Applied plant genomics: the secret is integration

Although concerted efforts to understand selected botanical models have been made, the resulting basic knowledge varies in its applicability to other diverse species including the major crops. Recent advances in high-throughput genomics are offering new avenues through which to exploit model systems for the study of botanical diversity, providing prospects for crop improvement. In particular, whole-genome sequencing has provided opportunities for the broader application of reverse genetics, expression profiling, and molecular mapping in diverse species.     

The secret to life is being different: asymmetric divisions in plant development

Asymmetric cell divisions (ACDs) are used to create organismal form and cellular diversity during plant development. In several embryonic and postembryonic contexts, genes that specify cell fates and networks that provide positional information have been identified. The cellular mechanisms that translate this information into a physically ACD, however, are still obscure. In this review we examine the cell polarization events that precede asymmetric divisions in plants. Using principles derived from studies of other organisms and from postmitotic polarity generation in plants, we endeavor to provide a framework of what is known, what is on the horizon and what is critically needed to develop a rigorous mechanistic understanding of ACDs in plants.     

The first "Slit" is the deepest: the secret to a hollow heart

Tubular organs are essential for life, but lumen formation in nonepithelial tissues such as the vascular system or heart is poorly understood. Two studies in this issue (Medioni, C., M. Astier, M. Zmojdzian, K. Jagla, and M. Sémériva. 2008. J. Cell Biol. 182:249-261; Santiago-Martínez, E., N.H. Soplop, R. Patel, and S.G. Kramer. 2008. J. Cell Biol. 182:241-248) reveal unexpected roles for the Slit-Robo signaling system during Drosophila melanogaster heart morphogenesis. In cardioblasts, Slit and Robo modulate the cell shape changes and domains of E-cadherin-based adhesion that drive lumen formation. Furthermore, in contrast to the well-known paracrine role of Slit and Robo in guiding cell migrations, here Slit and Robo may act by autocrine signaling. In addition, the two groups demonstrate that heart lumen formation is even more distinct from typical epithelial tubulogenesis mechanisms because the heart lumen is bounded by membrane surfaces that have basal rather than apical attributes. As the D. melanogaster cardioblasts are thought to have significant evolutionary similarity to vertebrate endothelial and cardiac lineages, these findings are likely to provide insights into mechanisms of vertebrate heart and vascular morphogenesis.     

The secret garden's gardeners

The role of the microbial fauna in our gut for health and well-being is undisputed. Now, scientists are discovering that gut viruses also play a crucial role in modulating our risk for a wide range of diseases.Research has shown that the microbiota—the population of micro-organisms inhabiting the gut—has a profound influence on health in both humans and animals. However, most studies have largely ignored the viral population of the gut—the virome—although it is much larger, both in number of organisms and in genetic diversity. This is because the virome was thought to be less important for health and immunity, as it mainly comprises bacteriophages that only affect bacteria. However, researchers are beginning to realize that the viruses present might well be important in human health, as they manipulate the microbiota, swapping genetic virulence factors among bacteria, and through interaction with the host immune system.There are two distinct categories of virus in the gut: phages, which infect bacteria, and viruses that target host cells. Although these two categories are apparently independent of each other, there is a relationship between them, as indicated by growing evidence that the microbiota as a whole, including phages, has a crucial role in protecting against bacterial and viral infections [1].The phage and bacteria populations of the gut have an intricate relationship, which raises the potential therapeutic use of phages to treat a variety of conditions caused by bacteria in the gut, especially those involving chronic inflammation. The first step, however, is to explore and analyse the phage populations in the gut in terms of diversity and number, along with their interactions with their bacterial targets. This has proven to be a major challenge, given the enormous difficulties in identifying, isolating and amplifying genetic material from the phage population.Nevertheless, researchers from the Weizmann Institute of Science and Tel Aviv University in Israel have made substantial progress by indirectly identifying phages through clustered regularly interspaced short palindromic repeats (CRISPRs) in their bacterial hosts [2]. CRISPRs function as a prokaryotic adaptive immune system against genetic invaders such as phages by recognizing foreign DNA and then silencing its expression in a manner analogous to RNA interference (RNAi) in eukaryotes. Short segments of the foreign DNA, known as spacers, are incorporated into the bacterial genome to provide the memory of past exposures to enable recognition of phage DNA.The phage and bacteria populations of the gut have an intricate relationship, which raises the potential therapeutic use of phages to treat a variety of conditions…The Israeli study reconstructed the CRISPR bacterial immune system in the human gut microbiomes of 124 European individuals, and from that identified 991 phages targeted in at least one of the individuals. Of these phages, 78% were present in at least two individuals and some turned out to be the same ones that had already been identified in Japanese and American people. This global distribution of particular phages was a surprise, given that in other ecological niches, notably seawater, where phages are highly abundant, there is great genetic diversity among the populations, even over short distances.The Israeli team further succeeded in deducing the bacterial hosts of 130 of the phages, which allowed them to study the associated phage–bacteria interactions. It turned out that a subset of the phages had developed closer associations with their host bacteria as lysogenized prophages after fusing their DNA with the bacterial chromo-some or as plasmids. Rotem Sorek, a specialist in microbial warfare at the Weizmann Institute of Science and co-author of the Israel study, commented that this behaviour allows bacteria to take advantage of the phage by incorporating and transmitting genes that provide vital functions and occasionally aid pathogenesis. “There are clear instances of phages ‘helping'' pathogenic bacteria to attack humans,” Sorek said. “The toxins of the Cholera, Diphtheria and Shigella (disenteria) are all carried by phages that are integrated into the bacterial genome.”Horizontal gene transfer among bacteria has long been known to increase the adaptability of several potentially virulent bacterial species, but it is only recently that the mechanisms involving prophages have begun to be elucidated. A significant advance was made in a Japanese study from the University of Miyazaki, inspired by the observation that many sequenced bacterial genomes contain multiple prophages carrying a wide range of genes involved in virulence, and that these often seem to contain genetic defects [3]. The team analysed a virulent strain of Escherichia coli, known as O157, which contains 18 prophages that encode various genes involved in the production of virulence factors, including two potent cytotoxins: Shiga toxins 1 and 2. Most of the prophages they identified contained multiple genetic defects, yet they seemed to be capable of transporting virulence elements between not only members of the same strain but also different E. coli strains.The conclusion from their study was that defective prophages in close proximity within E. coli cells were still capable of recombining to yield a new phage that was released from the cell and could infect other cells nearby in the gut. It seems that these defective prophages were not just evolutionary leftovers, but were important components of the bacterial genome, conferring additional adaptive flexibility through horizontal gene transfer. Many other bacteria contain multiple prophages with genetic defects, so it is probable that this mechanism is not confined to E. coli.Other studies have focused on the composition of phage virus populations outside bacteria in the gut, as part of initiatives to compare and contrast the virome and bacteriome in response to individual genetic variation and environmental factors such as diet. One might imagine that phage and bacteria populations should be closely correlated, but it turns out that there are significant differences in the level of variation between individuals, as well as over time within the same individual. A study at the Washington University School of Medicine, USA, on monozygotic twins, found that in contrast to bacteriomes, viromes tended to be unique to individuals and less varied over time in response to changes in diet or other factors. By contrast, the bacterial population changed much more with diet and was also quite similar between twins.“There are clear instances of phages ‘helping'' pathogenic bacteria to attack humans”…Given that there is a direct relationship between the bacteria of the gut and the immune system of the individual—which is not the case for phage viruses—these findings make a degree of sense. Furthermore, as noted by Jeffrey Gordon, co-author of the Washington University study, there is not a one-to-one relationship between bacteria and the phages they host: “It''s been shown in other environments that you can have several different viruses capable of infecting the same bacterial host, while the specificity of each virus is usually quite narrow, typically extending only to a few strains within a species-level phylotype,” he explained. “This leads to a greater genetic diversity in the virome. Furthermore, a viral genome is enriched for genes involved in genome replication and virion assembly. Thus, the functional composition of the virome and the microbiome are quite different.”The situation is different for non-phage viruses in the gut that have a direct relationship with the human or animal host. The main research interest here is the three-way relationship between the virus, the bacteriome and the host''s immune system. Research on this front has already led to a new understanding of the role played by the entire microbiome in immunity. Often, the microbiome provides protection against viruses, but in some cases it can encourage their propagation. This is relevant in the context of human immunodeficiency virus (HIV), for example, given that the virus infects immune cells such as helper T cells, macrophages and dendritic cells, the activity and production of which in turn are related to the microbiota. An important question is whether the course of HIV and its possible development into symptomatic acquired immunodeficiency syndrome (AIDS) might be encouraged by the microbiota, if it stimulates production of such immune cells. Whilst this has yet to be established for AIDS, there is evidence that it is the case in monkeys carrying the related simian immunodeficiency virus (SIV), which infects at least 45 species of African primates. Unlike HIV in humans, SIV is usually non-pathogenic, as many primates evolved to coexist with the virus; but it does cause AIDS in rhesus macaque monkeys.Another Washington University School of Medicine study, this time looking at the link between viruses, the bacteriome and host immunity, began with the insight that animals developing AIDS experience immune hyperactivation, including higher levels of inflammatory chemokines, cytokines and activated T cells. This observation suggested that excessive inflammation is an important factor in progression to AIDS, presumably because it increases the number of cells vulnerable to HIV and SIV infection. The US team investigated whether there were any corresponding changes in the virome, finding that whilst it remains unchanged in uninfected animals, including rhesus macaque monkeys that had not succumbed to AIDS, its diversity increases significantly in infected macaques with full-blown AIDS [4].Often, the microbiome provides protection against viruses, but in some cases it can encourage their propagationThe team is following up by probing the relationship between enteric viruses and AIDS and how the immune system is stimulated. The animals suffer from progressive damage to their intestinal walls, which could increase the absorption of viruses that in turn stimulate the immune system, promoting replication of SIV and possibly encouraging more opportunistic viral infection, thereby creating a vicious circle. “This is one of several possible scenarios that we are actively investigating,” commented Scott Handley, lead author of the study. “What is uncertain is what is causing the damage to the intestinal wall. It could be the viruses which expand in the enteric virome during SIV infection, or some other factor, which could be immune-mediated or some other microbe or microbial product in the enteric microbiome.”Handley''s team has identified some of the viruses involved, including both common ones and some previously undiscovered. “Many of the viruses we identified have been associated with [gastrointestinal] disease in one form or another,” Handley said. “It is true that many of the viruses we identified are common; however, we identified at least 32 novel subtypes of these viruses never seen before.” He added that it remains to be established whether SIV infection encourages opportunistic infection by these viruses or not: “We don''t really have a good handle on what viruses would be considered ‘commensal'' viruses in any animal, including research primates. So whether they are already there when infection with SIV occurs, or are just more susceptible to opportunistic infection, is unclear.”Handley further commented that this work could lead to new therapeutic targets for treating HIV infection and preventing AIDS, and he is investigating whether the same expansion of the enteric virome occurs in humans infected with HIV. “In addition, we are interested to see if vaccination can reverse the enteric virome expansion,” he explained. “We would also like to better understand if the viruses we have identified were already circulating in these primates, or are succumbing to opportunistic infections.”Handley argued that his team''s work and that of others provides a compelling case for devoting more resources to studying the role of viruses in the gut, which would require further advances in laboratory and analytical techniques. “One challenge with studying the viral members of a microbiome is that there are no well-defined marker sequences,” he said. “Therefore, we are largely dependent on random shotgun sequencing approaches, which are less efficient and more expensive. Not only do you have to gather much more data, the computational analysis required is much more complex than the well-established techniques developed for studying the bacterial microbiome. While we know there is a great deal of interest in studying the virome, current techniques and technology tend to limit the number of labs that can participate in these efforts. We are very interested in developing new tools and techniques to help alleviate this issue.”An important question is whether the course of HIV […] might be encouraged by the microbiota, if it stimulates production of such immune cellsWork undertaken so far has already shown that probiotic or prebiotic treatments that provide or encourage beneficial gut bacteria can benefit patients infected with HIV. Improvements in intestinal health could reduce the leakage of all antigens, including viral ones, through the intestinal wall. More generally, a better understanding of how phages, viruses and bacteria in the gut interact could lead to new therapies that manipulate the microbiome to restore intestinal health in sufferers of a variety of conditions, including those involving chronic inflammation.     

The secret life of histones

Recent evidence reveals an unexpected role for the linker histone H1.2 in DNA damage-induced apoptosis. DNA double strand breaks induce translocation of nuclear H1.2 to the cytoplasm, where it promotes release of cytochrome c from mitochondria by activating the Bcl-2 family protein, Bak.     

The secret life of memories

Recent evidence has challenged the view that memories are made permanent by a consolidation process that happens just once and instead have suggested that memories are "re-consolidated" after reminders. The current findings of Morris et al. in this issue of Neuron suggest that reconsolidation may involve a complex interaction between synaptic and system processing of recent as well as remote experiences.     

The secret life of the hair follicle.

The mammalian hair follicle is a treasure waiting to be discovered by more molecular geneticists. How can a tiny cluster of apparently uniform epithelial cells, adjacent to a tiny cluster of uniform mesenchymal cells, give rise to five or six concentric cylinders, each of which is composed of cells of a distinctive type that synthesize their own distinctive set of proteins? There is now evidence that several growth factors, cell adhesion molecules and other molecules play important roles in the regulation of this minute organ.     

The sex ratio distortion in the human head louse is conserved over time

Background

At the turn of the 19^th century the first observations of a female-biased sex ratio in broods and populations of the head louse, Pediculus humanus capitis, had been reported. A study by Buxton in 1940 on the sex ratio of lice on prisoners in Ceylon is still today the subject of reanalyses. This sex ratio distortion had been detected in ten different countries. In the last sixty years no new data have been collected, especially on scalp infestations under economically and socially more developed conditions.

Results

Here we report a female bias of head lice in a survey of 480 school children in Argentina. This bias is independent of the intensity of the pediculosis, which makes local mate competition highly unlikely as the source of the aberrant sex ratio; however, other possible adaptive mechanisms cannot be discounted. These lice as well as lice from pupils in Britain were carrying several strains of the endosymbiotic bacterium Wolbachia pipientis, one of the most wide spread intracellular sex ratio distorters. Similar Wolbachia strains are also present in the pig louse, Haematopinus suis, suggesting that this endosymbiont might have a marked influence on the biology of the whole order. The presence of a related obligate nutritional bacterium in lice prevents the investigation of a causal link between sex ratio and endosymbionts.

Conclusions

Regardless of its origin, this sex ratio distortion in head lice that has been reported world wide, is stable over time and is a remarkable deviation from the stability of frequency-dependent selection of Fisher's sex ratio. A female bias first reported in 1898 is still present over a hundred years and a thousand generations later.

     

Three-stranded DNA structure; is this the secret of DNA homologous recognition?

A novel type of triple-stranded DNA structure was proposed by several groups to play a crucial role in homologous recognition between single- and double-stranded DNA molecules. In this still putative structure a duplex DNA was proposed to co-ordinate a homologous single strand in its major groove side. In contrast to the well-characterized pyrimidine-purine-pyrimidine triplexes in which the two like strands are antiparallel and which are restricted to poly-pyrimidine-containing stretches, the homology-specific triplexes would have like strands in parallel orientation and would not be restricted to any particular sequence provided that there is a homology between interacting DNA molecules. For many years the stereo-chemical possibility of forming homology-dependent three- or four-stranded DNA structures during the pairing stage of recombination reactions was seriously considered in published papers. However, only recently has there been a marked increase in the number of papers that have directly tested the formation of triple-stranded DNA structures during the actual pairing stage of the recombination reaction. Unfortunately the results of these tests are not totally clear cut; while some laboratories presented experimental evidence consistent with the formation of triplexes, others studying the same or very similar systems offered alternative explanations. The aim of this review is to present the current state of the central question in the mechanism of homologous recombination, namely, what kind of DNA structure is responsible for DNA homologous recognition. Is it a novel triplex structure or just a classical duplex?     

The secret lives of single cells

Looking back fondly on the first 15 years of Microbial Biotechnology, a trend is emerging that biotechnology is moving from studies that focus on whole-cell populations, where heterogeneity exists even during robust growth, to those with an emphasis on single cells. This instils optimism that insights will be made into myriad aspects of bacterial growth in communities.