Characterization of the Heterogeneity and Specificity of Interpolypeptide Interactions in Amyloid Protofibrils by Measurement of Site-Specific Fluorescence Anisotropy Decay Kinetics

The aggregation of proteins often results in highly ordered fibrillar structures. While significant insights have been obtained on structural aspects of amyloid fibrils, little is known about the structures of protofibrils, which are presumed to be the precursors of fibrils. An understanding of the molecular mechanism of the formation of protofibrils and fibrils requires information on the landscape of interpeptide interactions. This work addresses this question by using, as a model protein, barstar, which forms protofibrils and fibrils at low (< 3) pH. Use was made of the heterogeneity of aggregate populations encountered during fibril formation. Population heterogeneity was scored through rotational dynamics monitored by time-resolved fluorescence anisotropy of an environment-sensitive fluorophore, 5-((((2-iodoacetyl)amino)ethyl)amino)naphthalene-1-sulfonic acid (1,5-IAEDANS), attached to specific locations in the protein. Firstly, it was observed that barstar, when labeled at certain locations with 1,5-IAEDANS, did not form mixed protofibrils with the corresponding unlabeled protein. Labeled and unlabeled proteins formed protofibrils as separate populations. A two-population model of fluorescence anisotropy decay kinetics exhibiting a ‘dip-and-rise’ behavior was the main readout in arriving at this conclusion. Additional support for this conclusion came from the fluorescence lifetime of the probe 1,5-IAEDANS. Subsequently, the location of the fluorophore was moved along the length of the protein in nine mutant proteins, and the capability to form mixed fibrils was assessed. The results revealed that about two-thirds of the protein sequence at the C-terminal end of the protein was intimately involved in the formation of ordered protofibrils, probably forming the core, while the remaining one-third of the protein (i.e., the N-terminal region) remained largely noninteractive and flexible. This methodology can be used as a general strategy to identify regions of a given protein sequence involved in interprotein interactions in amyloid protofibrils.     

Corridors for migration between large subdivided populations, and the structured coalescent

We study the ancestral genetic process for samples from two large, subdivided populations that are connected by migration to, from, and within a small set of subpopulations, or demes. We consider convergence to an ancestral limit process as the numbers of demes in the two large, subdivided populations tend to infinity. We show that the ancestral limit process for a sample includes a recent instantaneous adjustment to the sample size and structure followed by a more ancient process that is identical to the usual structured coalescent, but with different scaled parameters. This justifies the application of a modified structured coalescent to some hierarchically structured populations.     

Corridors for migration between large subdivided populations,and the structured coalescent

We study the ancestral genetic process for samples from two large, subdivided populations that are connected by migration to, from, and within a small set of subpopulations, or demes. We consider convergence to an ancestral limit process as the numbers of demes in the two large, subdivided populations tend to infinity. We show that the ancestral limit process for a sample includes a recent instantaneous adjustment to the sample size and structure followed by a more ancient process that is identical to the usual structured coalescent, but with different scaled parameters. This justifies the application of a modified structured coalescent to some hierarchically structured populations.     

Subfractionation of cell populations by partitioning in dextran-poly (ethylene glycol) aqueous phases

Partitioning of cells in dextran-poly(ethylene glycol) aqueous two-phase systems depends on the interaction between the surface properties of the cells and the physical properties of the phases. The latter can be manipulated to a considerable extent by selection of polymer concentrations and ionic composition and concentration. If salts (e.g., phopshate) are used that have an unequal affinity for the two phases, an electrostatic potential difference between the phases results and, at appropriately high polymer concentrations, the partition coefficient of cells is determined predominantly by membrane charge-associated properties. By “balancing” the magnitude of the electrostatic potential difference against that of the interfacial tension (primarily a function of polymer, but also phosphate, concentrations) one can obtain phase systems that give usable partition coefficients for most cell populations (1). In work under way in our laboratory on the effects of different chemical and enzymatic modifications on the relative surface properties of rat red blood cells of different ages, we have now found that certain phase compositions did not resolve such treated cell subpopulations while other phase compositions did. Thus not all charged phase systems in which cell populations as a whole have usable partition coefficients are equally capable of detecting or subfractionating cell subpopulations. It is therefore essential, before drawing conclusions on the nonseqarability of cell subpopulations, to test cell separability in charged phase systems of different compositions if the system initially chosen does not afford a subfractionation.     

The role of predation in the decline and extirpation of woodland caribou

To select appropriate recovery strategies for endangered populations, we must understand the dynamics of small populations and distinguish between the possible causes that drive such populations to low numbers. It has been suggested that the pattern of population decline may be inversely density-dependent with population growth rates decreasing as populations become very small; however, empirical evidence of such accelerated declines at low densities is rare. Here we analyzed the pattern of decline of a threatened population of woodland caribou (Rangifer tarandus caribou) in British Columbia, Canada. Using information on the instantaneous rate of increase relative to caribou density in suitable winter foraging habitat, as well as on pregnancy rates and on causes and temporal distribution of mortalities from a sample of 349 radiocollared animals from 15 subpopulations, we tested 3 hypothesized causes of decline: (a) food regulation caused by loss of suitable winter foraging habitat, (b) predation-sensitive foraging caused by loss of suitable winter foraging habitat and (c) predation with caribou being secondary prey. Population sizes of caribou subpopulations ranged from <5 to >500 individuals. Our results showed that the rates of increase of these subpopulations varied from −0.1871 to 0.0496 with smaller subpopulations declining faster than larger subpopulations. Rates of increase were positively related to the density of caribou in suitable winter foraging habitat. Pregnancy rates averaged 92.4% ±2.24 and did not differ among subpopulations. In addition, we found predation to be the primary cause of mortality in 11 of 13 subpopulations with known causes of mortality and predation predominantly occurred during summer. These results are consistent with predictions that caribou subpopulations are declining as a consequence of increased predation. Recovery of these woodland caribou will thus require a multispecies perspective and an appreciation for the influence of inverse density dependence on population trajectories.     

Abeta protofibrils possess a stable core structure resistant to hydrogen exchange

Protofibrils are transient structures observed during in vitro formation of mature amyloid fibrils and have been implicated as the toxic species responsible for cell dysfunction and neuronal loss in Alzheimer's disease (AD) and other protein aggregation diseases. To better understand the roles of protofibrils in amyloid assembly and Alzheimer's disease, we characterized secondary structural features of these heterogeneous and metastable assembly intermediates. We chromatographically isolated different size populations of protofibrils from amyloid assembly reactions of Abeta(1-40), both wild type and the Arctic variant associated with early onset familial AD, and exposed them to hydrogen-deuterium exchange analysis monitored by mass spectrometry (HX-MS). We show that HX-MS can distinguish among unstructured monomer, protofibrils, and fibrils by their different protection patterns. We find that about 40% of the backbone amide hydrogens of Abeta protofibrils are highly resistant to exchange with deuterium even after 2 days of incubation in aqueous deuterated buffer, implying a very stable, presumably H-bonded, core structure. This is in contrast to mature amyloid fibrils, whose equally stable structure protects about 60% of the backbone amide hydrogens over the same time frame. We also find a surprising degree of specificity in amyloid assembly, in that wild type Abeta is preferentially excluded from both protofibrils and fibrils grown from an equimolar mixture of wild type and Arctic mutant peptides. These and other data are interpreted and discussed in terms of the role of protofibrils in fibril assembly and in disease.     

Fluoroalcohol-induced modulation of the pathway of amyloid protofibril formation by barstar

To understand how the conformational heterogeneity of protofibrils formed by any protein, as well as the mechanisms of their formation, are modulated by a change in aggregation conditions, we studied the formation of amyloid protofibrils by barstar at low pH by multiple structural probes in the presence of hexafluoroisopropanol (HFIP). In the presence of 10% HFIP, aggregation proceeds with the transient formation of spherical oligomers and leads to the formation of both protofibrils and fibrils. Curly short protofibrils and fibrils are seen to form early during the aggregation reaction, and both are seen to grow gradually in length during the course of the reaction. Atomic force microscopy images reveal that the HFIP-induced protofibrils are long (～300 nm in length), curly, and beaded and appear to be composed primarily of β-sheet bilayers, with heights of ～2.4 nm. The protofibrils formed in the presence of HFIP differ in both their structures and their stabilities from the protofibrils formed either in the absence of alcohol or in the presence of a related alcohol, trifluoroethanol (TFE). Aggregation appears to proceed via an isodesmic polymerization mechanism. Internal structure in the growing aggregates changes in two stages during protofibril formation. In the first stage, an α-helix-rich oligomeric intermediate is formed. In the second stage, the level of β-sheet structure increases at the expense of some α-helical structure. The second stage itself appears to occur in two distinct steps. The creation of thioflavin T binding sites occurs concomitantly with aggregate elongation and is seen to precede the change in secondary structure. The long straight fibrils with characteristic heights of 8-10 nm, which form in the course of the HFIP-induced aggregation reaction, have not been observed to form either in the absence of alcohol or in the presence of TFE.     

Recombination Landscape Divergence Between Populations is Marked by Larger Low-Recombining Regions in Domesticated Rye

The genomic landscape of recombination plays an essential role in evolution. Patterns of recombination are highly variable along chromosomes, between sexes, individuals, populations, and species. In many eukaryotes, recombination rates are elevated in sub-telomeric regions and drastically reduced near centromeres, resulting in large low-recombining (LR) regions. The processes of recombination are influenced by genetic factors, such as different alleles of genes involved in meiosis and chromatin structure, as well as external environmental stimuli like temperature and overall stress. In this work, we focused on the genomic landscapes of recombination in a collection of 916 rye (Secale cereale) individuals. By analyzing population structure among individuals of different domestication status and geographic origin, we detected high levels of admixture, reflecting the reproductive biology of a self-incompatible, wind-pollinating grass species. We then analyzed patterns of recombination in overlapping subpopulations, which revealed substantial variation in the physical size of LR regions, with a tendency for larger LR regions in domesticated subpopulations. Genome-wide association scans (GWAS) for LR region size revealed a major quantitative-trait-locus (QTL) at which, among 18 annotated genes, an ortholog of histone H4 acetyltransferase ESA1 was located. Rye individuals belonging to domesticated subpopulations showed increased synaptonemal complex length, but no difference in crossover frequency, indicating that only the recombination landscape is different. Furthermore, the genomic region harboring rye ScESA1 showed moderate patterns of selection in domesticated subpopulations, suggesting that larger LR regions were indirectly selected during domestication to achieve more homogeneous populations for agricultural use.     

Increased level of linkage disequilibrium in rural compared with urban communities: a factor to consider in association-study design

Few studies have investigated genetic differentiation within nonisolate European populations, despite the initiation of large national sample collections such as U.K. Biobank. Here, we used short tandem repeat markers to explore fine-scale genetic structure and to examine the extent of linkage disequilibrium (LD) within national subpopulations. We studied 955 unrelated individuals of local ancestry from nine Scottish rural regions and the urban center of Edinburgh, as well as 96 unrelated individuals from the general U.K. population. Despite little overall differentiation on the basis of allele frequencies, there were clear differences among subpopulations in the extent of pairwise LD, measured between a subset of X-linked markers, that reflected presumed differences in the depths of the underlying genealogies within these subpopulations. Therefore, there are strategic advantages in studying rural subpopulations, in terms of increased power and reduced cost, that are lost by sampling across regions or within urban populations. Similar rural-urban contrasts are likely to exist in many other populations with stable rural subpopulations, which could influence the design of genetic association studies and national biobank data collections.     

On the survival of populations in a heterogeneous and variable environment

Summary The survival time of small and isolated populations will often be relatively low, by which the survival of species living in such a way will depend on powers of dispersal sufficiently high to result in a rate of population foundings that about compensates the rate of population extinctions. The survival time of composite populations uninterruptedly inhabiting large and heterogeneous areas, highly depends on the extent to which the numbers fluctuate unequally in the different subpopulations. The importance of this spreading of the risk of extinction over differently fluctuating subpopulations is demonstrated by comparing over 19 years the fluctuation patterns of the composite populations of two carabid species, Pterostichus versicolor with unequally fluctuating subpopulations, and Calathus melanocephalus with subpopulations fluctuating in parallel, both uninterruptedly occupying the same large heath area. The conclusions from the field data are checked by simulating the fluctuation patterns of these populations, and thus directly estimating survival times. It thus appeared that the former species can be expected to survive more than ten times better than the latter (other things staying the same). These simulations could also be used to study the possible influence of various density restricting processes in populations already fluctuating according to some pattern. As could be expected, the survival time of a population, which shows a tendency towards an upward trend in numbers, will be favoured by some kind of density restriction, but the degree to which these restrictions are density-dependent appeared to be immaterial. Density reductions that are about adequate on the average need even not occur at high densities only, if only the chance of occurrence at very low densities is low. The density-level at which a population is generally fluctuating appeared to be less important for survival than the fluctuation pattern itself, except for very low density levels, of course. The different ways in which deterministic and stochastic processes may interact and thus determine the fluctuations of population numbers are discussed. It is concluded that some stochastic processes will operate everywhere and will thus necessarily result in density fluctuations; such an omnipresence is much less imperative, however, for density-dependent processes, by which population models should primarily be stochastic models. However, if density-dependent processes are added to model populations, that are already fluctuating stochastically the effects are taken up into the general, stochastic fluctuation pattern, without altering it fundamentally.Communication No. 228 of the Biological Station WijsterDedicated to Professor Michael Evenari     

Structure and assembly-disassembly properties of wild-type transthyretin amyloid protofibrils observed with atomic force microscopy

Transthyretin (TTR) is an important human transport protein present in the serum and the cerebrospinal fluid. Aggregation of TTR in the form of amyloid fibrils is associated with neurodegeneration, but the mechanisms of cytotoxicity are likely to stem from the presence of intermediate assembly states. Characterization of these intermediate species is therefore essential to understand the etiology and pathogenesis of TTR-related amyloidoses. In the present work we used atomic force microscopy to investigate the morphological features of wild-type (WT) TTR amyloid protofibrils that appear in the early stages of aggregation. TTR protofibrils obtained by mild acidification appeared as flexible filaments with variable length and were able to bind amyloid markers (thioflavin T and Congo red). Surface topology and contour-length distribution displayed a periodic pattern of ～ 15 nm, suggesting that the protofibrils assemble via an end-binding oligomer fusion mechanism. The average height and periodic substructure found in protofibrils is compatible with the double-helical model of the TTR amyloid protofilament. Over time protofibrils aggregated into bundles and did not form mature amyloid-like fibrils. Unlike amyloid fibrils that are typically stable under physiological conditions, the bundles dissociated into component protofibrils with axially compacted and radially dilated structure when exposed to phosphate-buffered saline solution. Thus, WT TTR can form metastable filamentous aggregates that may represent an important transient state along the pathway towards the formation of cytotoxic TTR species.     

Competitive coexistence in antiviral immunity

Malignant brain tumors consist of a number of distinct subclonal populations. Each of these subpopulations may be characterized by its own behaviors and properties. These subpopulations arise from the constant genetic and epigenetic alteration of existing cells in the rapidly growing tumor. However, since each single-cell mutation only leads to a small number of offspring initially, very few newly arisen subpopulations survive more than a short time. The present work quantifies "emergence", i.e. the likelihood of an isolated subpopulation surviving for an extended period of time. Only competition between clones is considered; there are no cooperative effects included. The probability that a subpopulation emerges under these conditions is found to be a sigmoidal function of the degree of change in cell division rates. This function has a non-zero value for mutations which confer no advantage in growth rate, which represents the emergence of a distinct subpopulation with an advantage that has yet to be selected for, such as hypoxia tolerance or treatment resistance. A logarithmic dependence on the size of the mutated population is also observed. A significant probability of emergence is observed for subpopulations with any growth advantage that comprise even 0.1% of the proliferative cells in a tumor. The impact of even two clonal populations within a tumor is shown to be sufficient such that a prognosis based on the assumption of a monoclonal tumor can be markedly inaccurate.     

Subfilamentous protofibril structures in fibrous proteins: cross-linking evidence for protofibrils in intermediate filaments

The packing of the constituent molecules in some fibrous proteins such as collagen and intermediate filaments (IF) is thought to consist of several hierarchical levels, the penultimate of which is the organization of subfilamentous units termed protofibrils. However, to date only indirect evidence, such as electron microscopic images of unraveling fibers or the existence of mass quanta, has been adduced in support of the existence of protofibrils. We have reexamined this issue in IF. Cross-links have been induced in trichocyte keratin, cytokeratin, and vimentin IF proteins. Using improved experimental conditions, several additional and reproducible cross-links have been characterized. Notably, many of these link between columns of molecular strands four apart on two-dimensional surface lattices. These data provide robust support for the concept of an 8-chain (4-molecule) protofibril entity in IF. Further, their positions correspond to the axial displacements predicted for protofibrils in the different types of IF. Also, the data are consistent with intact IF containing four protofibrils. In addition, the positions of these novel cross-links suggest that there are multiple possible groupings of four molecular strands to form a protofibril, suggesting a promiscuous association of molecules to form a protofibril. This may underlie the reason that organized elongated protofibrils cannot be visualized by conventional microscopic methods.     

Solvent-induced tuning of internal structure in a protein amyloid protofibril

An important goal in studies of protein aggregation is to obtain an understanding of the structural diversity that is characteristic of amyloid fibril and protofibril structures at the molecular level. In this study, what to our knowledge are novel assays based on time-resolved fluorescence anisotropy decay and dynamic quenching measurements of a fluorophore placed at different specific locations in the primary structure of a small protein, barstar, have been used to determine the extent to which the protein sequence participates in the structural core of protofibrils. The fluorescence measurements reveal the structural basis of how modulating solvent polarity results in the tuning of the protofibril conformation from a pair of parallel β-sheets in heat-induced protofibrils to a single parallel β-sheet in trifluorethanol-induced protofibrils. In trifluorethanol-induced protofibrils, the single β-sheet is shown to be built up from in-register β-strands formed by nearly the entire protein sequence, while in heat-induced protofibrils, the pair of β-sheets motif is built up from β-strands formed by only the last two-third of the protein sequence.     

Ultrastructure of the different zones of the tectorial membrane

The tectorial membrane (t.m.) of mammals, which lies over the organ of Corti, is made up of an agglomerate of protofibrils of varying degrees of hydration. Two types of protofibrils are clearly distinguishable in the mouse t.m. While type-A protofibrils are straight and unbranched (thickness: 110A) demonstrating a periodic structure (period = 70 A), type-B protofibrils are branched and coiled (thickness: 150-200 A). These protofibrils could be systematically ordered according to the different t.m. zones. Type-A protofibrils predominate in the basal layer and in the entire middle zone, where they are interlaced with strongly hydrated type-B protofibrils. Weakly hydrated type-B protofibrils essentially make up the marginal zone (with the marginal net), the covering net, Hensen's stripe and the immediate contact layer with the limbus.     

Study of interaction of wild soybean subpopulations (Glycine soja) in the valley of the Tsukanovka river in the south of Far East of Russia

A comparative study of the genetic structure of natural and anthropogenic populations of G. soja gives significant information about formation of different populations, and allows developing measures for preservation of unique natural gene bank of wild soybean, the species closely related to cultivated soybean. In this study, ISSR markers were used to carry out a comparative analysis of genetic structure of natural and anthropogenic subpopulations of G. soja for studying possible mutual influence of subpopulations of anthropogenic and natural phytocenosis on the formation of their genetic diversity and to study genetic structure of natural subpopulations of wild soybean in the contact places between the two types ofcenoses. As a result, the characteristics that describe the genetic diversity of studied populations have been identified and the important role of an interaction between subpopulations of different phytocenoses on formation of the spatial genetic structure of population in the valley of Tsukanovka river has been demonstrated.     

Comparison of population structure in Ohio's late archaic and late prehistoric periods

Previous studies of population structure among prehistoric groups in the Ohio valley region have shown that hunting-gathering populations exhibited a different structure than horticultural populations. Among both Late Archaic hunter-gatherers and Late Prehistoric horticulturists, covariance structures for cranial metrics were found to be homogenous within the populations, but the Late Archaic subpopulations showed little differentiation while the Late Prehistoric subpopulations exhibited a marked differentiation. Biodistance based on cranial discrete trait frequency showed similar patterns, but in the Late Archaic discrete trait distance was associated significantly with the geographical distance separating populations. The present investigation is an extension of the previous studies increasing the Late Prehistoric sample (n = 8 samples and n = 341 individuals) and using the Harpending-Ward model, modified for use with multivariate quantitative data, to estimate the effects of differential gene flow and the amount of differentiation within populations. Results of the present analyses indicate that differentiation among subpopulations, measured by minimum F(ST), was greater in the Late Prehistoric compared to the Late Archaic period. However, for both periods the minimum F(ST) is comparable to values found for historic native populations of the northeast woodlands. Analysis of differential gene flow in the Late Archaic period indicates that geographically peripheral populations were affected more by external gene flow than more central populations. Late Prehistoric populations exhibit a very complex pattern of differential gene flow. We discuss the latter pattern in terms of proposed culture change in the Late Prehistoric period of Ohio.     

Development of β-sheet structure in Aβ aggregation intermediates diminishes exposed hydrophobic surface area and enhances proinflammatory activity

Three decades of research, both in vitro and in vivo, have demonstrated the conformational heterogeneity that is displayed by the amyloid β peptide (Aβ) in Alzheimer's disease (AD). Understanding the distinct properties between Aβ conformations and how conformation may impact cellular activity remain open questions, yet still continue to provide new insights into protein misfolding and aggregation. In particular, there is interest in the group of soluble oligomeric prefibrillar Aβ species comprising lower molecular weight oligomers up to larger protofibrils. In the current study, a number of strategies were utilized to separate Aβ protofibrils and oligomers and show that the smaller Aβ oligomers have a much different conformation than Aβ protofibrils. The differences were consistent for both Aβ40 and Aβ42. Protofibrils bound thioflavin T to a greater extent than oligomers, and were highly enriched in β-sheet secondary structure. Aβ oligomers possessed a more open structure with significant solvent exposure of hydrophobic domains as determined by tryptophan fluorescence and bis-ANS binding, respectively. The protofibril-selective antibody AbSL readily discerned conformational differences between protofibrils and oligomers. The more developed structure for Aβ protofibrils ultimately proved critical for provoking the release of tumor necrosis factor α from microglial cells. The findings demonstrated a dependency on β-sheet structure for soluble Aβ aggregates to cause a microglial inflammatory response. The Aβ aggregation process yields many conformationally-varied species with different levels of β-structure and exposed hydrophobicity. The conformation elements likely determine biological activity and pathogenicity.     

Induced response to herbivory in stinging hair traits of Japanese nettle (Urtica thunbergiana) seedlings in two subpopulations with different browsing pressures by sika deer

Evolutionary theories predict that natural selection favors inducible defense when the risk of predation is unpredictable. In this context, the magnitude of the induced defense in populations experiencing intermittent herbivory is predicted to be larger than that in populations experiencing constant herbivory when there is genetic differentiation between populations. To test this prediction, we conducted a clipping experiment to investigate induced response to shoot damage by the stinging hair traits of Japanese nettle (Urtica thunbergiana) seedlings. For this purpose, we studied two nettle subpopulations, one under constant browsing and another under intermittent browsing by sika deer in Nara Park, central Japan. The clipping experiment demonstrates that both subpopulations exhibited induced defenses in response to the clipping of the shoot apex as the number and length of stinging hairs increased after clipping. The subpopulation experiencing intermittent browsing exhibited smaller trait values and larger induced defenses, indicated by the number of stinging hairs on the upper leaf surface and the length of stinging hairs on both leaf surfaces compared with the subpopulation experiencing constant browsing. These results are consistent with the prediction and suggest that genetic differentiation of the induced defense between subpopulations is caused by adaptation to the herbivory regime. We discuss other plausible factors affecting the magnitude of the induced defense of the nettle subpopulations.