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AMOVA is a widely used approach that focuses on variance within and among strata to study the hierarchical genetic structure of populations. The recently developed Shannon Informational Diversity Translation Analysis (SIDTA) instead tackles exploration of hierarchical genetic structure using entropic allelic diversity. A mix of artificial and natural population data sets (including allopolyploids) is used to compare the performance of SIDTA (a 'q = 1' diversity measure) vs. AMOVA (a 'q = 2' measure) under different conditions. An additive allelic differentiation index based on entropic allelic diversity measuring the mean difference among populations (ΩAP) was developed to facilitate the comparison of SIDTA with AMOVA. These analyses show that the genetic population structure seen by AMOVA is notably different in many ways from that provided by SIDTA, and the extent of this difference is greatly affected by the stability of the markers employed. Negative among group values are lacking with SIDTA but occur with AMOVA, especially with allopolyploids. To provide more focus on measuring allelic differentiation among populations, additional measures were also tested including Bray-Curtis Genetic Differentiation (BCGD) and several expected heterozygosity-based indices (e.g., GST, G″ST, Jost's D, and DEST). Corrections, such as almost unbiased estimators, that were designed to work with heterozygosity-based fixation indices (e.g., FST, GST) are problematic when applied to differentiation indices (eg., DEST, G″ST, G'STH).

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A survey, primarily based on work in the authors' laboratory during the last 10 years, is provided of recent developments in NMR studies of exchange processes involving protein-ligand and protein-protein interactions. We start with a brief overview of the theoretical background of Dark state Exchange Saturation Transfer (DEST) and lifetime line-broadening (ΔR2) NMR methodology. Some limitations of the DEST/ΔR2 methodology in applications to molecular systems with intermediate molecular weights are discussed, along with the means of overcoming these limitations with the help of closely related exchange NMR techniques, such as the measurements of Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion, exchange-induced chemical shifts or rapidly-relaxing components of relaxation decays. Some theoretical underpinnings of the quantitative description of global dynamics of proteins on the surface of very high molecular weight particles (nanoparticles) are discussed. Subsequently, several applications of DEST/ΔR2 methodology are described from a methodological perspective with an emphasis on providing examples of how kinetic and relaxation parameters for exchanging systems can be reliably extracted from NMR data for each particular model of exchange. Among exchanging systems that are not associated with high molecular weight species, we describe several exchange NMR-based studies that focus on kinetic modelling of transient pre-nucleation oligomerization of huntingtin peptides that precedes aggregation and fibril formation.

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Recent studies highlight the initiation of Parkinson's disease (PD) in the gastrointestinal tract, decades before the manifestations in the central nervous system (CNS). This gut-brain axis of neurodegenerative diseases defines the critical role played by the unique microbial composition of the "second brain" formed by the enteric nervous system (ENS). Compromise in the enteric wall can result in the translocation of gut-microbiota along with their metabolites into the system that can affect the homeostatic machinery. The released metabolites can associate with protein substrates affecting several biological pathways. Among these, the bacterial endotoxin from Gram-negative bacteria, i.e., Lipopolysaccharide (LPS), has been implicated to play a definite role in progressive neurodegeneration. The molecular interaction of the lipid metabolites can have a direct neuro-modulatory effect on homeostatic protein components that can be transported to the CNS via the vagus nerve. α-synuclein (α-syn) is one such partner protein, the molecular interactions with which modulate its overall fibrillation propensity in the system. LPS interaction has been shown to affect the protein's aggregation kinetics in an alternative inflammatory pathway of PD pathogenesis. Several other lipid contents from the bacterial membranes could also be responsible for the initiation of α-syn amyloidogenesis. The present review will focus on the intermolecular interactions of α-syn with bacterial lipid components, particularly LPS, with a definite clinical manifestation in PD pathogenesis. However, deconvolution of the sequence of interaction events from the ENS to its propagation in the CNS is not easy or obvious. Nevertheless, the characterization of these lipid-mediated structures is a step towards realizing the novel targets in the pre-emptive diagnoses of PD. This comprehensive description should prompt the correlation of potential risk of amyloidogenesis upon detection of specific paradigm shifts in the microbial composition of the gut.

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Altered intestinal permeability has been correlated with Parkinson's pathophysiology in the enteric nervous system, before manifestations in the central nervous system (CNS). The inflammatory endotoxin or lipopolysaccharide (LPS) released by gut bacteria is known to modulate α-synuclein amyloidogenesis through the formation of intermediate nucleating species. Here, biophysical techniques in conjunction with microscopic images revealed the molecular interaction between lipopolysaccharide and α-synuclein that induce rapid nucleation events. This heteromolecular interaction stabilizes the α-helical intermediates in the α-synuclein aggregation pathway. Multitude NMR studies probed the residues involved in the LPS-binding structural motif that modulates the nucleating forms, affecting the cellular internalization and associated cytotoxicity. Collectively, our data characterizes this heteromolecular interaction associated with an alternative pathway in Parkinson's disease progression.

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Exchange-mediated saturation transfer (EST) provides critical information regarding dynamics of molecules. In typical applications EST is studied by either scanning a wide range of (15)N chemical shift offsets where the applied (15)N irradiation field strength is on the order of hundreds of Hertz or, scanning a narrow range of (15)N chemical shift offsets where the applied (15)N irradiation field-strength is on the order of tens of Hertz during the EST period. The (1)H decoupling during the EST delay is critical as incomplete decoupling causes broadening of the EST profile, which could possibly result in inaccuracies of the extracted kinetic parameters and transverse relaxation rates. Currently two different (1)H decoupling schemes have been employed, intermittently applied 180° pulses and composite-pulse-decoupling (CPD), for situations where a wide range, or narrow range of (15)N chemical shift offsets are scanned, respectively. We show that high-power CPD provides artifact free EST experiments, which can be universally implemented regardless of the offset range or irradiation field-strengths.

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Protein motions over various time scales are crucial for protein function. NMR relaxation dispersion experiments play a key role in explaining these motions. However, the study of slow conformational changes with lowly populated states remained elusive. The recently developed exchange-mediated saturation transfer experiments allow the detection and characterization of such motions, but require extensive measurement time. Here we show that, by making use of Fourier transform, the total acquisition time required to measure an exchange-mediated saturation transfer profile can be reduced by twofold in case that one applies linear prediction. In addition, we demonstrate that the analytical solution for R1ρ experiments can be used for fitting the exchange-mediated saturation transfer profile. Furthermore, we show that simultaneous analysis of exchange-mediated saturation transfer profiles with two different radio-frequency field strengths is required for accurate and precise characterization of the exchange process and the exchanging states.

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Little is known about the microevolutionary processes shaping within river population genetic structure of aquatic organisms characterized by high levels of homing and spawning site fidelity. Using a microsatellite panel, we observed complex and highly significant levels of intrariver population genetic substructure and Isolation-by-Distance, in the Atlantic salmon stock of a large river system. Two evolutionary models have been considered explaining mechanisms promoting genetic substructuring in Atlantic salmon, the member-vagrant and metapopulation models. We show that both models can be simultaneously used to explain patterns and levels of population structuring within the Foyle system. We show that anthropogenic factors have had a large influence on contemporary population structure observed. In an analytical development, we found that the frequently used estimator of genetic differentiation, F(ST), routinely underestimated genetic differentiation by a factor three to four compared to the equivalent statistic Jost's D(est) (Jost 2008). These statistics also showed a near-perfect correlation. Despite ongoing discussions regarding the usefulness of "adjusted"F(ST) statistics, we argue that these could be useful to identify and quantify qualitative differences between populations, which are important from management and conservation perspectives as an indicator of existence of biologically significant variation among tributary populations or a warning of critical environmental damage.