Role of Small Oligomers on the Amyloidogenic Aggregation Free-Energy Landscape

We combine atomic-force-microscopy particle-size-distribution measurements with earlier measurements on 1-anilino-8-naphthalene sulfonate, thioflavin T, and dynamic light scattering to develop a quantitative kinetic model for the aggregation of β-lactoglobulin into amyloid. We directly compare our simulations to the population distributions provided by dynamic light scattering and atomic force microscopy. We combine species in the simulation according to structural type for comparison with fluorescence fingerprint results. The kinetic model of amyloidogenesis leads to an aggregation free-energy landscape. We define the roles of and propose a classification scheme for different oligomeric species based on their location in the aggregation free-energy landscape. We relate the different types of oligomers to the amyloid cascade hypothesis and the toxic oligomer hypothesis for amyloid-related diseases. We discuss existing kinetic mechanisms in terms of the different types of oligomers. We provide a possible resolution to the toxic oligomer-amyloid coincidence.     

SIS epidemics with household structure: the self-consistent field method

We consider a stochastic SIS infection model for a population partitioned into m households assuming random mixing. We solve the model in the limit m→∞ by using the self-consistent field method of statistical physics. We derive a number of explicit results, and give numerical illustrations. We then do numerical simulations of the model for finite m and without random mixing. We find in many of these cases that the self-consistent field method is a very good approximation.     

Multistability, cross-modal binding and the additivity of conjoined grouping principles

We present a sceptical view of multimodal multistability--drawing most of our examples from the relation between audition and vision. We begin by summarizing some of the principal ways in which audio-visual binding takes place. We review the evidence that unambiguous stimulation in one modality may affect the perception of a multistable stimulus in another modality. Cross-modal influences of one multistable stimulus on the multistability of another are different: they have occurred only in speech perception. We then argue that the strongest relation between perceptual organization in vision and perceptual organization in audition is likely to be by way of analogous Gestalt laws. We conclude with some general observations about multimodality.     

An in vivo structure-function study of armadillo, the beta-catenin homologue, reveals both separate and overlapping regions of the protein required for cell adhesion and for wingless signaling

Armadillo, the Drosophila homologue of vertebrate beta-catenin, plays a pivotal role both in Wingless signaling and in assembly of adherens junctions. We performed the first in vivo structure-function study of an adherens junction protein, by generating and examining a series of Armadillo mutants in the context of the entire animal. We tested each mutant by assaying its biological function, its ability to bind proteins that normally associate with Armadillo in adherens junctions, its cellular localization, and its pattern of phosphorylation. We mapped the binding sites for DE-cadherin and alpha-catenin. Although these bind to Armadillo independently of each other, binding of each is required for the function of adherens junctions. We identified two separate regions of Armadillo critical for Wingless signaling. We demonstrated that endogenous Armadillo accumulates in the nucleus and provide evidence that it may act there in transducing Wingless signal. We found that the Arm repeats, which make up the central two-thirds of Armadillo, differ among themselves in their functional importance in different processes. Finally, we demonstrated that Armadillo's roles in adherens junctions and Wingless signaling are independent. We discuss the potential biochemical role of Armadillo in each process.     

Anesthesia in the mouse using a combination of ketamine and promazine

An anesthetic combination of ketamine and promazine was tested in 25 male and 25 female mice of each of two strains. The mean induction time was 5 minutes for the C57BL/6We mouse and 8 minutes for the DBA/2We mouse. No sex differences were observed. The mean duration time was 45 minutes for the C57BL/6We male, 53 minutes for the C57BL/TWe female, 29 minutes for the DBA/2We male, and 35 minutes for the DBA/2We female. The mean recovery time was 39 minutes for the C57BL/6We male, 38 minutes for the C57BL/6We female, 21 minutes for the DBA/2We male, and 24 minutes for the DBA/2We female. The drug combination provided effective anesthesia for these strains of the laboratory mouse for a period of 30--50 minutes after a single intramuscular injection.     

The canid genome: behavioral geneticists' best friend?

We review a range of studies on the genetic contribution to behavior in canid species. We begin by identifying factors that make canids a promising model in behavioral genetics and proceed to review research over the last decade that has used canids to identify genetic contributions to behavior. We first review studies that have selectively bred dogs to identify genetic contributions to behavior and then review studies that estimate heritability from populations of non‐laboratory bred dogs. We subsequently review studies that used molecular genetics to identify gene–behavior associations and note associations that have been uncovered. We then note challenges in canid behavioral genetics research that require further consideration. We finish by suggesting alternative phenotyping methods and identify areas in which canids may have as yet unexploited advantages, such as in gene–environment interaction studies where genetic factors are found to moderate the effects of environmental variables.     

The Social Burden of Resilience: A Historical Perspective

We examine the social burden associated with resilience to environmental shocks in pre-modern societies. We argue that analyses of state-level interventions to mitigate the consequences of catastrophic events tend to isolate these measures from their larger social contexts and thereby overlook the uneven distribution of their burden across different groups. We use three cases of pre-modern societies in the northeastern Mediterranean - the sixth century Roman Empire, the tenth century Byzantine Empire, and the sixteenth century Ottoman Empire. We demonstrate how the adaptive processes that reinforced resilience at the state level incurred different burdens for those at lower levels of the social hierarchy. We found that some groups sustained losses while others gained unexpected benefits in the context of temporary systemic instability. We also found that although elites enjoyed enhanced buffers against the adverse effects in comparison with non-elites, this did not consistently guarantee them a better outcome. We conclude that the differentiated burden of resilience could in some cases entrench existing political or economic configurations, and in other cases, overturn them. Our case studies indirectly address the pressing issue of environmental justice.     

A model for the origin and properties of flicker-induced geometric phosphenes

We present a model for flicker phosphenes, the spontaneous appearance of geometric patterns in the visual field when a subject is exposed to diffuse flickering light. We suggest that the phenomenon results from interaction of cortical lateral inhibition with resonant periodic stimuli. We find that the best temporal frequency for eliciting phosphenes is a multiple of intrinsic (damped) oscillatory rhythms in the cortex. We show how both the quantitative and qualitative aspects of the patterns change with frequency of stimulation and provide an explanation for these differences. We use Floquet theory combined with the theory of pattern formation to derive the parameter regimes where the phosphenes occur. We use symmetric bifurcation theory to show why low frequency flicker should produce hexagonal patterns while high frequency produces pinwheels, targets, and spirals.     

The joint allele-frequency spectrum in closely related species

We develop the theory for computing the joint frequency spectra of alleles in two closely related species. We allow for arbitrary population growth in both species after they had a common ancestor. We focus on the case in which a single chromosome is sequenced from one of the species. We use classical diffusion theory to show that, if the ancestral species was at equilibrium under mutation and drift and a chromosome from one of the descendant species carries the derived allele, the frequency spectrum in the other species is uniform, independently of the demographic history of both species. We also predict the expected densities of segregating and fixed sites when the chromosome from the other species carries the ancestral allele. We compare the predictions of our model with the site-frequency spectra of SNPs in the four HapMap populations of humans when the nucleotide present in the Neanderthal DNA sequence is ancestral or derived, using the chimp genome as the outgroup.     

T-cell receptor and immunoglobulin genes are rearranged together in Abelson virus-transformed pre-B and pre-T cells.

We have assessed the state of rearrangement and expression of B- and T-cell antigen receptor genes in cells of Abelson murine leukemia virus-transformed thymomas and other tumors. We found that unrearranged TcR gamma genes are expressed, as are unrearranged C mu genes, in pre-T, pre-B, and myeloid cells. We also found TcR gamma genes rearranged and expressed in putative pre-T cells and in cells apparently committed to the B-cell lineage. This is in contrast to the data from more mature T- and B-cell tumors. We conclude that in immature lymphoid cells both immunoglobulin and TcR gamma genes are accessible for rearrangement. We discuss the implications of these observations for an understanding of the B-T lymphoid differentiation event.     

An evolutionary strategy for all-atom folding of the 60-amino-acid bacterial ribosomal protein l20

We have investigated an evolutionary algorithm for de novo all-atom folding of the bacterial ribosomal protein L20. We report results of two simulations that converge to near-native conformations of this 60-amino-acid, four-helix protein. We observe a steady increase of "native content" in both simulated ensembles and a large number of near-native conformations in their final populations. We argue that these structures represent a significant fraction of the low-energy metastable conformations, which characterize the folding funnel of this protein. These data validate our all-atom free-energy force field PFF01 for tertiary structure prediction of a previously inaccessible structural family of proteins. We also compare folding simulations of the evolutionary algorithm with the basin-hopping technique for the Trp-cage protein. We find that the evolutionary algorithm generates a dynamic memory in the simulated population, which leads to faster overall convergence.     

Functional and structural analyses of novel Smith-Kingsmore Syndrome-Associated MTOR variants reveal potential new mechanisms and predictors of pathogenicity

Smith-Kingsmore syndrome (SKS) is a rare neurodevelopmental disorder characterized by macrocephaly/megalencephaly, developmental delay, intellectual disability, hypotonia, and seizures. It is caused by dominant missense mutations in MTOR. The pathogenicity of novel variants in MTOR in patients with neurodevelopmental disorders can be difficult to determine and the mechanism by which variants cause disease remains poorly understood. We report 7 patients with SKS with 4 novel MTOR variants and describe their phenotypes. We perform in vitro functional analyses to confirm MTOR activation and interrogate disease mechanisms. We complete structural analyses to understand the 3D properties of pathogenic variants. We examine the accuracy of relative accessible surface area, a quantitative measure of amino acid side-chain accessibility, as a predictor of MTOR variant pathogenicity.We describe novel clinical features of patients with SKS. We confirm MTOR Complex 1 activation and identify MTOR Complex 2 activation as a new potential mechanism of disease in SKS. We find that pathogenic MTOR variants disproportionately cluster in hotspots in the core of the protein, where they disrupt alpha helix packing due to the insertion of bulky amino acid side chains. We find that relative accessible surface area is significantly lower for SKS-associated variants compared to benign variants. We expand the phenotype of SKS and demonstrate that additional pathways of activation may contribute to disease. Incorporating 3D properties of MTOR variants may help in pathogenicity classification. We hope these findings may contribute to improving the precision of care and therapeutic development for individuals with SKS.     

Spatial and spatio-temporal patterns in a cell-haptotaxis model

We investigate a cell-haptotaxis model for the generation of spatial and spatio-temporal patterns in one dimension. We analyse the steady state problem for specific boundary conditions and show the existence of spatially hetero-geneous steady states. A linear analysis shows that stability is lost through a Hopf bifurcation. We carry out a nonlinear multi-time scale perturbation procedure to study the evolution of the resulting spatio-temporal patterns. We also analyse the model in a parameter domain wherein it exhibits a singular dispersion relation.     

The proteinase-catalysed synthesis of peptide hydrazides.

1. We report the trypsin-catalysed conversion, in high yield, of peptides to peptide hydrazides, t-butyloxycarbonylhydrazides and phenylhydrazides. The substitution is at the alpha-carboxy group. 2. We discuss the relative merits of carrying out the conversion either simultaneously with tryptic cleavage of the parent protein or after such cleavage. 3. We report analogous results with chymotrypsin, elastase and subtilisin. 4. We propose the use of such products in protein semi-synthesis and in the preparation of specific proteinase inhibitors.     

Partial‐Likelihood Analysis of Spatio‐Temporal Point‐Process Data

Summary We investigate the use of a partial likelihood for estimation of the parameters of interest in spatio‐temporal point‐process models. We identify an important distinction between spatially discrete and spatially continuous models. We focus our attention on the spatially continuous case, which has not previously been considered. We use an inhomogeneous Poisson process and an infectious disease process, for which maximum‐likelihood estimation is tractable, to assess the relative efficiency of partial versus full likelihood, and to illustrate the relative ease of implementation of the former. We apply the partial‐likelihood method to a study of the nesting pattern of common terns in the Ebro Delta Natural Park, Spain.     

Hierarchically organized populations: interactions between individual,population, and ecosystem levels

We consider a population of individuals which can be distributed in different equivalence classes. These classes are gathered in groups so that intragroup transformations are much more frequent than intergroup ones. We study linear systems in general, illustrated by the example of coupled individual and population levels. Then, we study nonlinear systems with the example of coupled population and ecosystem levels. We give methods to derive the dynamical equations for the different levels and to calculate interlevel coupling terms. We compare the coupling effects in the linear and in the nonlinear case.     

Deletion formation in bacteriophage T4

We have manipulated the dispensable region of the rIIB gene of bacteriophage T4 in order to study the generation of deletions involving direct repeats. We show that recombination between different parental chromosomes is one source of the deletions we have studied. We have also investigated the effects of structure, base composition and distance on deletion formation. We demonstrate that the potential to form structure in single-stranded DNA has variable effects on the frequency of deletion formation and conclude that, in some cases, slipped mispairing during DNA synthesis can make a substantial contribution to deletion frequencies. The G + C richness of the direct repeats involved in deletion formation is an important parameter of the frequency of deletion formation. We have confirmed that increasing the distance between direct repeats decreases deletion frequency.     

Microtubule-dependent transport and dynamics of vimentin intermediate filaments

We studied two aspects of vimentin intermediate filament dynamics—transport of filaments and subunit exchange. We observed transport of long filaments in the periphery of cells using live-cell structured illumination microscopy. We studied filament transport elsewhere in cells using a photoconvertible-vimentin probe and total internal reflection microscopy. We found that filaments were rapidly transported along linear tracks in both anterograde and retrograde directions. Filament transport was microtubule dependent but independent of microtubule polymerization and/or an interaction with the plus end–binding protein APC. We also studied subunit exchange in filaments by long-term imaging after photoconversion. We found that converted vimentin remained in small clusters along the length of filaments rather than redistributing uniformly throughout the network, even in cells that divided after photoconversion. These data show that vimentin filaments do not depolymerize into individual subunits; they recompose by severing and reannealing. Together these results show that vimentin filaments are very dynamic and that their transport is required for network maintenance.