The top three news stories of the week, as chosen by our resident students. This week’s top stories include visualising mutations, cellular tunnels and an experiment that combines all the experiments! 

By Tapan Pipalia

Mutations under scanner

 Did you know that it has been estimated that we receive about 100 new mutations from our parents (1,2)? However, it has been hard to study what these mutations actually do. The rate of mutations and their effects on the fitness of the cells ultimately determine their pace of evolution. Since it has been hard to study and visualise mutations in real time, estimating the relative frequencies of deleterious, neutral and beneficial mutations, also known as distribution of fitness effects (DFE) has proved difficult. Although some approaches have attempted to observe the dynamics of the mutations, they have been limited in their scope and biased since in those methods natural selection gets rid of the bad mutations. DFE amongst other reasons is important to help understand effects of different types of mutation on our well-being and how they may be the cause of complex diseases. I hope it ultimately might even allow us to estimate our chances of joining the X-men troupe and saving the world for example!

A new study(3) has combined microfluidics (a method of creating tiny experimental chambers sometimes smaller than 1 millimetre), time lapse imaging and a fluorescent tag to show the mutation to see the number of mutations. It has also been shown to be able to track their effects on individual E. coli cells over as many as 200 generations (this is a lot!). The mutations they were analysing were spontaneous and mainly borne out of DNA replication errors which are the most common source of the mutations in general. From their published supplementary movies one can see how E. coli cells within each microfluidic channel varied in their growth pattern and how mutations marked by bright spots were tracked within each new cell in each lane. Researchers were able to scan more than 1000 such micro channels simultaneously over 3 days!

Their approach led them to study of mutation dynamics in individual cells, the effect of those mutations on their growth and survival and interactions between mutation types. Amongst other results they were able to show that a smaller proportion of mutations were found to be bad than predicted previously from indirect observations.

Overall this approach looks very promising and for all my fellow mutants out there, by running your cells through such a setup you might have an opportunity to peep into how healthy your future will be.

For more information please read the article (3)

double helix
Photo credit: @typographyimages via pixabay

Deconstructing the nuclear tunnels

Just like London needs its intricate tube network to shuttle people to the city centre and out, the cells in our body need channels to allow transport of all kinds of cargo between two basic domains- nucleus and cytoplasm. For this role cells have their own transport channels- Nuclear Pore Complex (NPC). NPCs play a central role as gatekeepers of RNA, protein transport whilst allowing regulation of various nuclear processes. Defects in them have been associated with multiple diseases(4). Just as knowing and relying on information about station staff, departure boards, signal systems, size of the platforms and thereby size of tubes/number of passengers passing through it helps in estimating how smooth travel between stations is going to be, knowing the structure and assembly of the NPCs should help in understanding how transport is regulated through them.

Each NPC is made up of around 550 copies of 30 different proteins of the nucleoporin family (Nups) which are further organised into higher order structures. Previous attempts have managed to describe partial structures however a new study in Nature is the first to solve a complete structure of NPCs at sub-nanometre resolution in yeast Saccharomyces cerevisiae. The mammoth effort involved use of diverse range of techniques such as mass spectrometry, in vivo imaging cryo-electron tomography and sub-tomogram averaging and also a phenotypic analysis platform called ODELAY which allowed the researchers to determine critical elements of NPC stability. The platform helped to do so via quantifying the fitness defect (all about fitness these days!) of strains which had their Nups systematically truncated.

The end result is a 3D map of the entire final NPC with details about location, orientation and interactions of each of the Nups which involves information about which components provide the rigidity VS flexibility VS specific functionality within the structure. Basically they know now the size of the tunnel, shape of it, position of the platforms on either side, barriers, which bits do what and other such details of the NPC tunnel.

For more details, please read the article (5)

nuclear tunnels
Photo credit: @bkenney_ via Twenty20

‘Top Gear’ of the molecular imaging world

A new study appears to have built a ‘Top Gear’ for viewing molecules in tissue. Currently, methods to see what is in tissue either give very specific information about a single target (probe against a specific gene/protein/element) or can give more general information about many targets (by processing the entire tissue and then analysing components). The team from Vanderbilt University in Nashville combined integrated matrix assisted laser desorption/ionization imaging mass spectrometry (MALDI IMS), laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), bioluminescent imaging (BLI), magnetic resonance imaging (MRI) and blockface imaging (I know, too long to even write it down) to enable whole organ mapping of amount and layout of various proteins and elements.

The study focused on a mouse model of dissemination of Staphylococcus aureus infection to find the bacterial and host proteins that are located at the site of infection. More specifically, the interface they were studying were abscesses which are inflammatory lesions which consist of bacteria surrounded by few immune cells called neutrophils. They found that despite appearing normal using traditional methods, these lesions were a mix of both bacterial and host proteins. Even elements such as iron known to be critical in determining fate of infections were found to have uneven distribution explaining variations in the spread of infection.

Combining methods in this way allows in depth mapping of macromolecules and elements in intact tissues and can be adapted to any specific diseases which may have altered protein or element distribution. But yes, before you add this platform to your wish list, note the need to deploy invasive procedures to get the biopsy samples along with requirements of space and computational power to process data!

For more information please read the article (6)

Molecules
Photo credit: @tylerfrumusa via Twenty20

References:

  1. Crow, J. F. How much do we know about spontaneous human mutation rates? Environ. Mol. Mutagen. 21, 122–129, (1993).
  2. Kondrashov, A. S. & Crow, J. F. A molecular approach to estimating the human deleterious mutation rate. Hum. Mutat. 2, 229–234, (1993).
  3. Robert, L., Ollion, J., Robert, J., Song, X., Matic, I., Elez, M. Mutation dynamics and fitness effects followed in single cells. Science 359, 1283-1286, (2018)
  4. Nofrini, V., Di Giacomo, D. & Mecucci, C. Nucleoporin genes in human diseases. Eur. J. Hum. Genet. 24, 1388–1395, (2016)
  5. Kim, S.J., Fernandez-Martinez, J., et al. Integrative structure and functional anatomy of a nuclear pore complex. Nature 555, 475, (2018)
  6. Cassat, J.E., Moore, J.L., et al. Integrated molecular imaging reveals tissue heterogeneity driving host-pathogen interactions. Science Translational Medicine 10, (2018)