Structural insights into a unique cellulase fold and mechanism of cellulose hydrolysis

Published online before print March 10, 2011, doi:10.1073/pnas.1015006108

Clostridium thermocellum  is a well characterized cellulose degrading microorganism. The genome sequence of C.thermocellum encodes a number of proteins that contain type I dockerin domains, which implies that they are components of the cellulose degrading apparatus, but display no significant sequence similarity to known plant cell wall degrading enzymes. Here, we report the biochemical properties and crystal structure of one of these proteins, designated CtCel124. The protein was shown to be an endo-acting cellulase that displays a single displacement mechanism and acts in synergy with Cel485, the major cellulosomal exo-cellulase. The crystal structure of CtCel124 in complex with two cellotriose molecules, determined to 1.5 Angastrom, displays a superhelical fold in which a constellation of alpha-helices encircle a central helix that houses the catalytic apparatus. The catalytic acid, Glu96, is located at the C-terminus of the central helix, but there is no candidate catalytic base. The substrate binding cleft can be divided into two discrete topographical domains in which the bound cellotriose molecules display twisted and linear conformations, respectively,suggesting that the enzyme may target the interface between crystalline and disordered regions of cellulose.

Cap Binding and Immune Evasion revealed by Lassa Nucleoprotein structure

Nature; doi:10.1038/nature09605

Abstract:

Lassa virus, the causative agent of Lassa fever, causes thousands of deaths annually and is a biological  threat agent, for which there is no vaccine and limited therapy. The nucleoprotein of Lassa virus has essential roles in viral RNA synthesis and immune suppression, the molecular mechanisms of which are poorly understood. Here we report the crystal structure of Lassa virus NP at 1.80 Angstrom resolution, which reveals amino (N)-and carboxy(C)terminal domains with structures unlike any of the reported viral NPs. The N domain folds into a novel structure with a deep cavity for binding the m7GpppN cap structure that is required for viral RNA transcription, whereas the C domain contains 3’-5’ exoribonuclease activity involved in suppressing interferon induction. To our knowledge this is the first X-ray crystal structure solved for an arenavrial NP, which reveals its unexpected functions and indicates unique mechanisms in cap binding and immune evasion. These findings provide great potential for vaccine and drug development.

Gene Expression Divergence Recapitulates the Developmental hourglass model

Nature 468, 811-814; doi:10.1038/nature09634

Abstract:

The observation that animal morphology tends to be conserved during the embryonic phylotypic period(a period of maximal similarity between the species within each animal phylum) led to the proposition that embryogenesis diverges more extensively early and late than in the middle, known as the hourglass model. This patter of conservation is though to reflect a major constraint on the evolution of animal body plans. Despite a wealth of morphological data confirming that there is often remarkable divergence in the early and late embryos of species from the same phylum, it is not yet known to what extent gene expression evolution , which has a central role in the elaboration of different animal forms, underpins the morphological  hourglass pattern. Here we address this question using species  specific microarrays designed from six sequenced Drosophila species separated by up to 40 million years. We quantify divergence at different times during embryogenesis and show that expression is maximally conserved during the arthropod phylotypic period. By fitting different evolutionary models to each gene, we show that at each time point more than 80% of gene fit best to models incorporating stabilizing selection and that for genes whose evolutionarily optimal expression level is the same across all species, selective constraint is maximized during the phylotypic period. The genes that conform most to the hourglass pattern are involved in key developmental processes. These results indicate that natural selection acts to conserve patterns of gene expression during mid embryogenesis and provide a genome wide insight into the molecular basis of the hourglass pattern of developmental evolution.

intermittent fasting on prostate cancer tumor

Prostate Cancer and Prostatic Diseases (2010) 13, 350–355; doi:10.1038/pcan.2010.24; published online 24 August 2010

Effect of intermittent fasting on prostate cancer tumor growth in a mouse model

Abstract:

Caloric restriction (CR) has been shown to have anti-cancer properties. However, CR may be difficult to apply in humans secondary to compliance and potentially deleterious effects. An alternative is intermittent CR, or in the extreme case intermittent fasting (IF). In a previous small pilot study, we found 2 days per week of IF with ad libitum feeding on the other days resulted in trends toward prolonged survival of mice bearing prostate cancer xenografts. We sought to confirm these findings in a larger study. A total of 100 (7- to 8-week-old) male severe combined immunodeficiency mice were injected subcutaneously with 1 × 10⁵ LAPC-4 prostate cancer cells. Mice were randomized to either ad libitum Western Diet (44%carbohydrates, 40% fat and 16% protein) or ad libitum Western Diet with twice-weekly 24 h fasts (IF). Tumor volumes and mouse bodyweights were measured twice weekly. Mice were killed when tumor volumes reached 1000 mm³. Serum and tumor were collected for analysis of the insulin/insulin-like growth factor 1 (IGF-1) hormonal axis. Overall, there was no difference in mouse survival (P=0.37) or tumor volumes (P0.10) between groups. Mouse body weights were similar between arms (P=0.84). IF mice had significantly higher serum IGF-1 levels and IGF-1/IGFBP-3 ratios at killing (P<0.001). However, no difference was observed in serum insulin, IGFBP-3 or tumor phospho-Akt levels (P0.39). IF did not improve mouse survival nor did it delay prostate tumor growth. This may be secondary to metabolic adaptations to the 24 h fasting periods. Future studies are required to optimize CR for application in humans.

Turmeric (Curcuma longa) has protective effect on Prostrate Cancer

Prostate Cancer and Prostatic Diseases (2010) 13, 343–349; doi:10.1038/pcan.2010.26; published online 3 August 2010

Curcumin interrupts the interaction between the androgen receptor and Wnt/β-catenin signaling pathway in LNCaP prostate cancer cells

 

Abstract:

Recently, studies have investigated the significance of the Wnt/β-catenin pathway in prostate cancer. The transcriptional activity of the androgen receptor (AR) is modulated by interaction with coregulators, one of which is β-catenin. Curcumin, a dietary yellow pigment of Curcuma longa, has emerged as having a chemopreventive role. Although curcumin has been shown to inhibit AR expression, its molecular mechanism has not been fully elucidated. In this study, whether curcumin mediates the Wnt/β-catenin signaling pathway with regard to AR/β-catenin interactions was studied. Curcumin was shown to induce significant inhibition of AR expression in a dose-dependent manner. Marked curcumin-induced suppression of β-catenin was shown in the nuclear and cytoplasmic extracts as well as whole cell lysates. Further analysis revealed that phosphorylation of Akt and glycogen synthase kinase-3β were attenuated, but phosphorylated β-catenin was increased after curcumin treatment. Finally, cyclin D1 and c-myc, the target gene of the β-catenin/T-cell factor transcriptional complex, were also decreased. These findings suggest that curcumin modulates the Wnt/β-catenin signaling pathway and might have a significant role in mediating inhibitory effects on LNCaP prostate cancer cells.

Myriocin

The fungal metabolite from which fingolimod — a pioneering oral disease-modifying multiple sclerosis drug — was derived.

Myriocin systematic name 2-Amino-3,4-dihydroxy-2-(hydroxymethyl)-14-oxoicos-6-enoic acid, is a metabolite of the fungusIsaria sinclairii and a sphingoid base analog with immunosuppressive properties. Its chemical derivative fingolimod, systematic name 2-amino-2-[2-(4-octylphenyl)ethyl]propane-1,3-diol, was approved on 22 September 2010 by the US Food and Drug Administration for the treatment of multiple sclerosis (MS) — a chronic autoimmune disease that affects millions of people worldwide. It is the first orally administered disease-modifying treatment for MS to be approved in the United States and uses a unique strategy to disrupt the disease's attack on the central nervous system (CNS).

One clue that Isaria sinclairii might yield a useful drug came from traditional Chinese medicine — it has been used for centuries as an “elixir for eternal youth”. Another clue was Isaria sinclairii's ability to attack other organisms — in this case, insects — with a chemical arsenal. In 1994, a team of Japanese scientists was the first to extract and observe the immunosuppressive effects of myriocin ¹ . Soon after this, a program of derivatization to improve effectiveness and reduce toxicity resulted in FTY720, or fingolimod ² .

Fifteen years later, extensive research exploring the therapeutic potential of fingolimod has now led to its US regulatory approval for the treatment of relapsing forms of MS ³ . During this period, the key to fingolimod's mode of action was uncovered — modulation of the cell-surface receptors for sphingosine-1-phosphate (S1P)⁴ . Because of its structural similarity to sphingosine, fingolimod can also be phosphorylated at its aminodiol head group by sphingosine kinases ⁵ . Phosphoro-fingolimod acts as a functional antagonist of S1P₁receptors, internalizing them. It is thought that this leads to the retention of certain immune cells in the lymph nodes, thereby preventing them from migration into the CNS and involvement in the autoimmune attacks characteristic of MS ³ .

Immune system modulation is not myriocin's only useful contribution to biochemistry — it can also deplete sphingolipids from cells, because it inhibits the enzyme serine palmitoyltransferase⁷ which catalyses the formation of sphingosine, a precursor of sphingolipids.

Lipidomics Gateway (27 October 2010) [doi:10.1038/lipidmaps.2010.34]

Mouse macrophage lipids: All systems go

By combining lipidomic with transcriptomic methods, researchers have uncovered a whole-system picture of immunologically- and pharmacologically-induced lipid perturbations in mouse macrophages.

The ultimate goal of the LIPID MAPS consortium is to improve understanding of lipid metabolism and the active role that lipids play in human disease, which could aid the development of new therapies. The first step is to define the lipidome of the mouse macrophage — a cell with important roles in innate and adaptive immunity, and cardiovascular and inflammatory disease.

Now, Edward A. Dennis and colleagues from the consortium, writing in the Journal of Biological Chemistry, reveal the most complete lipids “parts list” to date for the mouse macrophage. By harnessing advanced mass spectrometry techniques to accurately measure the levels of lipid molecules, and coupling these with gene-transcription analysis, they present snapshots through time of the lipidomic response to immune-system and pharmacological perturbations. The research uncovers both expected and unexpected changes, including evidence of cross-talk between different lipid categories.

To analyse the effects of an immune-system perturbation on cellular lipid levels, the researchers used Kdo2 Lipid A (KLA), the active component of an inflammatory lipopolysaccharide. This ligand mimics aspects of bacterial infection by specifically acting on Toll-like receptor 4. The team also tested compactin — a drug which inhibits cholesterol biosysnthesis — both with and without KLA stimulation.

Over 400 lipid species were analysed by six research teams using liquid chromatography-mass spectrometry techniques, applying a different protocol for each major lipid category. In addition, to investigate how and why lipid levels might change, the researchers also measured the cellular mRNA of over 20,000 genes, including those that encode lipid-synthesizing proteins. Both mRNA and lipid measurements were taken at time intervals following perturbation by KLA and compactin.

Using statistical techniques, the researchers calculated correlations between lipids and genes over time and were able to distinguish between the effects of KLA and compactin. Many genes coding for lipid biosynthetic proteins were differently expressed, correlating with associated lipid concentrations.

One pathway significantly altered by KLA was the arachidonate oxidation pathway, in which cyclooxygenase 2 activity, prostaglandins and secondary metabolites increased. However, unsaturated fatty acid levels decreased, correlating with down-regulated elongase and desaturase genes. Also decreased were acyl CoAs, which have a key position in the lipid synthetic system, and their associated genes.

Glycerolipids, glycerophospholipids, sphingolipids and sterol esters were all remodelled by KLA. In particular, the authors found evidence for de novo synthesis of sphingolipids and for sterol synthesis via acetyl CoA. Saturated and monounsaturated cholesteryl esters and their associated enzymes also increased, suggesting that these species might accumulate due to TLR4 activation. Because oxysterols promote sphingomyelin biosynthesis, the authors suggest that elevated sphingomyelins might be due to cross-talk between the two pathways. Galactoceramides, which promote phagocytosis by macrophages, were also elevated. Interestingly, increases in saturated and monounsaturated phosphatidic acid and phosphatidylinositol lipid species were seen as late as 24 hours following KLA stimulation.

As expected, compactin, which inhibits the conversion of HMG-CoA to mevalonic acid, blocked the biosynthesis of cholesterol, but did not prevent accumulation of cholesterol owing to lipoprotein particle degradation. It also slowed the KLA-induced increase in CoQ. Unexpectedly, however, compactin appeared to increase two inflammatory eicosanoids — PGD₂ and PGE₂ — and their synthetic enzymes. To explain this finding, the authors propose cross-talk between sterols and eicosanoids via a new, as yet undiscovered, pathway.

Overall, the paper highlights the growing maturity of the lipidomics field, showing how developments in mass spectrometry are allowing the accurate measurement of an ever-growing number of lipid molecules, and that such data can reveal not just concentrations of individual lipids, but processes involving the whole system.

Lipidomics Gateway (27 October 2010) [doi:10.1038/lipidmaps.2010.32]

Virology: Severing the bud

Although many viruses use the host endosomal complex required for transport (ESCRT) to mediate budding and scission, influenza is thought to use an ESCRT-independent mechanism that was not clear. Lamb and colleagues now reveal that influenza budding and scission depends on the ion channel protein matrix 2 (M2).

M2 is part of the viral envelope, which also contains the viral glycoproteins haemagglutinin and neuraminidase; these glycoproteins associate with M1, which recruits M2, thereby incorporating it in the virion. M2 is known to be involved in the viral life cycle through its ion channel activities, and recent studies indicate that it might also affect viral budding. Using an in vitro reconstitution system, the authors found that M2 affects membrane curvature in a cholesterol-dependent manner and can induce vesicle formation in giant unilamellar vesicles (GUVs) in the presence of low or intermediate (17 mol %) cholesterol levels through its amphipathic helix. Reconstitution of GUVs with this amphipathic helix alone could also induce vesicle formation in the presence of 17 mol % cholesterol (which is comparable to the cholesterol concentration in areas of the plasma membrane), confirming the role of the M2 amphipathic helix in budding and scission.

Because GUVs have only one lipid phase (that is, lipids are spread homogeneously), they do not accurately mimic the plasma membrane, so the authors examined whether M2 can also induce budding in phase-separated GUVs. At low cholesterol levels, the M2 amphipathic helix bound the lipid-disordered phase of the GUV, clustering at the phase boundary, and induced excision of the lipid-ordered phase, initiating budding. Similar observations were made using full-length M2 in plasma membrane spheres, indicating that M2 induces budding by modifying the line tension between lipid phases.

So what is the role of M2 in viral budding in vivo? Electron microscopy showed that, in cells infected with wild-type virus, M2 localizes at the base of budding virions, where scission occurs. Interestingly, influenza with a mutated M2 amphipathic helix could bud but showed impaired scission, resulting in a string of attached viral particles. This mutated M2 localized at the constrictions between incompletely budded virions, suggesting that M2 is not required for budding but is necessary for scission.

On the basis of their findings and previous work, the authors propose a model for M2-mediated influenza budding. They suggest that budding is initiated by haemagglutinin, which clusters at lipid rafts and associates with M1. In turn, M1 recruits M2, which, in the cholesterol-rich environment of the rafts, stabilizes the site of budding until other proteins are recruited. When the pool of haemagglutinin is depleted by the assembling virions, M2 can move to the lipid phase boundary (that is, between the virion and the plasma membrane), where cholesterol levels are low, and mediate scission through its amphipathic helix.

Nature Reviews Microbiology 8, 757 (November 2010) [doi:10.1038/nrmicro2458]

Cytoskeleton: Filopodia self-assemble

Filopodia are finger-like projections made up of bundled actin filaments that have many biological roles, including cell migration. How filopodia are formed has been difficult to determine, as current experimental systems do not recapitulate aspects of filopodium biology. Kirschner and colleagues now address this question using an in vitro model system in which filopodia can self-assemble in the absence of a pre-existing cytoskeletal network.

To examine how filopodia are formed, the authors incubated frog egg extracts with lipid bilayers (and not liposomes, as had been done previously) to recapitulate actin nucleation at membranes in vitro. Dense, long structures grew from the bilayer surface that were made up of bundled actin filaments. Actin polymerization occurred at the tip of the structures, where, similarly to filopodia, proteins such as vasodilator-stimulated phosphoprotein (VASP), neural Wiskott–Aldrich syndrome protein (NWASP), CDC42 and the formin diaphanous 2 (DIA2), localized. Moreover, the kinetics of actin monomer addition at the tip were similar to those of filopodium growth in vivo. Together, these findings indicate that these structures (which the authors term filopodium-like structures (FLSs)) resemble filopodia and mimic filopodium formation in vivo.

So how do filopodia assemble? Using FLSs as an in vitro model system, the authors could not detect preformed domains on the membranes, indicating that filopodium assembly is not template driven. Instead, filopodia self-assemble on permissive membrane surfaces enriched in phosphatidylinositol (4,5)-bisphosphate. Specifically, transducer of CDC42-dependent actin assembly 1 (TOCA1; also known as FNBP1L), which interacts with membrane lipids through its F-BAR domain, is recruited early to sites where FLSs later form. This in turn recruits NWASP, followed by the actin-related protein 2/3 (ARP2/3) complex, actin, VASP, DIA2 and the bundling protein fascin. Interestingly, ARP2/3 complex-driven actin polymerization is necessary for the initiation of FLS formation but is not strictly required for elongation. Instead, a significant reduction of FLS elongation was seen only when both ARP2/3 and diaphanous-related formins were inhibited, suggesting that they both have roles in this process.

On the basis of their findings, the authors propose that filopodia self-assemble in a step-wise manner: negatively charged membranes signal the recruitment of F-BAR domain superfamily proteins, such as TOCA1, which in turn recruit nucleation-promoting factors, such as NWASP, leading to the recruitment of the ARP2/3 complex and actin, thereby initiating FLS formation.

Rachel David

Nature Reviews Molecular Cell Biology 11, 756-757, (November 2010) [doi:10.1038/nrm2991]

Jasmonate perception by inositol-phosphate-potentiated COI1–JAZ co-receptor

Jasmonates are a family of plant hormones that regulate plant growth, development and responses to stress. The F-box protein CORONATINE INSENSITIVE 1 (COI1) mediates jasmonate signalling by promoting hormone-dependent ubiquitylation and degradation of transcriptional repressor JAZ proteins. Despite its importance, the mechanism of jasmonate perception remains unclear. Here we present structural and pharmacological data to show that the true Arabidopsis jasmonate receptor is a complex of both COI1 and JAZ. COI1 contains an open pocket that recognizes the bioactive hormone (3R,7S)-jasmonoyl-l-isoleucine (JA-Ile) with high specificity. High-affinity hormone binding requires a bipartite JAZ degron sequence consisting of a conserved α-helix for COI1 docking and a loop region to trap the hormone in its binding pocket. In addition, we identify a third critical component of the jasmonate co-receptor complex, inositol pentakisphosphate, which interacts with both COI1 and JAZ adjacent to the ligand. Our results unravel the mechanism of jasmonate perception and highlight the ability of F-box proteins to evolve as multi-component signalling hubs.

 

Nature advance online publication 6 October 2010 | doi:10.1038/nature09430; Received 30 June 2010; Accepted 19 August 2010; Published online 6 October 2010

The herbicide ketoclomazone inhibits 1-deoxy-d-xylulose 5-phosphate synthase in the 2-C-methyl-d-erythritol 4-phosphate pathway and shows antibacterial activity against Haemophilus influenzae

Two distinct metabolic pathways have been elucidated for the formation of isopentenyl diphosphate and dimethylallyl diphosphate, essential metabolic precursors for isoprenoid biosynthesis: the mevalonate pathway, found ubiquitously in mammals, and the 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway, found in most bacteria. As the MEP pathway is absent from mammals, all MEP pathway enzymes represent effective targets for the development of antibacterial drugs. In this study, we found that a herbicide, ketoclomazone, exhibited antibacterial activity against a pathogenic bacterium, Haemophilus influenzae, with an MIC value of 12.5 μg ml⁻¹ and that antibacterial activity was suppressed by adding 1-deoxyxylulose, a free alcohol of 1-deoxy-d-xylulose 5-phosphate (DXP). DXP is an MEP pathway intermediate synthesized from pyruvate and d-glyceraldehyde 3-phosphate (d-GAP) by the action of DXP synthase. Thus, we investigated the enzyme kinetics of DXP synthase of H. influenzae(HiDXS) to elucidate an inhibitory mechanism of ketoclomazone on HiDXS. The dxs gene was cloned from H. influenzae and overexpressed in Escherichia coli, and the enzyme was purified to homogeneity. The purified HiDXS was a soluble dimeric 70-kDa protein. Steady-state kinetic constants for HiDXS were calculated, and Lineweaver–Burk plots were consistent with a ping-pong bi bi mechanism. The kinetics of inhibition by ketoclomazone suggested that ketoclomazone binds to an unidentified inhibitor-binding site that differs from both the pyruvate-binding site and the d-GAP-binding site on DXP synthase. These data reveal the inhibitory mechanism of ketoclomazone on DXP synthase.

The Journal of Antibiotics (2010) 63, 583–588; doi:10.1038/ja.2010.100; published online 1 September 2010

Structure–activity relationships of 11 new congeners of the SMTP plasminogen modulator

The fungal metabolite Stachybotrys microspora triprenyl phenols (SMTPs) are small-molecule plasminogen modulators that enhance plasminogen activation. The SMTP molecule consists of a tricyclic γ-lactam moiety, an isoprene side-chain and an N-linked side-chain. Previous investigations have demonstrated that the N-linked side-chain is crucial for its activity. In this study, we have isolated 11 new SMTP congeners with a variety of N-linked side-chain structures, to investigate structure–activity relationships. Active compounds included congeners with a carboxyl or a sulfonic acid group in the N-linked side-chain, whereas not all the congeners with a carboxyl group were active. Of these congeners, that with methionine or tyrosine as the N-linked side-chain moiety was more active than that with an aliphatic amino acid. Congeners without ionizable group in the N-linked side-chain were essentially inactive.

The Journal of Antibiotics (2010) 63, 589–593; doi:10.1038/ja.2010.101; published online 15 September 2010

Regulatory Oversight and Safety of Probiotic Use

Veena Venugopalan, Kimberly A. Shriner, and Annie Wong-Beringer

Abstract:
Depending on intended use of probiotic(drug vs. dietary supplement), regulatory requirements differs greatly. For dietary supplements, premarketing demonstration of safety and efficacy and approval by the Food and Drug Administration are not required; only premarket notification is required. Saccharomyces boulardii is a probiotic regulated as a dietar supplement intended for use by the general healthy population, not as a drug to prevent, treat or mitigate disease. However, since recent increases in incidence and severity of Clostridium difficile infection, probiotics have been used to treat recurrent and/or refractory disease in hospitalized patients. Saccharomyces fungemia secondary to use of the probiotic has been described for patients who are critically ill, are receiving nutrition enterally, or have a central venous catheter. Before use of a probiotic is considered for hospitalized patients, careful assessment of risk versus benefit must be made. To ensure patient safety, probiotics should be properly handled during administration.
Probiotics are defined by the Food and Agriculture Organization of the World Health Organization as live microorganisms that, when administered in adequate amounts confer a health benefit on the host. The term probiotic can be subcategorized to include probiotic drugs, probiotic foods(e.g. foods, food ingredients and dietary supplements), direct fed microbials (probiotics for animal use) and designer probiotics (genetically modified probiotics). In the US, probiotic products are marketed to a generally healthy population as foods or dietary supplements.
Recent increases in the incidence and severity of Clostridium difficile infection (CDI)have led some clinicians to consider use of probiotics as "drugs", either alone or in combination with traditional antimicrobial agents for the prevention and treatment of CDI. Several recent reviews have summarized results from clinical studies evaluating the efficacy of probiotics in diarrheal illness. The goal is to highlight the current regulatory oversight for probiotics in US, identify potential risk situations associated with their administration and offer suggestions on practical aspects of probiotic administration to ensure patient safety.
Accordingly to the Food and Drug Administration definition, a drug is an article intended for use as a drug, then it must undergo the regulatory process as a drug, which is similar to that of any new therapeutic agent.




http://www.cdc.gov/eid/content/16/11/1661.htm

Notch and EGFR pathway interaction

Notch and EGFR pathway interaction regulates neural stem cell number and
self-renewal

Specialized cellular microenvironments, or ‘niches’, modulate stem cell properties, including cell number, self-renewal and fate decisions1, 2. In the
adult brain, niches that maintain a source of neural stem cells (NSCs) and neural
progenitor cells (NPCs) are the subventricular zone (SVZ) of the lateral
ventricle and the dentate gyrus of the hippocampus3, 4, 5. The size of the NSC
population of the SVZ at any time is the result of several ongoing processes,
including self-renewal, cell differentiation, and cell death.
Maintaining the balance between NSCs and NPCs in the SVZ niche is critical to



Nature 467, 323-327 (16 September 2010) |
doi:10.1038/nature09347;

Small but dominant RNA

As Mendel observed over a century ago, the manifestation of a phenotype can crucially depend on the dominant-recessive relationship between alleles at a given locus. A study of plant self-incompatibility suggests a new mechanism by which such dominant-recessive relationships arise: in this system, a small RNA encoded by the dominant allele acts in trans to epigenetically silence the expression of the recessive allele.
A plant uses a 'self-incompatibility'mechanism to reject fertilization by pollen that is genetically too similar to itself. In Brasssica species, this trait is controlled by three tightly linked, multiallelic loci and particularly by the gene encoding the male-specific protein S locus protein 11 (SP11) and its female-specific receptor S receptor kinase SRK and SRK alleles known as the S haplotye/





Nature Reviews Genetics 11, 670-671 (October 2010) |
doi:10.1038/nrg2875

Predicting functional modules

The precise spatiotemporal patterns of gene expression that are required during the development of multicellular organisms are largely governed by the binding of transcription factors to cis-regulatory sequences. Although many methods have been successful in identifying specific cis-regulatory modules (CRMs), it remains difficult to systematically describe the location and function of
CRMs in a specific developmental process. This paper presents a novel computational approach that tackles this challenge and has led to the most
complete, quantitative description to date of the control network for fruitfly embryo anteroposterior patterning.
Kazemian and colleagues developed a regression-based model that estimates
the potential of a genomic region to control the spatially restricted
expression of a nearby gene, which they term the 'pattern-generating



Nature Reviews Genetics 11, 669 (October 2010) | doi:10.1038/nrg2872

Tumor cells engineered to codisplay on their surface 4-1BBL and LIGHT

Tumor cells engineered to codisplay on their surface 4-1BBL and LIGHT
costimulatory proteins as a novel vaccine approach for cancer immunotherapy

Primary tumor cells genetically modified to express a collection of immunological
ligands on their surface may have the utility as therapeutic autologous cancer
vaccines. However, genetic modification of primary tumor cells is not only cost,
labor and time intensive, but also has safety repercussions. As an alternative,
we developed the ProtEx technology that involves generation of immunological
ligands with core streptavidin (SA) and their display on biotinylated cells in a
rapid and efficient manner. We herein demonstrate that TC-1 tumor cells can be
rapidly and efficiently engineered to codisplay on their surface two costimulatory proteins, SA-4-1BBL and SA-LIGHT, simultaneously. Vaccination with irradiated TC-1 cells codisplaying both chimeric proteins showed 100% efficacy in a prophylactic and >55% efficacy in a therapeutic tumor setting. In
contrast, vaccination with TC-1 cells


Cancer Gene Therapy 17, 730-741 (October 2010) |
doi:10.1038/cgt.2010.29

Inhibition of follicular T-helper

Inhibition of follicular T-helper cells by CD8+ regulatory T cells is essential
for self tolerance

The ability to produce vigorous immune responses that spare self tissues and
organs depends on the elimination of autoreactive T and B cells. However,
purging of immature and mature self-reactive T and B cells is incomplete
and may also require the involvement of cells programmed to suppress immune
responses1. Regulatory T cells (Treg ) belonging to the CD4+ T-cell subset may
have a role in preventing untoward inflammatory responses, but T-cell
subsets programmed to inhibit the development of autoantibody formation
and systemic-lupus-erythematosus-like disease have not yet been defined2. Here
we delineate a CD8+ regulatory T-cell



Nature 467, 328-332 (16 September 2010) |
doi:10.1038/nature09370;

Vitamin D and disease

A recent study demonstrates the power of combining chromatin immunoprecipitation followed by sequencing (ChIP–seq) with genome-wide
association (GWA) study data sets to explore the molecular basis of complex disease.
Ramagopalan and colleagues used ChIP–seq to produce high-resolution
maps of the genomic binding of the vitamin D receptor (VDR) — a ligand-
activated transcription factor — in human lymphoblastoid cell lines, with
and without active ligand. In the presence of ligand, they identified 2,776
binding sites, many of which are in regions associated with active chromatin,
consistent with the expected role of VDR at gene regulatory elements.Vitamin D has been linked to several diseases, particularly autoimmune diseases, but the basis for the link is unclear. The authors compared their ChIP–seq data with GWA study data sets for 47 common traits and found significant enrichment of VDR sites in associated genomic intervals for multiple sclerosis and type 1 diabetes, along with other autoimmune diseases, cancers and traits such as height.



Nature Reviews Genetics 11, 670 (October 2010) | doi:10.1038/nrg2873

In vitro assembly of cubic RNA-

In vitro assembly of cubic RNA-based scaffolds designed in silico



The organization of biological materials into versatile three-dimensional
assemblies could be used to build multifunctional therapeutic scaffolds for
use in nanomedicine. Here, we report a strategy to design three-dimensional
nanoscale scaffolds that can be self-assembled from RNA with precise
control over their shape, size and composition. These cubic nanoscaffolds
are only ~13 nm in diameter and are composed of short oligonucleotides,
making them amenable to chemical synthesis, point modifications and
further functionalization. Nanocube assembly is verified by gel assays,
dynamic light scattering and cryogenic electron microscopy. Formation of
functional RNA nanocubes is also demonstrated by incorporation of a
light-up fluorescent RNA aptamer that is optimally active only upon full RNA
assembly. Moreover, we show that the RNA nanoscaffolds can self-assemble in
isothermal conditions (37 °C) during in


Nature Nanotechnology 5, 676 - 682 (2010)
Published online: 29 August 2010 | doi:10.1038/nnano.2010.160