction of the last of the Pardel Lynx felines, since these little carnivores (from which only around thirty may yet subsist in the region) feeding off of rabbits - also animals on the verge of extinction there.


On the other hand, for finding adequate place for the strawberry plants, at least 2000 hectares of forest have been devastated.


Production and exportation of these strawberries cropped in Spain starts slightly before the end of the Winter season and ends up around early June. Workers, at that specific time, need to go back to their houses or anywhere else, for if they get sick due to the noxious substances inhaled before, they will have to seek for treatment on their own expenses.


Most of the producers of these Spanish strawberries make use of Moroccan manpower, seasonal workers, sometimes clandestine workers, poorly paid and housed under precarious conditions. For heat at night during Winter, these workers burn the plastic used for covering the strawberry plants.


Anyway, every single year at the time of the end of the cropping, the 5 thousand tons of plastic used are taken by the wind, buried somehow, anywhere, or burned on the spot...


Needless to say that in this part of Andalusia, where aberrant agriculture thrives, lung and skin diseases are in frank progression. And who cares about it? No one!


And what is the reasoning behind the media's complete silence? Mysteries that are not only due to politics but also to economics.


But when the region becomes totally vandalised and the production becomes costly, the producers will just transfer everything to Morocco; country where they have started to settle. Later on, they will probably just move on to China... European population is happy for buying cheap products, however they will eventually fall ill for consuming these products, as well as see employment raising.


What can we do for fighting this tendency?


Each one of us is free to act in his own conscience and knowingly: to buy or to boycott the purchasing of any article that is not brought up according with the laws of nature and/or human rights. We all can opt for a personal boycott. And if the majority of the citizens thus proceed, the gigantic "sharks" in the economy will be forced to change their methods under penalty of presenting themselves to danger.


Citizens are to make the final choice!


Kind regards,


Mario Pinto

The previous text was translated by myself from the Portuguese and reflects entirely the opinion of the person hereby signing the message. However, by presenting this information I intended solely to open the discussion that in a biochemical toxicological perspective will be fully developed in part 2. See you then!

1st image taken from Fresh Plaza, Global Fresh Produce and Banana News,  http://www.freshplaza.com/news_detail.asp?id=15656, last visited on the 07th of November 2011, last update on the 02nd of January 2008.

2nd image taken from Viagens Lacoste, Parque Nacional de Donana - fotos soltas, http://viagenslacoste.blogspot.com/2010/04/parque-nacional-de-donana-fotos-soltas.html, last visited on the 07th of November 2011, last updated on the 30th of April 2010.

3rd image taken from unknown source.



Saturday 5 November 2011

If anything can go wrong... the Freezer will (adapted from Murphy's Laws)

I decided to create a brand new label to this blog where I can post a few light events that occur to me or members of my crew whilst completing this PhD in Molecular Microbiology. It works not only as something nice to share with the audience of this blog, but also as a therapeutic introspection where things that are usually taken very seriously by every single one of us can be accepted lightly, yet responsibly. In this day and time where pressure collides against our humour day in and day out, it is difficult to remain sane when dumb stupid random things happen to us in an uncalled for fashion. PhD - Pretty Humorous Disaster, is not only for sharing with you guys the unexpected things that take place during 4 years of my life as a PhD student (that has just started) but for you guys to give it a go to and share your ludicrous moments too. Use it as I will, as a purge, to cleanse the negativity and the burden of the random surprises that we don't want to happen, use it in a community manner as a passport to laughter rather than a judgement. Then, in 4 years time read it again and everything will seem a lot lighter than it does today, I promise you and I promise myself.

So here it goes!

On the 04th of November, when the day at work was nearly done, I saw my mate Josie struggling with an ice pick trying to brake through the ice blocks of an old freezer that contained samples from 1995. In 1995 I was bloody 16! A gentleman sees a lady in danger or affliction and must come forward, and that's what I did! I put my gym membership to work and broke those blocks for her in a much faster and effective pace. Everything was going so well, I felt like bonding with my guys, the supervisor was there proud of my work, and there I was revealing old eppendorfs after old eppendorfs, boxes and boxes of biological material, buffers and the like. Dressed in my lab coat, goggles protecting my eyes, ice pick hitting the watery rocks. I felt gooood, I felt part of them. But unaware of the mighty powers of Murphy's Laws, my supervisor came to me and warned me to just be very careful and avoid cutting through the tube with CFC in it because  that had happened to him in the past, you know, cutting a tube and releasing the cooling aerosol to the atmosphere. And I took that as my uttermost mission. My supervisor trusted me the long postponed mission of removing those ice blocks and clean that old freezer. I was doing so well, and at last the very last ice block was there, staring at me like an arch-rival,  the last enemy between myself and the glory of success and accomplishment; I was part of the team and I was really proud.

And suddenly that leaking sound happened, that horrendous ffffsssssssssssssssssssssssssssss that just took my light away. A tiny crack on the tube lasting forever (it was like 2 seconds but it felt like 2 minutes) to only end up with my supervisor saying - Well, that's it, there is nothing we can do with it any more.

James, a very funny Post-doc "cutting" through the ice of the moment replyed generously to light up the moment - You just killed around 5 penguins in the North Pole.

So, this proves that your good intentions and your team spirit sometimes might be undermined by the bloody Murphy's Laws that shouldn't even exist at all. Another thing is that you can tell your kids to go play ball outside in the front garden, and you know they shouldn't kick the ball too hard to avoid breaking a window or something. If you just shut it and say nothing, they will play and have lots of fun; the moment you tell them to be careful with the car window, just walk to the phone and call Autoglass Repair because it's gonna happen!

See you soon, guys... same place, same mood... The Toxicologist Today!