ACHOO - Autosomal dominant Compelling Helio-Ophthalmic Outburst

ACHOO - Autosomal dominant Compelling Helio-Ophthalmic Outburst - syndrome is another name for Photic sneeze reflex. This is the condition that affects around a fifth to a third of the population in which stimuli such as bright lights trigger uncontrolled sneezing. (Also known as “sun sneezing”.)

According to the source from which I discovered ACHOO, the ABC Science Weekly Update, it is “a funny acronym invented by doctors to help them remember the essentials of the photic sneeze reflex!” Personally, I think that “Photic sneeze reflex” is clearer than “Autosomal dominant Compelling Helio-Ophthalmic Outburst”! I suspect they were just having a bit of fun but, either way, it gets the coveted pre hoc status for such a well-aligned (if somewhat over contrived) acronym. (It’s just a shame about the “dominant” bit, which, ironically is probably the most likely bit to be forgotten!)

ASSET - Accelerated Segment Switch in Exons to alter Targeting

See the entry for RAVER. These guys had clearly tried so hard to contrive an acronym that was a dictionary word (surely it should really be ASSEAT?) that I thought they deserved their own entry.

ASSET - Accelerated Segment Switch in Exons to alter Targeting:

Doley R, Mackessy SP & Kini RM (2009).Role of accelerated segment switch in exons to alter targeting (ASSET) in the molecular evolution of snake venom proteins. BMC Evol Biol. 9:146.

RAVER - Rapid Accumulation of Variations in Exposed Residues

Things are beginning to settle after my recent move to Australia and today’s PubCrawler alert contained a reminder that ORCA had been somewhat neglected over the past few weeks:

RAVER - Rapid Accumulation of Variations in Exposed Residues - is the acronym given to a new theory to explain the molecular evolution of “three-finger” (snake) toxins:

Sunagar K, Jackson TN, Undheim EA, Ali SA, Antunes A & Fry BG (2013). Three-Fingered RAVERs: Rapid Accumulation of Variations in Exposed Residues of Snake Venom Toxins. Toxins (Basel) 5(11):2172-2208.

Three-finger toxins (3FTx) represent one of the most abundantly secreted and potently toxic components of colubrid (Colubridae), elapid (Elapidae) and psammophid (Psammophiinae subfamily of the Lamprophidae) snake venom arsenal. Despite their conserved structural similarity, they perform a diversity of biological functions. Although they are theorised to undergo adaptive evolution, the underlying diversification mechanisms remain elusive. Here, we report the molecular evolution of different 3FTx functional forms and show that positively selected point mutations have driven the rapid evolution and diversification of 3FTx. These diversification events not only correlate with the evolution of advanced venom delivery systems (VDS) in Caenophidia, but in particular the explosive diversification of the clade subsequent to the evolution of a high pressure, hollow-fanged VDS in elapids, highlighting the significant role of these toxins in the evolution of advanced snakes. We show that Type I, II and III α-neurotoxins have evolved with extreme rapidity under the influence of positive selection. We also show that novel Oxyuranus/Pseudonaja Type II forms lacking the apotypic loop-2 stabilising cysteine doublet characteristic of Type II forms are not phylogenetically basal in relation to other Type IIs as previously thought, but are the result of secondary loss of these apotypic cysteines on at least three separate occasions. Not all 3FTxs have evolved rapidly: κ-neurotoxins, which form non-covalently associated heterodimers, have experienced a relatively weaker influence of diversifying selection; while cytotoxic 3FTx, with their functional sites, dispersed over 40% of the molecular surface, have been extremely constrained by negative selection. We show that the a previous theory of 3FTx molecular evolution (termed ASSET) is evolutionarily implausible and cannot account for the considerable variation observed in very short segments of 3FTx. Instead, we propose a theory of Rapid Accumulation of Variations in Exposed Residues (RAVER) to illustrate the significance of point mutations, guided by focal mutagenesis and positive selection in the evolution and diversification of 3FTx.

This is really a twofer, as RAVER itself is proposed as a replacement for ASSET, which is pretty weak as fitting words to acronyms goes: ASSET - Accelerated Segment Switch in Exons to alter Targeting:

Doley R, Mackessy SP & Kini RM (2009).Role of accelerated segment switch in exons to alter targeting (ASSET) in the molecular evolution of snake venom proteins. BMC Evol Biol. 9:146.

Unless there are more snakes in banking or dance music than I realise, I think these must both be rated as ad hoc.

PICRUSt - Phylogenetic Investigation of Communities by Reconstruction of Unobserved States

I think that my favourite talk from the 1st International Environmental ‘Omics Synthesis Conference was the Keynote address by Jack Gilbert on the Earth Microbiome Project and other cool microbial metagenomic/metagenetic stuff. It also featured an impressively contrived acronym:

PICRUSt - Phylogenetic Investigation of Communities by Reconstruction of Unobserved States.

Profiling phylogenetic marker genes, such as the 16S rRNA gene, is a key tool for studies of microbial communities but does not provide direct evidence of a community’s functional capabilities. Here we describe PICRUSt (phylogenetic investigation of communities by reconstruction of unobserved states), a computational approach to predict the functional composition of a metagenome using marker gene data and a database of reference genomes. PICRUSt uses an extended ancestral-state reconstruction algorithm to predict which gene families are present and then combines gene families to estimate the composite metagenome. Using 16S information, PICRUSt recaptures key findings from the Human Microbiome Project and accurately predicts the abundance of gene families in host-associated and environmental communities, with quantifiable uncertainty. Our results demonstrate that phylogeny and function are sufficiently linked that this ‘predictive metagenomic’ approach should provide useful insights into the thousands of uncultivated microbial communities for which only marker gene surveys are currently available.

Langille MGI et al. (2013). Predictive functional profiling of microbial communities using 16S rRNA marker gene sequences. Nature Biotechnology 31, 814–821.

GOBLET - Global Organisation for Bioinformatics Learning, Education & Training

I’m at the 1st International Environmental Omics Synthesis (iEOS) Conference conference in Cardiff, which means (a) very little time for posting, and (b) a wealth of acronyms on display. A particularly notable contribution from one of the earlier sessions was GOBLET: Global Organisation for Bioinformatics Learning, Education & Training.

GOBLET, the Global Organisation for Bioinformatics Learning, Education and Training, is a legally registered foundation. Its mission is to:

1. Provide a global, sustainable support and networking structure for bioinformatics educators/trainers and students/trainees (including a training portal for sharing materials, tools, tips and techniques; guidelines and best practice documents; facilities to help train the trainers; and offering different learning pathways for different types of learner)

2. Facilitate capacity development in bioinformatics in all countries

3. Develop standards and guidelines for bioinformatics education and training

4. Act as a hub for fund gathering

5. Reach out to, amongst others, teachers at high schools, to bridge the gap to the next generation of bioinformaticians, and

6. Foster the international community of B3CB trainers

As well as the natty acronym, it could be quite useful.

BEDASSLE - Bayesian Estimation of Differentiation in Alleles by Spatial Structure and Local Ecology

Courtesy of Graham Coop on Twitter comes BEDASSLE: Bayesian Estimation of Differentiation in Alleles by Spatial Structure and Local Ecology.

"This is a method [Gideon Bradburd] worked on in collaboration with Peter Ralph and Graham Coop. It allows users to quantify the relative contributions of geographic and environmental distance to patterns of genetic differentiation."

This is a very solid ad hoc contrived acronym - making a word that is easy to pronounce but also (thanks to the altered spelling) easy to Google whilst not sounding too contrived. Hats off to Gideon, Peter and Graham. (I'm not really sure that I understand the connection to the logo, though!)

PURRS - Personal Unconditional Rescue Rehabilitation Re-homing Satisfactorily

Posts are a bit thin on the ground at present due to moving house and travelling around, but here’s an acronym that I came across whilst packing up my worldly goods. It’s the motto of Barbara’s Cat Rescue and deserves a mention here firstly because of it’s clear pre hoc contrived nature and, (a more important) secondly, to give a bit of extra publicity to Barbara.

PURRS - Personal Unconditional Rescue Rehabilitation Re-homing Satisfactorily

If looking after homeless animals is your kind of thing, please visit (and “Like”) Barbara’s Facebook page. Better still, make a donation!