RAD51 and the DNA Hokey-Pokey

DNA repair and recombination rely on homology search between separate DNA molecules, one of which is double-stranded. How is that done?

BRCA2 is one of the more significant cancer-causing genes, when mutated. It is a huge protein of 3,418 amino acids, with lots of interactions, and functions that are not, even at this late date, very well understood. Like many eukaryotic proteins, it does alot of facilitation and organization of other proteins, roles which have clearly snowballed over evolutionary time. But its core function seems to be to bind right at the site of DNA breaks, and load the recombination protein RAD51 onto the ragged single stranded end. RAD51 then coats the remaining single stranded DNA and does the important work of helping it to find matching DNA elsewhere in the nucleus, which can then be copied to properly repair the break.

It is clear that DNA repair is a critical and highly regulated process, thus the continuing elaboration of proteins like BRCA2 which have mangerial roles. But RAD51 has the more fascinating structural role to play. How does it enable a job that seems impossible- to search efficiently through a whole genome of 3 billion basepairs, crammed in a crowded and jostling nucleus, and wound into double-stranded form on nucleosomes and other chromosomal proteins, to find the exact partner with which to pair and perform the dance of filling in the missing bit of DNA?

RAD51 is, unlike BRCA2, highly conserved, from bacteria to humans. Due to the different genetic methods used to find it, it is named RecA in bacteria, (for a specifically recombination-oriented screen), but is called RAD51 in eukaryotes, following a screen done in yeast cells for all sorts of mutants sensitive to high-energy radiation. Work over the last couple of decades has clarified the structure of RecA/RAD51 and thus how it functions.

Schematic of a DNA break, after processing, searching and finding a homolog to complete the repair. Not mentioned in this post, but the two ends need to be held in a coordinated way to facilitate repair across the break, even while the single stranded ends engage in a nucleus-wide homology search.

RAD51/RecA coating DNA, in scanning electron microscopy. Note how linear and stiff it is. Comparison is with similar DNA coated with another protein, single-strand binding protein, which imposes much less structure.

As mentioned above, RAD51 coats the single stranded end left after a DNA break has been detected and processed / cleaned up by the initial enzymes, and after BRCA2 binds to the recessed junction where the single strand starts. RAD51 forms a stiff and bulky filament, holding the DNA in a stretched conformation that is a thousand times stiffer than single stranded DNA, and 20 times stiffer than double stranded DNA. Interestingly, the single stranded DNA is held deep within the RAD51 filament, quite hard to see from the outside. Only the bases peep out, in triplet sets, amongst the protein structure that holds it so tightly. RAD51 is an ATP-ase, using the energy of ATP to polymerize and construct the filament, and also to de-construct it, but not for the searching operations.

Structure of a RAD51/RecA filament- macro above, and micro below. The single stranded DNA whose homolog is being sought is in orange, tucked deep within the protein filament. In closeup, a slight opening of the incoming double stranded DNA (blue) allows its bases to sample a little bit of the target. The pinkish blobs are positively charged lysines / argenines, ready to mate with the negatively charged incoming DNA backbone. Video here.

So much for the single strand doing the homology search. What about the double stranded DNA being searched against? The RAD51 filament makes provision for that as well, binding it lightly (in the proper directional orientation) and additionally having local splaying interactions that encourage its strands to separate slightly, binding the non-searching single strand, and allowing the searching strand to pair with the triplets peeking out from the core RAD51 filament. At this atomic scale, there is a lot of brownian motion / jostling- the DNA does breathe a bit naturally- so this is not very hard to do in a rapid way. But RAD51 obviously facilitates this in an optimized way.

Another structural view of the core sampling interaction, emphasizing the DNA strands. In brown is the target single strand DNA. In green is the slightly opened strand from the incoming double stranded DNA doing the sampling of one target triplet (with its single strand complement in red held off a little to the side). Note how the target DNA is held in very stretched form, with triplets of bases separated by slight gaps, which are RAD51 protein residues.

The binding of the invading double strand DNA is then very heavily dependent on how well it pairs with the single strand triplets. Pairing with three exposed bases is not a big deal. But pairing with eight consecutive bases stabilizes the match, and pairing with 26 or more seals the deal to be a long-lived match, which can induce de-polymerization of RAD51 and the arrival of repair polymerases. It is clear that RAD51 coordinates a complex dance of on-off sampling of nearby double stranded DNAs, including non-specific capture of local DNA, detailed samping by encouraging strand opening, as well as linear back and forth shifting, allowing some linear scanning as well. These diffusion mechanisms somehow add up to a thorough search of the nucleus for the right partner.

In bacteria, with genomes of a few million base pairs, sequences of 15 nucleotides are usually unique. In a genome of three billion bases, longer sequences are needed to be sure of true homology, nuclear volume is much larger, and there is more complex chromatin to deal with. Yet, the homology search time is not much less- about an hour. Why this is is not yet really clear. In eukaryotes, homologous chromosomes may typically reside close to each other in a semi-stable nuclear architecture. Or other aspects of the chromatin milieu may facilitate the search, paradoxically. And how damaging is an incorrect match? If a closely related sequence is chosen, (sequences which in eukaryotes are common due to replication errors, recombination errors, gene amplification and duplication, and repetitive sequences of many other kinds), it may not matter at all, depending on the size of repair span being copied from the intact homolog. Tract lengths repaired by copying from the other homolog are typically between 50 to 800 nucleotides long.

An even more focused view of the evolving match between a RAD-51 bound single strand (red) and an incoming DNA from a double-stranded sequence match (blue).

• Work from home? It varies.
• Yes, vaccines should be required.
• Signs of social isolation.
• Signs of idiocy.

American Occupations and Preoccupations

Douglass North on the role of institutions in our society, part 2. "Understanding the process of economic change". Also, "Violence and Social Orders". American occupations of Germany, Japan, and Afghanistan and Iraq are case studies of institutions at work. 

In part 1, I discussed the role of ideology and thought patterns in the context of institutional economics, which is the topic of North's book. This post will look at the implications for developmental economics. In this modern age, especially with the internet, information has never been more free. All countries have access to advanced technological information as well as the vast corpus of economics literature on how to harness it for economic development and the good of their societies. Yet everywhere we look, developing economies are in chains. What is the problem? Another way to put it that we have always had competition among relatively free and intelligent people, but have not always had civilization, and have had the modern civilization we know today, characterized by democracy and relatively free economic diversity, for only a couple of centuries, in a minority of countries. This is not the normal state of affairs, despite being a very good state of affairs.

The problem is clearly not that of knowledge, per se, but of its diffusion (human capital), and far more critically, the social institutions that put it to work. The social sciences, including economics, are evidently still in their infancy when it comes to understanding the deep structure of societies and how to make them work better. North poses the basic problem of the transition between primitive ("natural") economies, which are personal and small-scale, to advanced economies that grew first in the West after the Renaissance, and are characterized by impersonal, rule-based exchange, with a flourishing of independent organizations. Humans naturally operate on the first level, and it requires the production of a "new man" to suit him and her to the impersonal system of modern political economies. 

This model of human takes refuge in the state as the guarantor of property, contracts, money, security, law, political fairness, and many other institutions foundational to the security and prosperity of life as we know it. This model of human is comfortable interacting with complete strangers for all sorts of transactions from mundane products using the price system to complex and personal products like loans and health care using other institutions, all regulated by norms of behavior as well as by the state, where needed. This model of human develops intense specialization after a long education in very narrow productive skills, in order to live in a society of astonishing diversity of work. There is an organized and rule-based competition to develop such skills to the most detailed and extensive manner. This model of human relies on other social institutions such as the legal system, consumer review services, and standards of practice in each field to ensure that the vast asymmetry of information between the specialized sellers of other goods and services that she needs is not used against her, in fraud and other breaches of implicit faith. 

All this is rather unlike the original model, who took refuge in his or her clan, relying on the social and physical power of that group to access economic power. That is, one has to know someone to use land or get a job, to deal with other groups, to make successful trades, and for basic security. North characterizes this society as "limited access", since it is run by and for coalitions of the powerful, like the lords and nobility of medieval Europe or the warlords of Afghanistan today. For such non-modern states, the overwhelming problem is not that of economic efficiency, but of avoiding disintegration and civil war. They are made up of elite coalitions that limit violence by allocating economic rewards according to political / military power. If done accurately on that basis, each lord gets a stable share, and has little incentive to start a civil war, since his (or her) power is already reflected in his or her economic share, and a war would necessarily reduce the whole economic pie, and additionally risks reducing the lord to nothing at all. This is a highly personalized, and dynamic system, where the central state's job is mostly to make sure that each of the coalition members is getting their proper share, with changes reflecting power shifts through time.

Norman castles locations in Britain. The powers distributed through the country were a coalition that required constant maintenance and care from the center to keep privileges and benefits balanced and shared out according to the power of each local lord.

For example, the Norman invasion of Britain installed a new set of landlords, who cared nothing for the English peasants, but carried on an elite society full of jealousies and warfare amongst themselves to grab more of the wealth of the country. Most of the time, however, there was a stable balance of power, thus of land allotments, and thus of economic shares, making for a reasonably peaceful realm. All power flowed through the state, (the land allotments were all ultimately granted by the king, and in the early days were routinely taken away again if the king was displeased by the lord's loyalty or status), which is to say through this coalition of the nobles, and they had little thought for economic efficiency, innovation, legal niceties, or perpetual non-political institutions to support trade, scholarship, and innovation. (With the exception of the church, which was an intimate partner of the state.)

Notice that in the US and other modern political systems, the political system is almost slavishly devoted to "the economy", whereas in non-modern societies, the economy is a slave to the political system, which cavalierly assigns shares to the powerful and nothing to anyone else, infeudating them to the lords of the coalition. The economy is assumed to be static in its productivity and role, thus a sheer source of plunder and social power, rather than a subject of nurture and growth. And the state is composed of the elite whose political power translates immediately into shares of a static economic pie. No notion of democracy here!

This all comes to mind when considering the rather disparate fates of US military occupations that have occurred over the last century, where we have come directly up against societies that we briefly controlled and tried to steer in economically as well as socially positive directions. The occupations of Germany, Japan, Afghanistan, and Iraq came to dramatically different ends, principally due to the differing levels of ingrained beliefs and institutional development of each culture (one could add a quasi-occupation of Vietnam here as well). While Germany and Japan were each devastated by World War 2, and took decades to recover, their people had long been educated into an advanced instutional framework of economic and civic activity. Some of the devastation was indeed political and social, since the Nazis (as well as the imperial Japanese system) had set up an almost medieval (i.e. fascist) system of economic control, putting the state in charge of directing production in a cabal with leading industrialists. Yet despite all that, the elements were still in place for both nations to put their economies back together and in short order rejoin the fully developed world, in political and economic terms. How much of that was due to the individual human capital of each nation, (i.e. education in both technical and civic aspects), and how much was due to the residual organizational and institutional structures, such as impersonal legal and trade expectations, and how much due to the instructive activities of the occupying administration?

One would have to conclude that very little was due to the latter, for try as we might in Iraq and Afghanistan, their culture was not ready for full-blown modernity (elections, democracy, capitalism, rule of law, etc.) in the political-economic sense. Many of their people were ready, and the models abroad were and remain ready for application. Vast amounts of information and good will is at their disposal to build a modern state. But, alas, their real power structures were not receptive. Indeed, in Afghanistan, each warlord continued to maintain his own army, and civil war was a constant danger, until today, when a civil war is in full swing, conducted by the Taliban against a withering central state. The Taliban has historically been the only group with the wide-spread cultural support (at least in rural areas), and the ruthlessness to bring order to (most of) Afghanistan. Its coalition with the other elites is based partly on doctrinaire Islam (which all parties across the spectrum pay lip service to) and brutal / effective authoritarianism. When the US invaded, we took advantage of the few portions outside the existing power coalition, (in the north), arming them to defeat the Taliban. That was an instance of working with the existing power structures.

But replacing or reforming them was an entirely different project. The fact is that the development of modern economies took Western countries centuries, and takes even the most avid students (Taiwan, South Korea, China to a partial degree) several decades of work to retrace. North emphasizes that development from primitive to modern political-economic systems is not a given, and progress is as likely to go backward as forward, depending at each moment on the incentives of those in power. To progress, they need to see more benefit in stability and durable institutions, as opposed to their own freedom of action to threaten the other members of the coalition, keep armies, extort economic rents, etc. Only as chaos recedes, stability starts being taken for granted, and the cost of keeping armies exceeds their utility, does the calculus gradually shift. That process is fundamentally psychological- it reflects the observations and beliefs of the actors, and takes a long time, especially in a country such as Afghanistan with such a durable tradition of militarized independence and plunder.

So what should we have done, instead of dreaming that we could build, out of the existing culture and distribution of power, a women-friendly capitalist modern democracy in Afghanistan? First, we should have seen clearly at the outset that we had only two choices. First was to take over the culture root and branch, with a million soldiers. The other was to work within the culture on a practical program of reform, whose goal would have been to take them a few steps down the road from a "fragile" limited access state- where civil war is a constant threat- to a "basic" limited access state, where the elites are starting to accept some rules, and the state is stable, but still exists mostly to share out the economic pie to current power holders. Indeed the "basic" state is the only substantial social organization- all other organizations have to be created by it or affiliated with it, because any privilege worth having is jealously guarded by the state, in very personal terms.

Incidentally, the next step in North's taxonomy of states would be the mature limited access order, where laws begin to be made in a non-personal way, non-state organizations are allowed to exist more broadly, like commercial guilds, but the concepts of complete equality before the law and free access to standardized organization types has not yet been achieved. That latter would be an "open access order", which modern states occupy. There, the military is entirely under the democratic and lawful control of a central state, and the power centers that are left in the society have become more diffuse, and all willing to compete within an open, egalitarian legal framework in economic as well as political matters. It was this overall bargain that was being tested with the last administration's flirtation with an armed coup at the Capital earlier this year.

In the case of Afghanistan, there is a wild card in the form of the Taliban, which is not really a localized warlord kind of power, which can be fairly dealt out a share of the local and national economic pie. They are an amalgam of local powers from many parts of the country, plus an ideological movement, plus a pawn of Pakistan, the Gulf states, and the many other funders of fundamentalist Islam. Whatever they are, they are a power the central government has to reckon with, both via recognition and acceptance, as well as competition and strategies to blunt their power.

Above all, peace and security has always been the main goal. It is peace that moderates the need for every warlord to maintain his own army, and which nudges all the actors toward a more rule-based, regular way to harvest economic rents from the rest of the economy, and helps that economy grow. The lack of security is also the biggest calling card for the Taliban, as an organization that terrorizes the countryside and foments insecurity as its principal policy (an odd theology, one might think!). How did we do on that front? Well, not very well at all. The presence of the US and allies was in the first place an irritant. Second, our profusion of policies of reform, from poppy eradication, to women's education, to showpiece elections, to relentless, and often aimless, bombing, took our eyes off the ball, and generated ill will virtually across the spectrum. One gets the sense that Hamid Karzai was trying very hard to keep it all together in the classic pattern of a fragile state, by dealing out favors to each of the big powers across the country in a reasonably effective way, and calling out the US occasionally for its excesses. But from a modern perspective, that all looks like hopeless corruption, and we installed the next government under Ashraf Ghani which tried to step up modernist reforms without the necessary conditions of even having progressed from a fragile to a basic state, let alone to a mature state or any hint of the "doorstep conditions" of modernity that North emphasizes. This is not even to mention that we seem to have set up the central state military on an unsustainable basis, dependent on modern (foreign) hardware, expertise, and funding that were always destined to dry up eventually.

So, nation-building? Yes, absolutely. But smarter nation-building that doesn't ask too much of the society being put through the wringer. Nation-building happens in gradual steps, not all at once, not by fiat, and certainly not by imposition by outsiders (Unless we have a couple of centuries to spare, as the Normans did). Our experience with the post-world war 2 reconstructions was deeply misleading if we came away with the idea that those countries did nothing but learn at the American's knee and copy the American template, and were not themselves abundantly prepared for institutional and economic reconstruction.

• Tax evasion: our solemn duty and right.
• Defending our precious bodily fluids.
• Signs of isolation and loneliness.

Nature and the Corporation

Douglass North on the role of institutions in our society, part 1. "Understanding the process of economic change"

Institutions, in the thinking of this book and its general field of institutional economics, are the rules of the game of life, while people and their organizations are the players. The practice of going to workplaces and being forced to work there for eight hours, and then going home.. that is an institution of modern societies, based partly on unwritten traditions, and partly on explicit rules written in laws, regulations, organizational guidelines, etc.  The fabric of our lives, and particularly the efficiency and success of our economies, depend on the details and quality of institutions, which set the parameters and incentives throughout the system, which the actors then grapple with, trying to either to satisfy them in competition against other actors, or to evade them, or to alter them through legal, polical, or social means. 

For example, North cites other writers who have concluded that one of the fundamental defects of the Muslim world, as it fell behind the Northern Europeans in economic and cultural terms through the Middle Ages, was the complete lack of the cultural institution of the corporation. Muslim commercial law centers around partnerships, typically very small partnerships between an investor and a merchant, which form anew for each trade mission. But until modern times and reforms inspired by the West, there was no legal form for corporations, which are so fundamental to the Western economic model, providing durable legally and financially independent homes for entrepreneurial teamwork and innovation. Corporations obviously tap into natural human tribalism, offering the familiar setting of small group cohesion and competition, and helpfully cross-cutting against other cultural organizations and power centers such as actual clans, tribes, nations, and religious groupings.

This is a very powerful view of how culture and economics interact. Are corporations all good? Obviously not. They are given rules by the culture at large, though traditional practices and by legal structures when those unwritten rules prove insufficient. Child labor, fraud, tax evasion, family-destroying work schedules... the ways corporations have to make money in socially destructive ways, and thus the ways in which they need to be regulated, are endless. And it is our collective view of these harms and our capacity through social and legal structures / sanctions to address them that manifest in the strength and quality of our institutions.

And here is where one looks back in horror at what has happened to our institutional structures over the last few decades. Donald Trump was merely the apotheosis of lawlessness and institutional destruction that has been the program of the Right for decades. It was enunciated most charmingly by Ronald Reagan, (earning him high grades from historians), but he was only repeating the thoughts of intellectuals like Friedrich Hayek and Milton Friedman who made such persuasive cases for the "freedom" part of free enterprise. I recall especially the spellbinding nature of Friedman's narratives, which contrasted the sclerosis of communist economies with the vibrancy of free markets. Friedman was a hedgehog, advocating one big idea and bulldozing through any nuance or complication. And I regard him as the most influential cultural figure responsible for the general inequality and institutional weakness we find ourselves facing today.

A typical nostrum from Milton Friedman. As though "freedom" was self-explanatory and absolute. Rich people take it to mean something quite different from how others take it, and therein lies the destructive magic of this ideology. 

For he was spinning fairy tales, quite simply. The free market was always good, the government was always bad in his telling. Ham fisted regulation and intrusive economic policy were only one target of attack. Money and inflation was another, and one of the most damaging wedges of this argument. The government is necessarily in charge of the money, by printing it and managing its value through the interest rate, banking regulation, and other mechanisms. But the private sector and general economic conditions are obviously enormous factors as well, creating a complex system of feedbacks and unanticipated events. But Friedman gleefully pinned all the blame for inflation on the government, pronounced a false simplicity in his monetarist program, and used it to further bludgeon the state to get out of the regulatory business. If the government couldn't even get something as simple as the money supply right, how could it possibly have the intellectual wherewithal to regulate the internet, or corporate mergers and concentration, or industrial policy vs other countries? This was the kind of thinking that led to people buying gold, and eventually to the thought that we should get back on the gold standard, one of the greatest lunacies of right-wing politics. (Which Friedman would never have subscribed to, incidentally.)

This intellectual and rhetorical attack, so richly supported and cheered by business interests and the rich, led to the following decades of revolt by the Right against all forms of regulation and enfetterment by the government, to the point now that Republicans speak blithely of defunding the IRS, as if defunding the government and enabling vast tax avoidance consitutes the most natural and virtuous motivation that anyone could imagine. And the gross over-simplifications that Friedman engaged in, his rhetorical excesses, are reflected in more general anti-intellectual trends like the denialism and warfare waged by the right against climate change, among many other topics of urgent and common interest. He, Nobel Prize winner that he was, disastrously debased our intellectual debates on politics and economics. His narrative framing (and that of the whole Chicago school) shaped a generation and more, misleading us into false certainties and terrible policies.

Now, our institutions are in tatters, given that half of our political system is in open warfare against the very idea of productive regulation of economic affairs and a positive role for the state in managing elementary unfairnesses and corruptions that are mounting across our political and economic systems. No wonder that on the world stage, our system is no longer in the vanguard, but is faced with a fundamental challenge coming from states (principally China) whose political systems remain in the driver's seat in managing social institutions, including economic institutions of all kinds, even while harnessing markets in extremely successful ways. 

The question is not whether the government is good or bad, or whether corporations are good or bad. Both institutions have critical and positive roles to play in our prosperity. Both are tools, not ends in themselves. Both need rules to operate effectively- government to be refreshed (via elections, education, research, and new talent) by ever-expanding public perspectives on how society can be improved, and business by an active set of institutions and rules set down by the government to channel all that greed to productive directions instead of the socially destructive directions it inevitably takes when rules are absent. (See Haiti, post-war Iraq, and Afghanistan for examples.) Indeed, it is not going out on a limb to state that business people who spend their time railing against regulations, legal strictures and other institutions designed to make economic markets fair, socially responsible, and productive are not really interested in business at all, but in plunder.

"Because there is a widespread prejudice among many neo-classical economists that simply an absence of government intervention is a sufficient condition for good economic performance in a particular market, it is important to stress that the performance characteristics of any market are a function of the set of constraints imposed by institutions (formal rules- including those by government- informal norms, and the enforcement characteristics) that determine the incentive structure in that market. As noted in the discussion of institutional change in chapter 5, if the incentives reward piracy then that will be the outcome. Any economist who doubts the importance of this observation has only to examine the characteristics of various factor and product markets in Russia in the 1990s to be convinced that it is the incentive structure derived from the institutional framework that is decisive. The rash of entrepreneurial malfeasance in large U.S. corporations in 2001-2 has reflected the evolution of the institutional framework that has altered relative prices to provide incentives for such anti-social behavior."  p.77

 

• Notes on China's economic trajectory. Institutions will be the main determinant.
• Vaccines? Schmaxines!
• Democrats- and the planet- have a problem in coal country.
• What is it with Republicans and basic health & decency?

Sneakey Eating

An evolutionary perspective on overeating syndromes.

Most animals have a simple problem in life- find enough food to live and survive. But social animals, if they are even slightly advanced, share food, and thus alter this basic equation. They have to find ways to store and share food in a way that sustains the group, whether that is starving the old, or feeding the helpless larvae that can not feed themselves. Humans have always faced this dilemma, but don't have the rigid programming that insects do.

Humans can lie, and steal, and then lie some more. It isn't pretty, but sometimes it gets the job done. Humans can regard rules as optional, a flexibility that is a perpetual threat to institutions, norms, cultural patterns, and ultimately to group success. We recently went through an administration that regarded norms as suggestions, laws as annoyances, and then wondered why their behavior attracted so much hatred, and such low historical esteem.

This dynamic comes to mind more concretely in the case of overeating syndromes, which exemplify the conflict between the individual and the group. In a prehistoric setting, food was almost always scarce and precious. In all native cultures there are elaborate practices of public food sharing and eating, which contribute to surveillance by the community of what everyone is eating. Anyone who violates such social structures must have been severely penalized.

Public, communal eating is a fundamental human practice.

Imagine then that someone feels a compulsion to eat more than their share. Such a compulsion would be highly advantageous- if successful- to enable survival when the others in the group might be starving or malnourished. Some extra weight might well mean the difference of making it through the next winter or not. But being caught could dramatically alter the calculus. Primitive societies had harsh punishments for violating critical norms, including ostracism or execution. What then? 

I would suggest that this background sets the stage for overeating syndromes that commonly combine secret eating, often at night, stealth, and stealing. In a world of plenty like today, it is stigmatized and medicalized, and due to the abundance of food, relatively easy to navigate and thus easy to gain weight from. But pre-historically, it would have been far more fraught, and challenging, probably less likely to result in easily observable weight gains. Like other issues in social life, this conflict would take the form of an arms race between cheaters and rule-enforcers. It would be a cognitive battle between effective surveillance and punishment, vs stealth and the intelligence required to not get caught. So one can view it as one impetus among many other evolutionary forces that shaped human intelligence, and in light of its considerable incidence in modern populations, an arms race that was never resolved. Indeed, it is the type of trait that comes under balancing selection, where a high incidence in a population would be self-defeating, while a low incidence yields a much more successful outcome.

• Satire- not so funny when you are the target.
• Making every home a part of the energy solution.
• Constitution? Who ever heard of enforcing it?

How a Nervous System is Maintained

Researchers have mapped how transcriptional programming specifies C. elegans neurons.

Model systems in biology have led the way into knowledge of body development. Fruit flies have been the target of intensive work on the genetic origins of morphogenesis and body plan specification, finding successive action by maternally deposited proteins or mRNAs, gap genes, pair rule genes, and homeotic genes to specify ever finer segments of the body. 

An even simpler model system was later developed, in the tiny worm C. elegans, a nematode, which is smaller, faster-developing than the fruit fly, and also transparent. This organism is attractive for some neurobiology studies, (despite lacking a brain), since its nervous system is both simple and stereotypical- every worm has 302 neurons, of 118 types, laid out in pretty much the same pattern, all easily visible. 

The neurons of C. elegans, in overview. Only the cell body locations are shown, not their various axonal and dendritic processes.

A recent paper therefore looked into the question of how these neurons are specified- how they maintain their identity through the life of the worm, after their original development. The fruit fly genes mentioned above that lay out the body plan are almost all transcription regulators- proteins that regulate the expression of other genes by binding near them and turning on (or off) transcription. A cascade of such regulators allows complex programs of refinement and specification to be carried out, to the point that individual cells are told what they are supposed to be and what features they are supposed to express. These patterns of transcription eventually get cast in stone by the durable repression of unneeded genes, and feedback loops that perpetuate the expression of whatever ones at the end are required to maintain the particular specified type. These are also transcription regulators acting at the end of the line of the developmental pathway, and are called "terminal selectors", since they regulate /select the final sets of genes to be expressed in that cell type which manifest whatever it is supposed to be. 

So a question is- what kind of terminal selectors are active in the stereotyped neurons of C. elegans? Are there just a few for each neuron, used broadly to control all its distinctive genes, or are there many different ones deployed in a complex combinatorial code of transcription regulators to control the final gene expression and the cell type? What they found was that these worms use mostly the former method, and much less the latter. But there can be over 20 such regulators deployed in combination to set up some of these neuronal cells.

For each neuron type (top graph, bottom axis), the associated transcriptional regulators are either common (blue) or rare and particular (green). Common regulators are used to broadly bind to and activate many or most of that neuron's specifically expressed genes. The bottom graph shows the various regulators (bottom axis), and counts how many neuron types they operate in (Y-axis). Some of these regulators are used by many neurons, yet by their cooperation with other regulators can be relied on to specify a particular cell type.

The methods these researchers use are two-fold. One is to sequence all the RNAs of each specific neuron (generally called single cell sequencing). This was used to find all the specifically (differentially) expressed genes of each neuronal cell type, whose upstream regions were then investigated to find the binding sites for all the known transcription regulators of C. elegans. This catalog of target binding sites, genes and their binding regulators could then be compiled to ask whether each cell type had a characteristic pattern ... and generally they do. A second method was to consult a previously developed collection of many "reporter" genes, which had each been fused to bit of DNA encoding a fluorescent protein, which then were screened as being expressed specifically in one or another neuron of C. elegans. This collection of 1000 genes was likewise scanned for its regulatory sites and binding transcription regulators, and the authors found completely concordant results- that here too. the same combinations of regulators were used time and again to activate the specific genes of each neuron. 

Analysis of one gene, and one regulator, through evolutionary time. One key analysis to find regulator sites on a gene was to ask whether its sites were conserved in related species. Here, the ODR-7 DNA-binding regulator has binding sites both upstream and within the olrn-1 gene. Sites are shown in purple, the gene transcription start is shown with the big arrow at top, and the gene's coding exons are shown in black blocks downstream of the start site. The locations of the sites are not well conserved, but their presence is quite well conserved, here on a gene that is expressed in AWS neurons, and necessary for them to occur. 

So development, specification, and maintenance of the body are encoded by the genome largely via a program of regulators that are placed where they are supposed to be, and then successively activate, out of the genome, further parts of the control series in defined regions, and finally regulate the genes required to manifest the body plan in particular places, by expressing (or repressing) genes for the ion channels, cytoskeletal formation, neurotransmitters, and all other specific bric-a-brac of each cell type.

• How farmers think about nematodes.
• But some people love them.
• A strange and sinister religion.
• The Taliban preaches good governance.
• Let's be like Maine.
• RIP Rumsfeld.
• Voting has been a big constitutional issue, with at least five relevant amendments. But now the federal government has no role in enforcing the constitution. Just how many more amendments are needed?
• Covid graph of the week- Where were covid deaths undercounted?