INVITED CONTRIBUTION

Unhealthy habits in Molecular Biology laboratories: learning to separate lunch-time from research-time

Karl Kurtz
Deutsche Kommissionen für Gutten Habiten im Researchen, Pönensieguanten, Germany.

Experimental research in Molecular Biology laboratories has always been characterised by the utilisation of a large amount of weird reagents which constitute a threat for human health. These products are usually of chemical or biological nature, and their effects range from death-causative illnesses, such as cancer, to other lesser nuisances such as uncomfortable attacks of diarrhoea or irreversible staining of personal clothes. A methodical and painstaking observation of laboratory security procedures is absolutely crucial for the healthy and correct development of research. In this short assay, I shall document the main bad habits commonly observed in Molecular Biology laboratories, and provide some simple and useful recommendations regarding laboratory safety practices. The major concerns of researchers in terms of lab security seem to be completely focused on the manipulation of ethidium bromide (see bitesizebio). The rest of chemicals, such as methanol, phenylmethylsulfonyl fluoride or sodium azide are happily handled as if they were innocuous. A common but non-advisable practice often seen in many labs is the use of methanol as a substitute for ethanol in the preparation of energetic beverages, such as the half-morning carajillo (coffeecognac) or the solysombra (sunandshadow). The habit of baking bread (with lunching or almuerzing purposes, of course) with strains of yeast used for research, although undoubtedly money- and time-saving for research fellows, may not be completely secure. It is nowadays common to find incubators filled with baguettes and ciabattas resting aside Petri plates. The proximity of other microorganisms such as bacteria in this kind of incubators is probably the cause of colitis found in the labs were these habits exist. Other apparently harmless uses of laboratory material, like boiling potatoes in such devices as those used to denature protein preparations (commonly rich in 2-mercaptoethanol or other stinky reducing agents) are strongly discouraged, unless for decoration purposes of otherwise healthily-prepared dishes (e.g. complementing Russian salad or Bratwurst). A similar practice is often found involving the preparation of lunch (e.g. heating of home-made Spanish omelette or other egg-derived products; see CurrRevol 04/16/2009) in microwaves which are also used for melting agarose solutions that contain ethidium bromide. Given this short summary of unhealthy habits, which surely does not cover the whole spectra of dangerous vices and manipulations in Molecular Biology research premises, we recommend that hereafter researchers simply continue working in their labs as usual, but observing the rule of covering themselves in a clean lab coat, gloves and mask when going out to public spaces and private homes. That may be the easiest way to avoid the spreading of genetically manipulated organisms, harmful chemicals and other bizarre products by researchers from the place where these fellows should always be confined: the laboratories.

REPLY

Can true feelings be communicated in less than 250 words?

W. Shakespeare Jr.
Stratford-upon-Avon Academy for Awfully Pedant Writing

Despise me if I do not act in response of the writing that mine sorrowful eyes saw published in Current Revolution by thee, immoral Mr. Billings, in recent times. For I am touched in the depths of mine heart as a concise playwright of scientific account, and brave, valiant, courageous and gallant as I am (such a one do I profess myself), I must react with all my might. Be heaven my judge! For thou shouldst know that the most outstanding deeds of the most outstanding researchers bring forward the most outstanding discoveries. And such is their singular nature that they can not be explained by means of frivolous, flippant, utterly concise terms. Rather, the most talented pen amongst the laureate poets, the greatest of all bards would find no words to bring that warming light into the cold eyes of those that had not been initiated in their beauty. Tell’st me, oh, loutish fellow, out-tongue it: How willst thou put in plain words the magnitude and prominence of the truth, evidence and proof of the wonders that rule nature and life? Thee, Molecular Biologists that cast a name on all phenomena, thou who PCR everything, who read the secrets of life in disgusting gels as the augurs read on the entrails of sacrificed beasts. If you honestly believe that the facts that hold the truth can be said in less than 250 words, you are only half-right. And I still have two words to go, so... Fuck haikus.

An abstract with less than 250 words

Mr. Billings
Washington Library, Washington, USA

Writing up precise and concise abstracts for scientific reports in specialized journals is one of the most important talents required to become a successful scientist. The efficient elaboration of scientific abstracts requires powerful mental concentration, optimal aptitude for analysis and synthesis, good abstraction capability, and swiftness with the fingers on the computer keyboard. The limitation in the number of characters or words in the abstracts is an additional challenge for authors, and long-term training is necessary to condense, in a short format that fits the specified dimensions of the abstracts of the distinct journals, the excellent ideas, interesting results, and brilliant conclusions described in the manuscript that is going to be submitted. In this abstract of 249 words, a brief consideration is made that could help young scientists to summarize their findings in such a positive manner that success in publication is almost guaranteed. The consideration is based on the famous quoting of my own words by the neurobiologist Santiago Ramón y Cajal, in his celebrated assay on rules and advices for scientific investigation, as well as on the known fact that most journal editors anticipate a decision on the acceptance or rejection of a paper before ending the reading of its abstract. To write up a good summary for a scientific publication, it would be convenient: 1/ to have something new to say; 2/ to say it; and 3/ to shut up when it is said. Editors of scientific journals love reading abstracts with less than 250 words.

GENELLOQUY: a biologically encrypted genetic language to express inner thoughts

A.D. Nine and U. Racil
Babel Institute, Genesis, Israel

Currently, more than six thousands different human languages are estimated to exist. However, most of them have proved to be unpractical to express the deeper thoughts of the people, especially in those cases where a non-maternal language has to be used. Feasible alternatives to express deep thoughts, intense emotions, and profound desires, when words do not come to the mouth, involve the use of mimics, touching, kissing, and other physical- or visual-contact related stratagems. However, all these mechanical languages are too simplistic and cover a very limited range of communication possibilities. In its standard form of representation for biologists, geneticists, and other gene- and polypeptide-writers, the expression of proteins follows the rules of a four-letter genetic code that forms triplet-words that translate in each amino acid, which is then represented graphically by one capital letter plus two small letters, or just by a capital letter. This gene-to-protein language applies to all people, regardless their culture, nationality, or race, and provides enough combinatorial diversity as to account for the expression of any imagined kind of protein in any imagined kind of person. We have created a novel form of communication, named GENELLOQUY, based on the use of triplets and four-letters gene writing rules, standard forms of amino acid sequences representation, and an informative hierarchy from-gene-to-protein-to-poem. A short title, a preamble, and a concluding statement can be added to the GENELLOQUY to help in the optimal transmission and understanding of the message:

EXPLANATION OF THE GENELLOQUY

(Preamble: person A is trying to explain to person B what a GENELLOQUY is, but person B does not understand it. Person A, then, succeeds using an example)


Genetic explanation (person A):

ATA ACG ATA AGC ACC CAC ATC AGC AGC CAC ATA ACT

Genetic understanding (person B):

TAC GAA TCT ATA TCT GAG GAA GAG GAA


Proteic explanation (person A):

Ile Thr Ile Ser Thr His Ile Ser Ser His Ile Thr

Proteic understanding (person B) (swallowing the explanation):

Tyr Glu Ser Ile Ser Glu Glu Glu Glu


Poetic explanation (person A):

IT IS THIS, SHIT!

Poetic understanding (person A):

YES, I SEEEE…!


(to express yourself: think what you say and say what you think)

As shown, the punctuation signs in the poetic part of the GENELLOQUY are not represented in the proteic or genetic parts, and are considered as epigenetic editing. This editing adds diversity and expressive possibilities to the communication, and allows evolution of the information of the message without changing its basic genetic content; for instance:

IT IS THIS, SHIT!
vs.
IT IS THIS SHIT

The GENELLOQUY is translatable to almost all idioms, including Esperanto, and offers the advantage of being encrypted in a universal code at the protein- or gene-level. Thus, fluent and private GENELLOQUY communication between people speaking different languages can be achieved if the proteic or the genetic part of the GENELLOQUY message is used. Such peculiarity makes open chats, blogs, and other modern gossiping inventions, suitable instruments to obtain all benefits from this new human expression system. Many users of GENELLOQUY worldwide have already experienced the pleasure and the relief of being able to produce their own feelings and ideas as they never did before (see, for instance, jindetres). We anticipate that GENELLOQUY may become the universal language in the world in the not very distant biotechnological future.

The three-dimensional structure of vault particles unveils the secret of the Lady of Elche

Nuria Delajara, Lydia Vilanova and José Conrado
Finca El Palmeral, Elche, Spain

The Lady of Elche is one of the major treasures of pre-Roman figurative Iberian art. Both, religious and pagan influences seem to be fundamental in the design and elaboration of the sculpture, which is considered by many as a funerary bust. The unquestioned modern beauty of the lady, and her enigmatic gesture, have been the subject of controversial interpretations by art historians, including hesitations about the authenticity of the sculpture, as well as about the sex of the represented figure (see, for instance, El Garrofer). Although Hellenic influences seem to delineate the artistic style of the bust, the aesthetic fundaments of the Lady of Elche remain obscure, specially in those matters concerning the unique design of the two ornamental, cartwheel-like discs that decorate the lady´s head. Vaults are large ribonucleprotein particles present at multiple locations in all eukaryotic cells. Electron microscopy has revealed a barrel-shaped structure for individual vaults, and it has been postulated a matruska-like, open-and-close hollow architecture for these particles. However, both the secretive content of the vaults and the function of these particles in the cell are mysterious. We have recently developed a friendly-use OJIMETRIXTM virtual package, that provides all the tools required to analyze in one sight complex biological and artistic structures. Using OJIMETRIXTM, we have performed a visual study of vaults in crystalline state, in comparison with the decorative discs that adorn the head of the Lady of Elche. We have found a strong similarity between the shape of the vaults, when visualized from an apical view, and that of the ornamental discs from Lady of Elche´s head:

In spite of differences in size of several orders of magnitude, the delicate engraving of the lateral ornaments of the bust overlaps quite well with the highly-organized molecular structure of the vaults. Our findings demonstrate that the design of the Lady of Elche´s headdress adornments possesses vault particle-like features, and suggest that ancient Iberians had precise knowledge of the shape, and perhaps the function and the content, of primitive vaults. The conservation along centuries of a vault-shaped women hairdo in some fire-related tribal rituals in modern Iberia, such as Fallas, at the Spanish Levant region, support the hypothesis that the Lady of Elche was used as a funerary urn to preserve the ashes of the dead. Whether vaults could also play a role as molecular coffins, confining cellular bodies or other unknown corps generated during programmed cell death, deserves further studies.

FLU EPIDEMIC ALERT 2009

A versatile sandpaper therapeutic kit against all types of flu viruses

Nestor Nuda and Shon Sonete
WHO Sales Department, Hong Kong, China

Efficient vaccination and therapies against flu viruses are challenged by the rapid changes and reassortments in the genetic content experimented by the distinct virus strains which are hosted in birds, pigs, and humans, among others (see Cellularium). Every season, about 5% of population worldwide is infected by renovated influenza viral forms and suffers the symptoms of the flu, spreading the virus particles all over by regular nose blowing, impulsive sneezing, and occasional kissing. A major handicap in the prevention of flu epidemics is the human practice of using soft handkerchiefs to clean the nose respiratory tract, here and there. This bad habit produces a numerous amount of circulating handkerchiefs full of alive viral particles, which easily colonize new hosts at areas frequented by people, such as school classrooms, public transportation, bars, and unemployment offices. Therefore, the implementation of a nose blowing system that kills all and every viral particle, regardless of their antigenic variation, during the frequent nose manipulation carried out by the infected individuals, could be a primary barrier against the expansion of the seasonal flu. Here, we present a versatile and safe sandpaper kit (SANDGRIATALTM) that has abrasive therapeutic properties against all flu virus infections, including those from all varieties of avian-, swine- and pet-influenza viruses. The kit includes a dozen reusable, water-resistant, flexible polyester microgritted sandpaper sheets (P1000, ISO 6344 standard; average particle diameter 13.3 microns), an assortment of band-aids (in case of bleeding), an airtight pocket-sized sheet container, and a multi-language manual of instructions. Our quality controls assure the extermination of flu virus particles with an efficiency of 99.9% if uniform and vigorous nose blowing is performed frequently with the sandpaper therapeutic kit during a flu episode. After several uses on the nose, the SANDGRIATALTM sandpaper can be used, without risks of infection, to soften callosities, or as a practical nail polisher. SANDGRIATALTM is available in several sheet colors and sizes, and is sold without prescription in pharmacies and in selected grocery and hardware stores.

Anthropophagic habits alter the microbiota of the human gut

Mwongo, O.1, Mwongo, O.1, Mwongo, O.1 and Mwongo, J.C.2
1Yuyu University, somewhere in Africa (ND)
2Dpt. Of Anthropophagy, Wholemeat Breakfast University, South Dakota

Eating habits and the nature of the diet, both qualitatively and quantitatively, are known to influence the composition of the microbiota in the intestine. Although cannibalism is though to have played a role in social development and early evolution of the human species, the influence of human meat ingestion had never been investigated from a physiological and microbiological point of view. This is the first scientific study in this pioneering direction. Two-hundred regular daily customers of the junk- and fast-food restaurant McMickey’s were blindly fed with ground meat from human forensic waste in their hamburgers instead of the normal junk, whereas a second cohort of 200 individuals were fed with the habitual stuff, as a control. The Committee for Bioethics of the state of South Dakota allowed this experiment because “it would not be worse than the shit these guys were eating already, anyway”. Interestingly, the human meat-eating group asked for an extra piece three-times more frequently than the control, and 23% asked the cook if the recipe had been improved somehow, visibly delighted. In contrast, more complains about the quality of the food were presented by the control group in comparison with the human-meat eating group (p<0.000001), the only complain from the latter group corresponding to one individual who found a gold tooth in his BigMac. Automatic probes for collecting samples of faeces from all individuals involved in the experiment were cunningly installed in their domestic WCs by postgraduate students disguised as household cleaning personnel. Visual examination of the consistence and abundance of the faecal samples revealed that human meat-eating individuals went to the toilet more regularly. Faecal samples were collected and processed for the isolation of microbial species in culture and their further identification by serologic and molecular techniques. In parallel, rRNA 16S amplification and sequencing was performed straight on the faecal samples from both experimental groups to identify non-cultivable bacteria. Surprisingly, our study revealed an increase in microbial diversity that was patent in samples from individuals subjected to involuntary human meat diet, respect to the control. Novel anaerobic species were isolated, namely Nosferatella cannibalensis, Cometelcoccus dakotensis, Delacacca gordae and Morbidelicatella macmickeyii. Our results suggest that recycling human corpses onto the alimentary chain would have a positive impact in human health, save energy that is currently wasted in crematory ceremonies, and allow the recovery of massive urban burial grounds for other social uses.

CONCRETASE: an enzyme that degrades building materials by a novel waka-waka mechanism

D. P. Stevenson and P.D. Stevenson
Applied Demolitions, Cascot, USA

High throughput structural analysis of orphan proteins from extremophile organisms has emerged as a promising approach to unveil novel and unpredictable polypeptide biological activities in extreme natural environments. To search for new protein functions that could have biotechnological applications both at industry and at home in the post-constructomic era, we have performed a comprehensive structural analysis of the proteome of Brickeria debrisii, an archaea that likes living under tons of construction wreckage in the outer suburbs of modern cities. Thirteen hundred and a half proteins were crystallized on an automated 3D-POT, and their structures were analyzed using the OJIMETRIXTM platform. One unique protein, which was named as CONCRETASE, was selected for further studies because of the combination of a highly flattened three-dimensional folding with a really-hungry surface asymmetry (see below), which are likely to be imposed by the high pressure and dusting conditions suffered by D. debrisii under the rubble. Shape-oriented enzymatic analysis of CONCRETASE demonstrated that this protein readily degrades all kind of construction materials, from reinforced concrete to handicrafted glass, suggesting that D. debrisii lives on building junk food. CONCRETASE did not need cofactors nor activators, and also displayed good lytic activity towards the abundant useless objects that fill the apartment of lower and middle class families. In vitro stationary-state kinetics studies using refined tile dust as the substrate indicated that the high specific activity of CONCRETASE (Kcat = 1.1 x 1013 x s-1) is achieved by a non-saturable waka-waka reaction mechanism, which takes place in two steps:

To the best of our knowledge, this is the first description of a waka-waka catalytic mechanism in a non-virtual, real-life enzyme. The abundance of concrete- and building-related manufactures in human habitats prompts to their exploitation as regular food supplies. The avidity, wide substrate specificity, and high stability of CONCRETASE, as well as its easy and cheap purification from crude debris extracts, make this enzyme an attractive candidate as a human digestion adjuvant during food-resource supply limit situations (supplementary information at El Garrofer).