Gut commensal bacteria enhance pathogenesis of a tumorigenic murine retrovirus.

The influence of the microbiota on viral transmission and replication is well appreciated. However, its impact on retroviral pathogenesis outside of transmission/replication control remains unknown. Using murine leukemia virus (MuLV), we found that some commensal bacteria promoted the development of leukemia induced by this retrovirus. The promotion of leukemia development by commensals is due to suppression of the adaptive immune response through upregulation of several negative regulators of immunity. These negative regulators include Serpinb9b and Rnf128, which are associated with a poor prognosis of some spontaneous human cancers. Upregulation of Serpinb9b is mediated by sensing of bacteria by the NOD1/NOD2/RIPK2 pathway. This work describes a mechanism by which the microbiota enhances tumorigenesis within gut-distant organs and points at potential targets for cancer therapy.

Dance reveals symmetry especially in young men.

Dance is believed to be important in the courtship of a variety of species, including humans, but nothing is known about what dance reveals about the underlying phenotypic--or genotypic--quality of the dancer. One measure of quality in evolutionary studies is the degree of bodily symmetry (fluctuating asymmetry, FA), because it measures developmental stability. Does dance quality reveal FA to the observer and is the effect stronger for male dancers than female? To answer these questions, we chose a population that has been measured twice for FA since 1996 (ref. 9) in a society (Jamaican) in which dancing is important in the lives of both sexes. Motion-capture cameras created controlled stimuli (in the form of videos) that isolated dance movements from all other aspects of visual appearance (including FA), and the same population evaluated these videos for dancing ability. Here we report that there are strong positive associations between symmetry and dancing ability, and these associations were stronger in men than in women. In addition, women rate dances by symmetrical men relatively more positively than do men, and more-symmetrical men value symmetry in women dancers more than do less-symmetrical men. In summary, dance in Jamaica seems to show evidence of sexual selection and to reveal important information about the dancer.

CRISPR-based functional genomics in human dendritic cells.

Dendritic cells (DCs) regulate processes ranging from antitumor and antiviral immunity to host-microbe communication at mucosal surfaces. It remains difficult, however, to genetically manipulate human DCs, limiting our ability to probe how DCs elicit specific immune responses. Here, we develop a CRISPR-Cas9 genome editing method for human monocyte-derived DCs (moDCs) that mediates knockouts with a median efficiency of >94% across >300 genes. Using this method, we perform genetic screens in moDCs, identifying mechanisms by which DCs tune responses to lipopolysaccharides from the human microbiome. In addition, we reveal donor-specific responses to lipopolysaccharides, underscoring the importance of assessing immune phenotypes in donor-derived cells, and identify candidate genes that control this specificity, highlighting the potential of our method to pinpoint determinants of inter-individual variation in immunity. Our work sets the stage for a systematic dissection of the immune signaling at the host-microbiome interface and for targeted engineering of DCs for neoantigen vaccination.

The Biosynthesis of Lipooligosaccharide from Bacteroides thetaiotaomicron.

Lipopolysaccharide (LPS), a cell-associated glycolipid that makes up the outer leaflet of the outer membrane of Gram-negative bacteria, is a canonical mediator of microbe-host interactions. The most prevalent Gram-negative gut bacterial taxon, Bacteroides, makes up around 50% of the cells in a typical Western gut; these cells harbor ~300 mg of LPS, making it one of the highest-abundance molecules in the intestine. As a starting point for understanding the biological function of Bacteroides LPS, we have identified genes in Bacteroides thetaiotaomicron VPI 5482 involved in the biosynthesis of its lipid A core and glycan, generated mutants that elaborate altered forms of LPS, and used matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry to interrogate the molecular features of these variants. We demonstrate, inter alia, that the glycan does not appear to have a repeating unit, and so this strain produces lipooligosaccharide (LOS) rather than LPS. This result contrasts with Bacteroides vulgatus ATCC 8482, which by SDS-PAGE analysis appears to produce LPS with a repeating unit. Additionally, our identification of the B. thetaiotaomicron LOS oligosaccharide gene cluster allowed us to identify similar clusters in other Bacteroides species. Our work lays the foundation for developing a structure-function relationship for Bacteroides LPS/LOS in the context of host colonization.IMPORTANCE Much is known about the bacterial species and genes that make up the human microbiome, but remarkably little is known about the molecular mechanisms through which the microbiota influences host biology. A well-known mechanism by which bacteria influence the host centers around lipopolysaccharide (LPS), a component of the Gram-negative bacterial outer membrane. Pathogen-derived LPS is a potent ligand for host receptor Toll-like receptor 4, which plays an important role in sensing bacteria as part of the innate immune response. Puzzlingly, the most common genus of human gut bacteria, Bacteroides, produces LPS but does not elicit a potent proinflammatory response. Previous work showing that Bacteroides LPS differs structurally from pathogen-derived LPS suggested the outlines of an explanation. Here, we take the next step, elucidating the biosynthetic pathway for Bacteroides LPS and generating mutants in the process that will be of great use in understanding how this molecule modulates the host immune response.

Marker Imputation Before Genomewide Selection in Biparental Maize Populations.

Marker imputation can be used to increase the number of markers in genomewide selection. Our objectives were to determine (i) if marker imputation increases the response to selection (R) and prediction accuracy (rMP ) among the progeny of two maize (Zea mays L.) parental inbreds (A and B); (ii) the number of imputed single nucleotide polymorphism (SNP) markers needed to reach a plateau in rMP for grain yield, moisture, and test weight; and (iii) the lowest number of assayed SNP markers that can be used for imputation without a significant decrease in rMP . The progeny of 27 biparental crosses between A and B (A/B) were assayed with 49 to 100 SNP markers, and imputation was conducted to increase the number of markers to 2911. For each A/B test population, the training population in the general combining ability (GCA) model consisted of 4 to 26 maize crosses with A and B as one of the parents, whereas the training population in the A/B model was the A/B population itself. Marker imputation made the GCA model as good as or better than the A/B model in terms of R and rMP for all traits. The rMP values did not increase significantly beyond 500 imputed markers for grain yield and beyond 1000 imputed markers for moisture and test weight. We recommend that maize breeders assay an elite biparental cross with only around 50 polymorphic SNP markers, increase marker coverage to around 1000 markers by imputation, and use the GCA model with imputed markers for genomewide selection within the cross.

A Phase-Variable Surface Layer from the Gut Symbiont Bacteroides thetaiotaomicron.

UNLABELLED: The capsule from Bacteroides, a common gut symbiont, has long been a model system for studying the molecular mechanisms of host-symbiont interactions. The Bacteroides capsule is thought to consist of an array of phase-variable polysaccharides that give rise to subpopulations with distinct cell surface structures. Here, we report the serendipitous discovery of a previously unknown surface structure in Bacteroides thetaiotaomicron: a surface layer composed of a protein of unknown function, BT1927. BT1927, which is expressed in a phase-variable manner by ~1:1,000 cells in a wild-type culture, forms a hexagonally tessellated surface layer. The BT1927-expressing subpopulation is profoundly resistant to complement-mediated killing, due in part to the BT1927-mediated blockade of C3b deposition. Our results show that the Bacteroides surface structure is capable of a far greater degree of structural variation than previously known, and they suggest that structural variation within a Bacteroides species is important for productive gut colonization. IMPORTANCE: Many bacterial species elaborate a capsule, a structure that resides outside the cell wall and mediates microbe-microbe and microbe-host interactions. Species of Bacteroides, the most abundant genus in the human gut, produce a capsule that consists of an array of polysaccharides, some of which are known to mediate interactions with the host immune system. Here, we report the discovery of a previously unknown surface structure in Bacteroides thetaiotaomicron. We show that this protein-based structure is expressed by a subset of cells in a population and protects Bacteroides from killing by complement, a component of the innate immune system. This novel surface layer protein is conserved across many species of the genus Bacteroides, suggesting an important role in colonization and host immune modulation.

Congo Red Interactions with Curli-Producing E. coli and Native Curli Amyloid Fibers.

Microorganisms produce functional amyloids that can be examined and manipulated in vivo and in vitro. Escherichia coli assemble extracellular adhesive amyloid fibers termed curli that mediate adhesion and promote biofilm formation. We have characterized the dye binding properties of the hallmark amyloid dye, Congo red, with curliated E. coli and with isolated curli fibers. Congo red binds to curliated whole cells, does not inhibit growth, and can be used to comparatively quantify whole-cell curliation. Using Surface Plasmon Resonance, we measured the binding and dissociation kinetics of Congo red to curli. Furthermore, we determined that the binding of Congo red to curli is pH-dependent and that histidine residues in the CsgA protein do not influence Congo red binding. Our results on E. coli strain MC4100, the most commonly employed strain for studies of E. coli amyloid biogenesis, provide a starting point from which to compare the influence of Congo red binding in other E. coli strains and amyloid-producing organisms.

Mammalian Lipopolysaccharide Receptors Incorporated into the Retroviral Envelope Augment Virus Transmission.

The orally transmitted retrovirus mouse mammary tumor virus (MMTV) requires the intestinal microbiota for persistence. Virion-associated lipopolysaccharide (LPS) activates Toll-like receptor 4 (TLR4), stimulating production of the immunosuppressive cytokine IL-10 and MMTV evasion of host immunity. However, the mechanisms by which MMTV associates with LPS remain unknown. We find that the viral envelope contains the mammalian LPS-binding factors CD14, TLR4, and MD-2, which, in conjunction with LPS-binding protein (LBP), bind LPS to the virus and augment transmission. MMTV isolated from infected mice lacking these LBPs cannot engage LPS or stimulate TLR4 and have a transmission defect. Furthermore, MMTV incorporation of a weak agonist LPS from Bacteroides, a prevalent LPS source in the gut, significantly enhances the ability of this LPS to stimulate TLR4, suggesting that MMTV intensifies these immunostimulatory properties. Thus, an orally transmitted retrovirus can capture, modify, and exploit mammalian receptors for bacterial ligands to ensure successful transmission.

A longitudinal study of digit ratio (2D:4D) and other finger ratios in Jamaican children.

It has been hypothesised that the ratio between the length of the 2nd and 4th digits (2D:4D) is a correlate of prenatal sex steroids, and this relationship is strongest for the right hand. Furthermore, it has been suggested that 2D:4D is sexually dimorphic, the dimorphism is determined early, and 2D:4D among children is stable with growth. Here, we present the first longitudinal study of right and left hand 2D:4D. Our sample was 108 (54 males) Jamaican children. The first measurements were made in 1998 when mean age was 9.68 +/- 1.39 years, and a second set of measurements were made in 2002. We found that: (i) there was a small increase in 2D:4D with age which was lowest in the right hand; (ii) 2D:4D was sexually dimorphic, the means for males and females differed in the same direction in the 1998 and 2002 samples, and the sex difference was significant in the 1998 but not in the 2002 sample; (iii) the correlation between the 1998 and 2002 measurements of 2D:4D was high, indicating that rank order of the ratio was stable across year groups; and (iv) the rate of change in 2D:4D did not differ significantly across year groups. We conclude that 2D:4D increases slightly with age in children with the effect less marked for the right hand (i.e. the hand which is likely to show the strongest association with prenatal steroids), 2D:4D is sexually dimorphic from an early age, and the rank order of 2D:4D is stable in children. We discuss the implications of our findings for the status of 2D:4D as a correlate of prenatal sex steroids. The patterns of change in other finger ratios are also considered.