Genetics Archives - The Sciku Project

June 20, 2024June 20, 2024

Gene Editing by John Hawkhead

a cure for cancer…
cutting the gordian knot
in a gene sequence
by John Hawkhead

Gene editing provides us with the ability to make highly specific changes in the DNA of a living organism. It has the potential to revolutionize cancer treatment via manipulation of the genome to target specific genetic mutations that drive the growth and spread of tumours.

The cutting of the Gordian knot is a legend associated with Alexander the Great about a complex knot that tied an oxcart. It was claimed that whoever was able to untie it would be destined to rule all of Asia. When Alexander was challenged to untie the knot he cut through it with his sword rather than attempt to untie it. This is now used as a metaphor for solving a seemingly intractable problem through bold means or thinking differently.

Further reading:

‘What is genome editing?’, 2019, National Human Genome Research Institute, available: https://www.genome.gov/about-genomics/policy-issues/what-is-Genome-Editing

‘How CRISPR Is Changing Cancer Research and Treatment’, 2020, National Cancer Institute, available: https://www.cancer.gov/news-events/cancer-currents-blog/2020/crispr-cancer-research-treatment

‘The Potential Revolution of Cancer Treatment with CRISPR Technology’, 2023, Stefanoudakis, D., et al., Cancers (Basel), https://doi.org/10.3390/cancers15061813

Author bio:

John Hawkhead (@HawkheadJohn) has been writing haiku and illustrating for over 25 years. His work has been published all over the world and he has won a number of haiku competitions. John’s books of haiku and senryu, ‘Small Shadows’ and ‘Bone Moon’, are now available from Alba Publishing (http://www.albapublishing.com/). Read more of John’s sciku here!

February 2, 2023May 16, 2024

DNAncient by James Penha

Genetic freeze frame
shows Edenic genesis
in Arctic subsoil
By James Penha

“Two-million-year-old DNA from northern Greenland has revealed that the region was once home to mastodons, lemmings and geese, offering unprecedented insights into how climate change can shape ecosystems.”

Quote from The Guardian article ‘DNA from 2m years ago reveals lost Arctic world’ from 7th December 2022.

Further reading:

https://www.theguardian.com/science/2022/dec/07/dna-from-2m-years-ago-reveals-lost-arctic-world?CMP=Share_iOSApp_Other

https://www.nature.com/articles/s41586-022-05453-y

Author bio:

Expat New Yorker James Penha (he/him🌈) has lived for the past three decades in Indonesia. Nominated for Pushcart Prizes in fiction and poetry, his work is widely published in journals and anthologies. His newest chapbook of poems, American Daguerreotypes, is available for Kindle. His essays have appeared in The New York Daily News and The New York Times. Penha edits TheNewVerse.News, an online journal of current-events poetry. You can find out more about James’ poetry on his website https://jamespenha.com and catch up with him on Twitter @JamesPenha

Enjoyed James’ sciku? Check out more of his sciku here: ‘Quantumku‘, ‘If A Tree Talks in a Forest’, ‘Air-Gen-Ku’, and ‘Boys Whale Be Boys’.

November 11, 2022November 16, 2022

Ant-y-insulin

Long live queens! But why?
Ovaries might change growth cues
to extend lifespan!
By Dr Nathan Woodling

A queen takes the throne.
Insulin surges, eggs grow.
A switch extends life.
By Dr Andrew Holmes

Reproduction is linked to reduced lifespan in many animals, yet ant queens have a far greater longevity compared to workers in their colony – black garden ant queens can live up to 30 times longer than the 1-year lifespan of their workers. Ant queens have the same genome as their workers, and in some species of ant they aren’t reared differently but switch caste following the death of the current queen.

The Indian jumping ant (Harpegnathos saltator) exhibits this switching behaviour. When a queen dies, workers duel each other, with the winners transitioning into pseudo-queens known as gamergates. These gamergates begin laying fertile eggs and their lifespan is substantially increased – from 7 months to 4 years. Gamergates can even transition back into the worker caste if replaced by another queen, their lifespan reverting back to 7 months.

How is ant lifespan so mutable?

New research by Yan et al. (2022) points to an insulin-suppressing protein as a possible answer.

The researchers compared gene expression during caste switching and found that ants that switch from worker to gamergate produce more insulin. The increased insulin results in a change in the balance of activity between the two main insulin signalling pathways, MAPK (which controls metabolism and egg formation) and AKT (which controls ageing).

On transitioning to a gamergate, the MAPK insulin signalling pathway’s activity increases, inducing ovary development and the production of eggs. But this also results in the production of an insulin-suppressing protein (Imp-L2) which blocks the AKT insulin signalling pathway, increasing longevity.

IMP-L2 essentially acts as a switch between a worker being short-lived and sterile compared to a queen being long-lived and fertile.

Original research:

http://dx.doi.org/10.1126/science.abm8767

A note about the sciku:

Nathan and Andrew independently wrote their sciku about this research and discovered the coincidence when Nathen posted his poem on Twitter. The two different approaches to writing about the same subject demonstrate why sciku are such a consistently interesting medium for exploring and sharing research.

Author bios:

Dr Nathan Woodling is a lecturer in molecular biosciences at the University of Glasgow. You can follow him on Twitter here: @NathanWoodling.

Dr Andrew Holmes is a former researcher in animal welfare and the founder and editor of The Sciku Project. You can follow him on Twitter here: @AndrewMHolmes.

October 8, 2021October 8, 2021

Darwin’s Finches

islands diverging
beaks for seeds and bugs and blood
letters rearranged

Darwin’s finches are a group of 18 species of passerine birds found across the Galápagos Islands (hence their other name of Galápagos finches). The group are a poster child for Darwin’s theory of evolution by means of natural selection. During his voyage on the HMS Beagle he collected specimens from what later turned out to be 12 of the 18 species, although Darwin himself didn’t realise the significance at the time, not realising they were all types of finch (ornithologist John Gould corrected him about the species) and not recording which islands they came from (he was later able to correctly assign them based on the notes of others on the voyage).

As the finches colonised the islands and began to adapt to the varied habitats and food resources available, the different groups diverged from each other, resulting in the separate species we see today. The finches themselves have a huge variety of forms (likely leading to Darwin’s confusion), most notably in their beak shapes and sizes. Their beaks are highly specialised to the food sources available on the different islands, with different species feeding on nuts, seeds, flowers, nectar, leaves, cacti, and invertebrates (including insects, parasites, larvae and spiders).

Perhaps the strangest of all is the Vampire Ground Finch (Geospiza septentrionalis) which feeds on the blood of other birds such as blue-footed boobies and Nazca boobies. It’s theorised that this behaviour evolved from mutualistic behaviours where the finch would clean parasites from the plumage of larger birds. These days their sharp beaks are used to peck their victim’s skin until it starts bleeding and the finches feed on the blood. Their unpleasant behaviours don’t stop there, however, as they steal eggs and roll them into rocks to break the shells, and they’ll also eat guano – excrement from seabirds. Since fresh water is scarce on their home islands (Wolf Island and Darwin Island), they also feed on nectar from Galápagos prickly pear flowers.

Molecular studies of Darwin’s finches suggests that the timing and spatial expression of at least four genes are responsible for the differences in beak structure, alphabetic changes that led to anatomical changes: BMP4 (which encodes Bone morphogenetic protein 4), CaM (which encodes Calmodulin), ALX1 (which encodes ALX homeobox protein 1), and HMGA2 (which regulates the expression of other genes).

A note about the sciku: this sciku has been written using a scale and focussing structure – narrowing in from the vast islands to the beaks to the individual letters of DNA. Have you ever tried writing sciku with a focussing structure? If so, how did you get on? Let us know in the comments below!

Interested instances of evolution in action? Check out this sciku by Prof Matthew J. James on the classic example of evolution, the Peppered Moth: Dark Moths.

May 14, 2021May 14, 2021

Saba, the morning breeze by Dr Jolene Ramsey

We know you were small
Preying on Proteus too
Surprise, DNA!
by Dr Jolene Ramsey

Bacteriophages, or phages, are the viruses that infect bacteria. They come in different shapes and sizes, but are often icosahedral (spherical) and tailed. A tailed phage is structured like a filled lollipop, where the candy represents the phage head, the filling represents the nucleic acid genome, and the stick is like the tail. The overwhelming majority of phages scientists and students have discovered up to this point are tailed with a DNA genome, largely due to bias in our sampling methods. Recent investigations suggest many phages with RNA genomes remain to be isolated, and they were hypothesized to be small and round, similar to the ones that are already known. We want to find them.

In a very focused hunt, we looked for small RNA phages against the human opportunistic pathogen Proteus using a filtration selection method. After a few rounds of selection, there was a prime candidate that was definitely small, but it didn’t pass the other tests that define RNA phages. It was a puzzle. For clues, we looked at the phage shape in the electron microscope. To our astonishment the phage had a tail and a very small head! We immediately verified that it had a DNA genome as well. Though the search was a failure, we put phage Saba in the arsenal for use in other projects. To fully survey the diverse kinds of phage in the environment we will need to develop and refine targeted and general protocols for phage isolation. This will give us the most accurate picture of the phage universe.

Original research: https://doi.org/10.1128/MRA.01094-19

Jolene Ramsey studies bacterial viruses (phage) as a Center for Phage Technology postdoctoral researcher. She tries to understand how phages orchestrate their escape plan at the molecular level. You can catch up with her on Twitter: @jrrmicro

Enjoyed Jolene’s sciku? Check out her excellent sciku ‘Privateer, the phage’, ‘TF gets in on the bud’, ‘Click click go!’ and ‘The Phriendly Phage‘.

April 1, 2021May 14, 2021

The Phriendly Phage by Dr Jolene Ramsey

Phage are phriends, not phood
Not Phriendly to host, but nice
Plaques phor lab hunters
By Jolene Ramsey

Vibrio natriegens is an environmental microbe that naturally resides in marine habitats, including brackish waters and salty marshes. If you Google this bacterial species, all the top hits will tout its ‘fast’ growth. Unusual among bacteria, but common with other vibrios, V. natriegens has a >5 Megabase genome split across two chromosomes. It also has a high count of total ribosomes, the cellular machines that make protein. As a non-pathogenic environmental organism, researchers are exploring its use in various biotechnology applications, including as a protein production system. This is one reason some are hoping V. natriegens will become the next lab workhorse in molecular and industrial microbiology that could even rival E. coli.

With an interest in improving the resources available to use in this field of research, we decided to look for bacteriophages that target V. natriegens. Bacteriophages, or phage, are the viruses that infect bacteria. Because phage rely so heavily on their host cell to copy themselves, they turn out to be extremely useful tools for probing how the cell works. As a kind of natural predator, phages can be found everywhere the host lives. The phage this Sciku is about, named Phriendly, was found in a sample collected by a college student brand-new to research on a trip to the beach.

The phage hunt process involves layering spots of environmental samples on top of growing bacteria, then looking for clear spots where the bacteria did not grow (or died due to infection) called plaques. A few of the beach samples yielded these plaques. One was a hazy, weak plaque that was difficult to propagate. We nicknamed it ‘problem phage’. In contrast, another had large, clear plaques that appeared quickly and consistently. We dubbed it the ‘friendly phage’. Following our cute tradition, we replace all ‘f’ sounds with the ‘ph’ used in the word phage to come up with the name Phriendly. Along with others, Phriendly is in a collection of phages we hope can be tools to better harvest the great potential its host microbe has for advancing biotechnology.

Original research: https://doi.org/10.1128/MRA.01096-19

Enjoyed Jolene’s sciku? Check out her excellent sciku ‘Privateer, the phage’, ‘TF gets in on the bud’, ‘Click click go!’ and ‘Saba, the morning breeze’.

March 12, 2021May 14, 2021

Click click go! by Dr Jolene Ramsey

Galaxy applied
Eyes scan Apollo data
To annotate phage
By Jolene Ramsey

Studying the genetic makeup of an organism helps us understand how they tick. Scientists often make precise notes about the position and function of important features within a genome, called annotation, akin to marking and reviewing the restaurants on a city map. Viruses tend to have smaller genomes, but they are packed with information. We annotate the genomes of bacteriophages, the viruses that infect and kill bacteria, to reveal their genetic secrets. While there are automated annotation programs, manual review by human eyeballs is necessary to ensure high quality outcomes. With the number of interesting new phage genomes rising daily, the need for user-friendly tools to analyze their genomes has grown as well.

Using our curated toolbox in an open-source, online bioinformatic portal called Galaxy (https://cpt.tamu.edu/galaxy-pub), features common to bacterial and phage genomes can be spotted and cataloged by novices and experts. There are many feature types, each one detected by a different tool. Instead of manually passing the genome through each tool, we are able to speed up and standardize the process using automatic pipelines that run a prescribed list of analyses. We can visualize the results in context using another linked platform called Apollo, and also compare to known genomes. The coupled Center for Phage Technology Galaxy and Apollo suite have allowed us to annotate >130 bacteriophage genomes, and train many students and researchers along the way.

Original research: https://doi.org/10.1371/journal.pcbi.1008214

Enjoyed Jolene’s sciku? Check out her excellent sciku ‘Privateer, the phage’, ‘TF gets in on the bud’, ‘The Phriendly Phage’ and ‘Saba, the morning breeze’.

August 16, 2019August 16, 2019

Pickled – Not Pickled

Hidden, protected.
Ancient bird beneath acid,
DNA preserved.

DNA from extinct species can be hard to get – obtaining bone or tissue samples is tricky and degradation of those samples over time can result in vast swathes of the genome missing or heavily fragmented.

Yet, as a new study by Oswald et al (2019) suggests, there are circumstances where samples can be remarkably preserved across hundreds and even thousands of years.

The study used bones found in Sawmill Sink, a blue hole in the Bahamas. The Sawmill Sink has a top layer of fresh water, a hydrogen sulfide layer and then a bottom layer of saltwater. The hydrogen sulfide layer forms a barrier that limits UV light and oxygen from getting to the lower saltwater. As a result, the various bones found on floor of the blue hole are remarkably well preserved.

Oswald et al (2019) were able to recover a nearly complete mitochondrial genome from a 2,500 year old bone of an extinct bird species – Caracara creightoni. Genetic analysis of the ancient DNA suggests that the species is sister to a clade containing the Northern Crested Caracara and the Southern Crested Caracara, birds of prey in the Falconidae family found in Central and South America. The work highlights the huge potential for similarly recovered fossils to illuminate our understanding of species and populations in the past.

The title of this sciku is Pickled – Not Pickled. This refers to the hydrogen sulfide layer in Sawmill Sink which forms sulfuric acid where it comes into contact with the fresh water layer above, making it extremely hard for divers to get through and discover the bones beneath. Whilst the bones themselves were not in the sulfuric acid, they were preserved by it making them in essence pickled whilst not actually being pickled.

Original research: http://dx.doi.org/10.1016/j.ympev.2019.106576

May 10, 2019May 10, 2019

Adaptation by Prof Fred W. Allendorf

Survive, reproduce
Mendel rules, pass on your genes
That’s adaptation
by Prof Fred W. Allendorf

Natural selection is one of the primary mechanisms of evolution. Those individuals with higher survival and greater reproductive success are more successful at passing on their genes to future generations. This brings about adaptation which increases the fitness of individuals in future generations.

Further reading: A brief history of the genetic theory of adaptation by H. Allen Orr (2005): http://dx.doi.org/10.1038/nrg1523

Prof Fred W. Allendorf is Regents Professor of Biology Emeritus at the University of Montana. His primary scientific interest is the application of population genetics to conservation biology. He is senior author of the book Conservation and the Genetics of Populations. Check out Fred’s other sciku on Genetic Drift, Inbreeding Depression and Gene Flow.

March 8, 2019May 10, 2019

Gene flow by Prof Fred W. Allendorf

Move away from home
Find a mate and reproduce
That is called gene flow
by Prof Fred W. Allendorf

Gene flow is the movement of alleles or genes from one population to another (Slatkin, 1987). Gene flow is crucial in reducing the harmful effects of genetic drift and inbreeding depression in populations. As global change, habitat destruction, and fragmentation rapidly progress, many natural populations are becoming smaller, more isolated, and more affected by inbreeding depression. However, Sewall Wright (1951) demonstrated that even very small amounts of gene flow are sufficient to avoid the harmful effects of genetic drift and inbreeding within local populations.

Original research:

Slatkin, M. 1987. Gene flow and the geographic structure of natural populations. Science 236: 787-792.

Wright, S. 1951. The genetical structure of natural populations. Annals of Eugenics 15: 323-354.

Prof Fred W. Allendorf is Regents Professor of Biology Emeritus at the University of Montana. His primary scientific interest is the application of population genetics to conservation biology. He is senior author of the book Conservation and the Genetics of Populations. Check out Fred’s other sciku on Genetic Drift, Inbreeding Depression and Adaptation.

September 18, 2018September 18, 2018

These membrane proteins by Chris Gillen

These membrane proteins

might reclaim salt from urine

or suck it from ponds.

Mosquitoes face extraordinary challenges to their salt and water balance during their complex life-cycles. Larva of most species live in freshwater environments in which they lose salt by diffusion and gain water by osmosis. In contrast, adults live in terrestrial environments where water loss is a problem. Finally, female mosquitoes ingest large amounts of salt and water when they take a blood meal.

In vertebrates, the sodium-potassium-chloride cotransporters (NKCCs) participate in both salt secretion and absorption. Whereas secretory roles for this group of transporters are well-described in insects, their roles in salt absorption are less well studied. Piermarini et al (2017) recently identified yellow fever mosquito transport proteins that have sequence similarity to the vertebrate NKCCs. Two of these transporters apparently resulted from gene duplications early in the insect and mosquito lineages, suggesting that they have diverged into roles related to mosquito osmoregulation. The transporters may contribute to salt absorption, because the researchers found them in adult hindgut and larval anal papillae, both tissues that transport salt into the body.

Original research: Piermarini, P. M., Akuma, D. C., Crow, J. C., Jamil, T. L., Kerkhoff, W. G., Viel, K. C. M. F., and Gillen, C. M. (2017) Differential expression of putative sodium-dependent cation-chloride cotransporters in Aedes aegypti. Comp. Biochem. Physiol. A 214, 40-49. https://doi.org/10.1016/j.cbpa.2017.09.007

Chris Gillen teaches animal physiology and science writing at Kenyon College in Gambier, Ohio. He is author of The Hidden Mechanics of Exercise (Harvard, 2014) and Reading Primary Literature (Pearson, 2007).

July 17, 2018July 17, 2018

Eggy difference

The Baltic flounder:

Native to namesake region.

Eggy difference.

A new species of flounder has been identified as separate from the European flounder by Momigliano et al (2018). The Baltic flounder (Platichthys solemdali sp.) is native only to the Baltic Sea – the first fish species to be identified as endemic to the area.

Its reproductive behaviour differs from the European flounder, spawning eggs that sink in coastal areas as opposed to buoyant eggs in open water. There are also differences between the species in egg morphology, egg and sperm physiology. Unfortunately, the small morphological differences mean that it is difficult to unambiguously distinguish the species and genetic methods or egg/sperm analyses are required.

Original research: http://dx.doi.org/10.3389/fmars.2018.00225

July 12, 2018July 12, 2018

Extrapolation

from laboratory tests.

Not always correct?

Experiments within the laboratory are often used to understand biological interactions in a controlled manner. Yet research by Comforth et al (2018) suggests that what we learn from the laboratory may not always represent what happens in reality.

The researchers found that Pseudomonas bacteria (a pathogen that threatens immunocompromised people) behaved differently in humans compared to under laboratory conditions. This was particularly apparent in the levels of gene expression involved in antibiotic resistance, cell to cell communication and metabolism. The implications of this work suggest laboratory studies only take us so far and further understanding bacterial behaviour in humans is just as important.

Original research: https://doi.org/10.1073/pnas.1717525115

June 6, 2018June 6, 2018

Giant becomes five

endangered salamanders.

Hidden extinction?

The Chinese Giant salamander is the world’s largest amphibian, adults can be 2 meters long and weigh up to 50 kg. It’s critically endangered in the wild due to habitat destruction, fungal infection and because the species is used as a luxury food source in China. It is kept in far greater numbers in captivity as a result of it being farmed for food. Two studies published in Current Biology add additional concerns for the future of this species in the wild.

In what is thought to be the largest wildlife survey conducted in China, Turvey et al (2018) found that giant salamander populations were either critically depleted or had been eradicated, as well as finding plenty of evidence for illegal poaching. The researchers were unable to confirm the survival of wild Chinese giant salamanders at any of their survey sites, raising the question of whether this species is all but extinct in the wild.

In a companion piece of research, Yan et al (2018) performed a genetic analysis on Chinese giant salamanders and found that the species actually consists of at least five species-level lineages, potentially up to eight. This suggests that some of these distinct lineages (effectively separate species) may well have already gone extinct in the wild – a phenomenon known as cryptic or hidden extinction. This has crucial importance for conservation efforts, particularly with regards to re-releases from captive populations where the five lineages have been mixed and the resulting offspring are effectively hybrids.

Original research:

Turvey et al (2018): https://doi.org/10.1016/j.cub.2018.04.005

Yan et al (2018): https://doi.org/10.1016/j.cub.2018.04.004

February 13, 2018May 10, 2019

Inbreeding Depression by Prof Fred W. Allendorf

More homozygous

brings inbreeding depression.

Cousins should not mate.

Inbreeding (mating between relatives) results in offspring having reduced fitness. This is known as inbreeding depression and is primarily caused by increased homozygosity at loci with harmful recessive alleles. Small populations, where most or all mates are relatively closely related, are particularly vulnerable to inbreeding and inbreeding depression. The effects of inbreeding depression in small populations can accumulate to reduce the population growth rate and increase the probability of extinction (Keller and Waller 2002).

Despite being of interest since Darwin, inbreeding depression remains a crucial area of research in conservation biology, ecology, and evolutionary biology. As global change, habitat destruction, and fragmentation rapidly progress, many natural populations will become smaller and more isolated and consequently more affected by inbreeding depression.

Original Research: Keller, L. F., and D. M. Waller. 2002. Inbreeding effects in wild populations. Trends in Ecology & Evolution 17:230-241. http://dx.doi.org/10.1016/S0169-5347(02)02489-8

Fred W. Allendorf is Regents Professor of Biology Emeritus at the University of Montana. His primary scientific interest is the application of population genetics to conservation biology. He is senior author of the book Conservation and the Genetics of Populations.

Enjoyed this sciku? Check out Fred’s other sciku: Genetic drift, Gene Flow, and Adaptation.

January 16, 2018May 10, 2019

Genetic drift by Prof Fred W. Allendorf

Unavoidable

Time and chance happen to all

Wright, genetic drift.

Genetic drift is one of the primary mechanisms of evolution. It is the change in allele frequencies in a population between generations due to the sampling of individuals that become parents and the random binomial sampling of alleles during meiosis. The theory of genetic drift was primarily developed by Sewall Wright.

Genetic drift causes the loss of genetic variation, and it is more pronounced in small and isolated populations. The ongoing human-caused loss of habitat has brought about the loss of genetic variation in many species throughout the world via genetic drift.

Original research:

Wright, S. 1931. Evolution in Mendelian populations. Genetics 16:97-159. http://www.genetics.org/cgi/reprint/16/2/97

Enjoyed this sciku? Check out Fred’s other sciku: Inbreeding Depression, Gene Flow, and Adaptation.

December 20, 2017December 20, 2017

Transcription by Prof Sridhar Hannenhalli

To express or not

Here now a bit or a lot

That is the question.

Every cell in an organism contains an identical copy of the genome, except for rare somatic mutations, that encodes its entire gene complement. Yet, each of the hundreds of individual cell types in an organism utilizes a well-defined subset of the genes – imagine your neurons expressing genes that are normally expressed in skin cells. Thus the cell, starting from the single-celled embryo, must have a mechanism to control when, and how much of, each gene is expressed. This control is exercised, in large part, at the level of transcription – the process of reading the DNA encoding a gene on the genome and copying it into a messenger RNA (mRNA), which is eventually translated into the final protein product (or otherwise processed into a final RNA product).

Besides controlling normal development and defining the identity of individual cells, the response to a change in environment is also managed at the level of transcription. This was first demonstrated by Jacques Monod and Francois Jacob in their seminal 1961 paper, showing that a group of E. coli genes that encode for proteins required to break down lactose is transcriptionally switched on or off depending on whether the growth medium is rich in lactose or glucose. They went on to win the 1965 Nobel Prize in Physiology or Medicine for their discovery.

Transcriptional control plays a critical role not only in development and environmental response, but also at a longer time scale in mediating evolutionary divergence across species. In their classic 1975 paper, Mary-Claire King and Alan C Wilson, observing very high levels of similarity between several proteins of chimpanzees and humans, concluded that the vast phenotypic differences between the two species could not be explained by such small degree of molecular divergence and are likely to be driven by the changes in the mechanisms controlling the gene transcription.

The role of transcriptional control in dictating natural diversity at multiple natural scales from cells within an organism, individuals within a species, and across species is now well established. This extends even to phenotypic changes associated with all complex diseases, and is underscored by the observation that the vast majority of genotypic signals associated with human diseases reside in non-protein-coding regions of the genome, thus focusing the research efforts in interpreting these signals in the context of transcriptional control.

Original research:

Jacob, F. & Monod, J. (1961) Genetic regulatory mechanisms in the synthesis of proteins. J Mol Biol 3, 318–356. http://biotheory.phys.cwru.edu/phys320/JacobMonod1961.pdf

King, M. C. & Wilson, A. C. (1975) Evolution at two levels in humans and chimpanzees. Science (80) 188, 107–116. https://doi.org/10.1126/science.1090005

Hindorff, L. A. et al. (2009)Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. PNAS 106, 9362–9367. https://doi.org/10.1073/pnas.0903103106

Sridhar Hannenhalli is professor of Cell Biology and Molecular Genetics at the UMD, interested in transcriptional regulation and evolution. He is currently visiting IISc, Bangalore, as a Fulbright scholar. You can follow him on twitter @hannenhalli.

December 8, 2017December 8, 2017

Packaging signals by Maria White

Packaging signals:

Limiters of gene exchange

in influenza.

Influenza viruses, which have segmented genomes, can exchange genes through a process called reassortment, which can lead to the formation of novel influenza viruses. At the termini of each gene segment are regions called packaging signals, which direct the incorporation of each gene segment into virus particles during assembly.

A recent study by White et al (2017) demonstrated that heterologous packaging signals limit the efficiency of reassortment, but that this phenotype is dependent on the influenza virus gene segment being examined.

Of note, 85% of the reassortant viruses studied packaged a hemagglutinin (HA) segment carrying matched packaging signals relative to the background of the virus. The HA segment is of particular interest from a public health perspective due to its antigenic properties, and these data suggest that HA packaging signals could be an important factor in determining the likelihood that two influenza virus strains will undergo reassortment.

Original research: https://dx.doi.org/10.1128%2FJVI.00195-17

Maria White is a PhD candidate in the Immunology and Molecular Pathogenesis program at Emory University.

November 13, 2017November 13, 2017

An orphan crop

Yam: an orphan crop,

vital yet disregarded.

Gene map may assist.

Yams are a stable tuber crop in tropical Africa yet their cultivation has been constrained due to little interest from the rest of the world, their susceptibility to pests and diseases, and their awkward propagation. As such they can be referred to as an “orphan crop that would benefit from crop improvement efforts”.

To help the humble yam’s lot, researchers have sequenced the genome of the white Guinea yam (Tamiru et al, 2017). The research has revealed that yams belong to a unique genus (Dioscorea) that is distinct from rice, palm and banana groups. Yams have separate male and female plants (a limiting factor for yam breeding efforts) but the research has now revealed that yams use female heterogametic sex determination – unlike our XX females and XY males, yams have ZZ males and ZW females meaning that it’s the female gamete that determines the sex of individual offspring. The research hopes to assist yam breeding and cultivation efforts as well as improve food security and sustainability.

Original research: https://doi.org/10.1186/s12915-017-0419-x

October 23, 2017October 23, 2017

Arachnid genome

duplicated long-ago.

Arachnid genome.

Sometimes having two of something is a good thing. Genes are occasionally duplicated and whilst duplications are often lost, they may be retained and may help aid the evolutionary diversification of organisms. Normally only a few genes are duplicated but occasionally duplication can occur on a greater scale.

Schwager et al (2017) sequenced the genome of the common house spider and found evidence that whole genome duplication occurred in the house spider’s distant past. In fact, comparison with the genome of bark scorpions suggests that the duplication event took place in the common ancestor of spiders and scorpions more than 450 million years ago.

Original research: https://doi.org/10.1186/s12915-017-0399-x

October 16, 2017August 9, 2019

Flocks of new markers

Little white sponges,

filtering in mining zones:

Flocks of new markers.

New species are being discovered all the time and even the most innocuous can be important. A new species of sponge has been discovered and recorded by Lim et al (2017) at a depth of 4000m on the abyssal seafloor of the central Pacific Ocean. Morphologic and genetic analysis of the sponges (Plenaster craigi) has revealed they are a new genus, currently placed within the family Stelligeridae.

The region where the sponges are found is rich in polymetallic (metal-rich) nodules and may well be subjected to deep-sea mining. The sponges could be useful indicators of the impacts of such mining efforts – they are abundant on the nodules, are easily identified and are filter-feeders so sensitive to changing conditions.

The Latin name Plenaster is due to the abundance of star-shaped microscleres within their bodies, whilst the species name of craigi is in honour of the Chief Scientist on the expeditions that sampled the species Professor Craig R. Smith of the University of Hawaii.

Original research: http://dx.doi.org/10.1080/14772000.2017.1358218

October 13, 2017October 13, 2017

Tool of the future?

Environmental

DNA: Conservation

tool of the future?

Conservation efforts depend on the knowledge of species distribution patterns and population size estimates in order to know what needs protection and the subsequent impacts of conservation efforts. But there are a number of difficulties association with biodiversity monitoring techniques, including issues to do with correct species identification and invasive methods.

Environmental DNA – “genetic material obtained directly from environmental samples (soil, sediment, water etc.) without any obvious signs of biological source material” – could be a non-invasive and easy to standardise method of biodiversity monitoring. The advances of next-generation sampling technologies has meant individual or multiple species (through DNA metabarcoding) can be detected from such environmental samples quickly and cheaply.

Thomsen and Willerslev (2015) provide a thorough review of the main findings, future potential and limitations of eDNA for biodiversity monitoring and conservation. They document the successes of eDNA so far and discuss pitfalls such as contamination, inhibition, errors, interpretation and problematic reference DNA databases.

September 18, 2017September 18, 2017

Alchemist goldfish

change acid to alcohol

through doubled proteins.

Many species of carp (including goldfish) can survive for months over winter in frozen lakes despite a lack of oxygen. Without oxygen they use anaerobic respiration resulting in the production of lactic acid. To avoid a deadly build up of lactic acid the fish convert it into ethanol which diffuses across their gills into the surrounding water.

Researchers have now discovered how the fish do this. During energy production in the absence of oxygen a mutated set of proteins switches the metabolic pathway within mitochondria to produce ethanol instead. The fish have two sets of these proteins, one set which is very similar to that found in other species and one set that appears to be a duplicate of the first. These sets of proteins appear to have arisen during a whole genome duplication event approximately 8 million years ago and have enabled the fish to survive in conditions other species can’t. Fagernes et al, 2017.

September 8, 2017September 8, 2017

Ancestral origami

To fold life’s proteins:

Ancestral origami

around hockey pucks.

The basic way DNA is stored within cells is remarkably conserved suggesting a deep ancestral origin. Mattiroli et al (2017) have revealed that the way DNA is folded in eukaryotes (a domain containing animals, plants, fungi and protists) is very similar to the way its folded in archaea, a domain of single-celled microorganisms containing some of the oldest forms of life.

In both eukaryotes and archaea DNA is wrapped around proteins called histones creating the same DNA geometry. This suggests that eukaryote DNA folding method is ancestral, although a key difference is that in eukaryotes DNA is wrapped around bundles of 8 histones (sometimes referred to as a ‘hockey puck’) whilst in archaea its just wrapped around individual histones.

May 15, 2017June 14, 2017

Gregarious sharks

Gregarious sharks:

Cohabiting siblings and

multiple lovers

Whilst the bluntnose sixgill shark is a widely known species of shark, little is known about its biology. A genetic study looking at polymorphic microsatellites revealed that individuals sampled at the same time and place were often siblings, whilst one female was found to have had up to 9 males fathering her offspring. Larson et al, 2011.

May 12, 2017June 14, 2017

Fauna crime

Holmes solves fauna crime.

The case of invading smelt –

Released with intent

‘Translocation of freshwater fish… to new localities where they do not already exist’ is illegal in Norway. Understanding how a population of smelt has rapidly appeared in Lake Storsjoen is therefore important for population management. By using microsatellite markers Hagenlund et al (2015) were able to determine that it is likely that a large number of individuals were translocated at one time, potentially to create a population of large-sized trout, a species that feeds on smelt and is popular for fishing.

May 2, 2017June 14, 2017

Unhappy Whio

Unhappy Whio –

Your populations estranged,

split by the Cook strait.

The rare blue duck (named the Whio in Maori after the male call) is found on the North and South islands of New Zealand. The genetics suggest that the populations on the two islands diverged in the late Pleistocene, with very limited gene flow since. The current conservation strategy not to translocate individuals between the populations is therefore sensible so as to avoid potentially negative issues arising from crossing distant genetic pools. Grosser et al, 2016.