Posture Affects How Robots and Infants Map Words to Objects

For infants, the first problem in learning a word is to map the word to its referent; a second problem is to remember that mapping when the word and/or referent are again encountered. Recent infant studies suggest that spatial location plays a key role in how infants solve both problems. Here we provide a new theoretical model and new empirical evidence on how the body – and its momentary posture – may be central to these processes. The present study uses a name-object mapping task in which names are either encountered in the absence of their target (experiments 1–3, 6 & 7), or when their target is present but in a location previously associated with a foil (experiments 4, 5, 8 & 9). A humanoid robot model (experiments 1–5) is used to instantiate and test the hypothesis that body-centric spatial location, and thus the bodies’ momentary posture, is used to centrally bind the multimodal features of heard names and visual objects. The robot model is shown to replicate existing infant data and then to generate novel predictions, which are tested in new infant studies (experiments 6–9). Despite spatial location being task-irrelevant in this second set of experiments, infants use body-centric spatial contingency over temporal contingency to map the name to object. Both infants and the robot remember the name-object mapping even in new spatial locations. However, the robot model shows how this memory can emerge –not from separating bodily information from the word-object mapping as proposed in previous models of the role of space in word-object mapping – but through the body’s momentary disposition in space.     

Human Excreta as a Stable and Important Source of Atmospheric Ammonia in the Megacity of Shanghai

Although human excreta as a NH₃ source has been recognized globally, this source has never been quantitatively determined in cities, hampering efforts to fully assess the causes of urban air pollution. In the present study, the exhausts of 15 ceiling ducts from collecting septic tanks in 13 buildings with 6 function types were selected to quantify NH₃ emission rates in the megacity of Shanghai. As a comparison, the ambient NH₃ concentrations across Shanghai were also measured at 13 atmospheric monitoring sites. The concentrations of NH₃ in the ceiling ducts (2809−2661+5803 μg m^-3) outweigh those of the open air (~10 μg m^-3) by 2–3 orders of magnitude, and there is no significant difference between different seasons. δ¹⁵N values of NH₃ emitted from two ceiling ducts are also seasonally consistent, suggesting that human excreta may be a stable source of NH₃ in urban areas. The NH₃ concentration levels were variable and dependent on the different building types and the level of human activity. NH₃ emission rates of the six residential buildings (RB_NH3) were in agreement with each other. Taking occupation time into account, we confined the range of the average NH₃ emission factor for human excreta to be 2–4 times (with the best estimate of 3 times) of the averaged RB_NH3 of 66.0±58.9 g NH₃ capita^-1 yr^-1. With this emission factor, the population of ~21 million people living in the urban areas of Shanghai annually emitted approximately 1386 Mg NH₃, which corresponds to over 11.4% of the total NH₃ emissions in the Shanghai urban areas. The spatial distribution of NH₃ emissions from human excreta based on population data was calculated for the city of Shanghai at a high-resolution (100×100 m). Our results demonstrate that human excreta should be included in official ammonia emission inventories.     

CONVERGENT AND CORRELATED EVOLUTION OF MAJOR LIFE‐HISTORY TRAITS IN THE ANGIOSPERM GENUS LEUCADENDRON (PROTEACEAE)

Natural selection is expected to cause convergence of life histories among taxa as well as correlated evolution of different life‐history traits. Here, we quantify the extent of convergence of five key life‐history traits (adult fire survival, seed storage, degree of sexual dimorphism, pollination mode, and seed‐dispersal mode) and test hypotheses about their correlated evolution in the genus Leucadendron (Proteaceae) from the fire‐prone South African fynbos. We reconstructed a new molecular phylogeny of this highly diverse genus that involves more taxa and molecular markers than previously. This reconstruction identifies new clades that were not detected by previous molecular study and morphological classifications. Using this new phylogeny and robust methods that account for phylogenetic uncertainty, we show that the five life‐history traits studied were labile during the evolutionary history of the genus. This diversity allowed us to tackle major questions about the correlated evolution of life‐history strategies. We found that species with longer seed‐dispersal distances tended to evolve lower pollen‐dispersal distance, that insect‐pollinated species evolved decreased sexual dimorphism, and that species with a persistent soil seed‐bank evolved toward reduced fire‐survival ability of adults.     

Marine moult migration of the freshwater Scaly‐sided Merganser Mergus squamatus revealed by stable isotopes and geolocators

Scaly‐sided Mergansers Mergus squamatus breed on freshwater rivers in far eastern Russia, Korea and China, wintering in similar habitats in China and Korea, but nothing was known of their moulting habitat. To investigate the moult strategies of this species, we combined wing feather stable isotope ratios (males and females) with geolocator data (nesting females) to establish major habitat types (freshwater, brackish or saltwater) used by both sexes during wing moult. Although most Scaly‐sided Mergansers of both sexes probably moult on freshwater, some males and non‐breeding and failed breeding females appeared to undertake moult migration to brackish and marine waters. Given the previous lack of any surveys of coastal or estuarine waters for this species during the moult period, these findings suggest important survey needs for the effective conservation of the species during the flightless moult period.     

A new phylodynamic model of Mycobacterium bovis transmission in a multi-host system uncovers the role of the unobserved reservoir

Multi-host pathogens are particularly difficult to control, especially when at least one of the hosts acts as a hidden reservoir. Deep sequencing of densely sampled pathogens has the potential to transform this understanding, but requires analytical approaches that jointly consider epidemiological and genetic data to best address this problem. While there has been considerable success in analyses of single species systems, the hidden reservoir problem is relatively under-studied. A well-known exemplar of this problem is bovine Tuberculosis, a disease found in British and Irish cattle caused by Mycobacterium bovis, where the Eurasian badger has long been believed to act as a reservoir but remains of poorly quantified importance except in very specific locations. As a result, the effort that should be directed at controlling disease in badgers is unclear. Here, we analyse densely collected epidemiological and genetic data from a cattle population but do not explicitly consider any data from badgers. We use a simulation modelling approach to show that, in our system, a model that exploits available cattle demographic and herd-to-herd movement data, but only considers the ability of a hidden reservoir to generate pathogen diversity, can be used to choose between different epidemiological scenarios. In our analysis, a model where the reservoir does not generate any diversity but contributes to new infections at a local farm scale are significantly preferred over models which generate diversity and/or spread disease at broader spatial scales. While we cannot directly attribute the role of the reservoir to badgers based on this analysis alone, the result supports the hypothesis that under current cattle control regimes, infected cattle alone cannot sustain M. bovis circulation. Given the observed close phylogenetic relationship for the bacteria taken from cattle and badgers sampled near to each other, the most parsimonious hypothesis is that the reservoir is the infected badger population. More broadly, our approach demonstrates that carefully constructed bespoke models can exploit the combination of genetic and epidemiological data to overcome issues of extreme data bias, and uncover important general characteristics of transmission in multi-host pathogen systems.     

Open and Closed Conformations of the Isolated Transmembrane Domain of Death Receptor 5 Support a New Model of Activation

It has long been presumed that activation of the apoptosis-initiating Death Receptor 5, as well as other structurally homologous members of the TNF-receptor superfamily, relies on ligand-stabilized trimerization of noninteracting receptor monomers. We and others have proposed an alternate model in which the TNF-receptor dimer—sitting at the vertices of a large supramolecular receptor network of ligand-bound receptor trimers—undergoes a closed-to-open transition, propagated through a scissorslike conformational change in a tightly bundled transmembrane (TM) domain dimer. Here we have combined electron paramagnetic resonance spectroscopy and potential-of-mean force calculations on the isolated TM domain of the long isoform of DR5. The experiments and calculations both independently validate that the opening transition is intrinsic to the physical character of the TM domain dimer, with a significant energy barrier separating the open and closed states.Death receptor 5 (DR5) is a member of the tumor necrosis factor receptor (TNFR) superfamily that mediates apoptosis when bound by its cognate ligand, TNF-related apoptosis-inducing ligand (1). Upregulated in cancer cells, DR5 is among the most actively pursued anticancer targets (2). TNF-related apoptosis-inducing ligand binds to preassembled DR5 trimers at their extracellular domains, causing the formation of oligomeric ligand-receptor networks that are held together by receptor dimers (3). In the long-isoform of DR5, this dimer is crosslinked via ligand-induced disulfide bond formation between two transmembrane (TM) domain α-helices at Cys-209, and is further stabilized by a GxxxG motif one helix-turn downstream (3).Our recent study of the structurally homologous TNFR1 showed that receptor activation involves a conformational change that propagates from the extracellular domain to the cytosolic domain through a separation (or opening) of the TM domains of the dimer (4). We have therefore hypothesized that the activation of DR5, and indeed all structurally homologous TNF-receptors, involves a scissorslike opening of the TM domain dimer (Fig. 1).Open in a separate windowFigure 1Activation model of the DR5-L TM dimer. The sequence and positions of the disulfide bond and TOAC spin label (top), along with our previously published model (bottom, left) are shown. We propose an activation model (bottom, right) in which the transmembrane dimer pivots at its disulfide bond to reach an active open conformation.Using electron paramagnetic resonance (EPR) spectroscopy, a technique that has been used previously to study TM helix architecture and dynamics (5,6), and potential-of-mean force (PMF) calculations (7,8), this study addresses the question of whether the isolated disulfide-linked DR5-L TM domain dimer occupies distinct open and closed states (Fig. 1), and how its dynamic behavior contributes to the free-energy landscape of the opening transition of the full-length receptor.The DR5-L TM domain was synthesized with TOAC, an amino acid with a nitroxide spin label rigidly fixed to the α-carbon (9), incorporated at position 32 (Fig. 1), with some minor modification to facilitate EPR measurements. Previous work confirmed that this peptide forms disulfide-linked dimers (e.g., via comparison to 2-ME treated sample) and a negligible population of higher-order oligomers (further supported by model fitting of the EPR data below). For peptide work, residues were renumbered such that Thr-204 corresponds to Thr-1, and so on. The cytosolic Cys-29 (which we previously showed does not participate in a disulfide bond in cells) was replaced with serine to prevent the formation of antiparallel disulfide-linked dimers, and Trp-34 was replaced with tyrosine to prevent intrinsic fluorescence in fluorescence studies (not published). Continuous-wave (CW) dipolar EPR (sensitive only to spin-spin distances <25 Å) was used to measure TOAC-TOAC distances within the TM dimers and revealed an ordered Gaussian distribution centered at 16 Å (full width half-maximum (FWHM) = 4 Å), corresponding to a closed state (Fig. 2 A). Double electron-electron resonance (DEER) (sensitive to spin-spin distances from 15 to 60 Å) also detected a short distance consistent with the dipolar EPR data, along with a longer, disordered component (32.9 Å, FWHM = 28 Å) (Fig. 2 B). Together, these measurements indicate the presence of a compact, ordered closed state and a broader, disordered open state. EPR on oriented membranes also indicated two structural states. Global fitting revealed two populations of spin-label tilt angles (orientation of the nitroxide principal axis relative to the membrane normal): a narrow conformation (24°, FWHM = 20°), and a disordered conformation (50°, FWHM = 48°) (Fig. 2 C). This bimodal orientational distribution (Fig. 2 C) is remarkably consistent with the bimodal distance distribution (Fig. 2 B).Open in a separate windowFigure 2EPR spectra (left) of 32-TOAC-DR5 in lipid, and resulting structural distributions (right). (A) CW dipolar EPR spectra (left) of dimer (1 mM diamide) and monomer (1 mM 2-mercaptoethanol). Best-fit spin-spin distance distribution was a single Gaussian centered at 16 ± 2 Å (right). (B) The DEER waveform (left) of 32-TOAC-DR5 dimer was best fit (right) to a two-Gaussian distribution. The short distance was constrained to agree with the CW data, because DEER has poor sensitivity for distances <20 Å. The long-distance distribution is centered at 32.9 Å and is much broader. (C) CW EPR spectra (left) of 32-TOAC-DR5, with the membrane-normal oriented parallel (red) and perpendicular (blue) to the field. Simultaneous (global) fitting of these spectra reveals narrow and broad components (right). (In panels B and C, the overall distribution is plotted as black, while the closed and open components are plotted as green and magenta, respectively.)We subsequently conducted a PMF calculation (10) using the DR5-L TM dimer starting configuration developed by our group previously (3), embedded in a DMPC bilayer, with the Leu-32/Leu-32 C_α distance as the reaction coordinate. Three calculations were run from independent starting configurations, each using 50 windows spaced in 0.5° increments, and run for 20 ns at each window (totaling 3 μs). Each of the calculations yielded a similar result, and the averaged free energy curve (Fig. 3 A) agrees remarkably well with our EPR measurements: a narrow distribution at the closed conformation (∼16 Å, Fig. 3 B) separated by an ∼3 kcal/mol energy barrier from a broad distribution of accessible open conformations at ∼27 Å, (Fig. 3 C). Each of the three individual PMF plots can be found in Fig. S1 in the Supporting Material.Open in a separate windowFigure 3(A) PMF calculation of the DR5 TM domain dimer along the Leu-32/Leu-32 distance reaction coordinate. The PMF calculation reveals a narrow closed state and a broader open state separated by a free energy barrier. Representative snapshots of the (B) closed state and (C) open state.In the closed state, the helices are tightly packed at the GxxxG interfacial motif and all the way down the juxtaposed helix faces at residues Ala-18, Leu-22, Ala-25, and Val-26. The tight packing is aided by kinking and twisting of the two helices around their common axis, increasing the interacting surface area. In the open conformations, the Ala-18, Leu-22, Ala-25, and Val-26 pairs are dissociated and, interestingly, the GxxxG motif at Gly-10 and Gly-14 remains tightly packed. The open state energy well is only slightly less favorable than the closed state (by ∼2 kcal/mol), and its free energy profile is relatively broad and flat. The increased crossing angle in the open state is facilitated by straightening of the helix kink and is not accommodated by a change in bilayer thickness (see Fig. S3, A and B).The observed change in helix-helix distance (11 Å between the two minima in the PMF) is extremely close to that observed previously in live-cell FRET studies of a constitutively active form of TNFR1 (∼8 Å change between states using large fluorescence probes at the cytosolic domains) (4). The change observed in the EPR data (17 Å) may be an overestimate because the measurement is made between TOAC spin labels that likely protrude from the two helices, depending on rotational orientation. These results collectively show that activation of these receptors requires a small, but clearly significant conformational opening of the TM domains. One important note is that our EPR experiments recapitulate the equilibrium distribution of the two states despite there being no driving force to traverse the barrier between them (∼3 kcal/mol in the closed-to-open transition and ∼1 kcal/mol in the open-to-closed transition, Fig. 3). We do not interpret the results to mean that the dimer necessarily traverses these barriers at 4°C. Rather, there likely exist multiple reaction paths for dimerization of the abstracted TM domains. Finally, in the context of the full-length receptor, how the ligand induces a conformational change capable of overcoming the closed-to-open barrier remains an important question.Whether the observed structural transition in the TM domain dimer of the long-isoform of DR5 is a ubiquitous conformational switch that acts over the entire TNFR superfamily remains unknown. Vilar et al. (11) first proposed a similar scissors-model for activation of p75 neurotrophin receptor, which has a cysteine at the center of its TM helix. The short isoform of DR5 lacks a TM domain cysteine, but does form noncovalent dimers in cells, with likely TM domain dimer contacts (3). Among the other closely related and structurally homologous members of the TNFR superfamily, TNFR1 contains a cysteine at the center of the TM domain, but lacks any discernible small residue motifs (e.g., GxxxG). TNFR2 lacks a TM cysteine on the extracellular side, but does have a GxxxG motif positioned similarly to that of DR5. On the other hand, Death Receptor 4, whose functional distinction from DR5 has remained somewhat elusive, lacks both a cysteine and any recognizable small-residue hydrophobic motif.In summary, we have extended recent findings that point to the TM domain of DR5 as an essential structural component in the conformational change associated with activation. Our findings that the DR5-L TM domain occupies distinct open and closed states, separated by a substantial energy barrier, points the way to further studies across the TNF-receptor superfamily.     

ANOLIS SEX CHROMOSOMES ARE DERIVED FROM A SINGLE ANCESTRAL PAIR

To explain the frequency and distribution of heteromorphic sex chromosomes in the lizard genus Anolis, we compared the relative roles of sex chromosome conservation versus turnover of sex‐determining mechanisms. We used model‐based comparative methods to reconstruct karyotype evolution and the presence of heteromorphic sex chromosomes onto a newly generated Anolis phylogeny. We found that heteromorphic sex chromosomes evolved multiple times in the genus. Fluorescent in situ hybridization (FISH) of repetitive DNA showed variable rates of Y chromosome degeneration among Anolis species and identified previously undetected, homomorphic sex chromosomes in two species. We confirmed homology of sex chromosomes in the genus by performing FISH of an X‐linked bacterial artificial chromosome (BAC) and quantitative PCR of X‐linked genes in multiple Anolis species sampled across the phylogeny. Taken together, these results are consistent with long‐term conservation of sex chromosomes in the group. Our results pave the way to address additional questions related to Anolis sex chromosome evolution and describe a conceptual framework that can be used to evaluate the origins and evolution of heteromorphic sex chromosomes in other clades.     

3-Methyl-1-butanol production in Escherichia coli: random mutagenesis and two-phase fermentation

Interest in producing biofuels from renewable sources has escalated due to energy and environmental concerns. Recently, the production of higher chain alcohols from 2-keto acid pathways has shown significant progress. In this paper, we demonstrate a mutagenesis approach in developing a strain of Escherichia coli for the production of 3-methyl-1-butanol by leveraging selective pressure toward l-leucine biosynthesis and screening for increased alcohol production. Random mutagenesis and selection with 4-aza-d,l-leucine, a structural analogue to l-leucine, resulted in the development of a new strain of E. coli able to produce 4.4 g/L of 3-methyl-1-butanol. Investigation of the host’s sensitivity to 3-methyl-1-butanol directed development of a two-phase fermentation process in which titers reached 9.5 g/L of 3-methyl-1-butanol with a yield of 0.11 g/g glucose after 60 h.     

Lysosomal fusion and SNARE function are impaired by cholesterol accumulation in lysosomal storage disorders

The function of lysosomes relies on the ability of the lysosomal membrane to fuse with several target membranes in the cell. It is known that in lysosomal storage disorders (LSDs), lysosomal accumulation of several types of substrates is associated with lysosomal dysfunction and impairment of endocytic membrane traffic. By analysing cells from two severe neurodegenerative LSDs, we observed that cholesterol abnormally accumulates in the endolysosomal membrane of LSD cells, thereby reducing the ability of lysosomes to efficiently fuse with endocytic and autophagic vesicles. Furthermore, we discovered that soluble N‐ethylmaleimide‐sensitive factor attachment protein (SNAP) receptors (SNAREs), which are key components of the cellular membrane fusion machinery are aberrantly sequestered in cholesterol‐enriched regions of LSD endolysosomal membranes. This abnormal spatial organization locks SNAREs in complexes and impairs their sorting and recycling. Importantly, reducing membrane cholesterol levels in LSD cells restores normal SNARE function and efficient lysosomal fusion. Our results support a model by which cholesterol abnormalities determine lysosomal dysfunction and endocytic traffic jam in LSDs by impairing the membrane fusion machinery, thus suggesting new therapeutic targets for the treatment of these disorders.