Mitochondrial DNA variation and the evolutionary history of chromosome races of collared lemmings (Dicrostonyx) in the Eurasian Arctic

Collared lemmings (Dicrostonyx) demonstrate extensive chromosome variation along their circumpolar distribution in the high Arctic. To reveal the history of this genus and the origin of chromosome races in the Palearctic, we studied the geographical pattern of mtDNA variation in lemmings from 13 localities by using eight tetranucleotide restriction enzymes. The main split in mtDNA phylogeny is at the Bering Strait and corresponds to the main chromosome division between the Beringian and the Eurasian groups of karyotypes. Nucleotide divergence estimate of 6.8% suggests that, despite the Bering Land Bridge, Palearctic and Nearctic forms have been separated since the mid-Pleistocene. Five distinct phylogenetic groups of mtDNA haplotypes, with average divergence of 1.5%, corresponding to geographical regions, were found along the Palearctic coast. Low nucleotide and haplotype diversity and a star-like phylogeny within phylogeographical groups of haplotypes suggest regional bottleneck events in the recent past, most probably due to warming events during the Holocene. There is congruence between phylogeographical pattern of mtDNA variation and geographical distribution of chromosome races; 69% of the total mtDNA variation is allocated among chromosome races. This congruence implies that historical events such as fragmentation and allopatric bottleneck events have been important for the origin of chromosome races. However, historical factors do not explain the fixed autosome fusions found to distinguish certain populations.     

Phylogeography of a host-specific insect: genetic structure of Ips typographus in Europe does not reflect past fragmentation of its host

The phylogeography of the bark beetle Ips typographus was assessed using five microsatellite markers. Twenty-eight populations were sampled throughout Europe on the host tree Picea abies . I. typographus showed very low levels of genetic diversity, and the study revealed a lack of genetic structure across Europe. No significant barrier to gene flow was found, even though P. abies has a fragmented distribution. A weak but significant effect of isolation by distance was found. These results suggest a high dispersal capacity of I. typographus , which leads to low genetic differentiation between populations. Its high dispersal capacity is likely to have prevented I. typographus from developing important local adaptations to its host, which would have influenced its genetic structure. The nuclear data was compared to previously published mitochondrial data that showed strong differentiation between Central–Northern European populations and Russian–Baltic populations, and a founder effect in Scandinavia, probably reflecting the postglacial history of I. typographus . Discrepancies between nuclear and mitochondrial markers could be due to the maternal inheritance of mitochondrial DNA, and to sex-biased dispersal in I. typographus . The overall low genetic diversity observed on both markers on a large geographical scale is discussed. © 2007 The Linnean Society of London, Biological Journal of the Linnean Society , 2007, 90 , 239–246.     

Genetic structure and evidence of anthropogenic effects on wild populations of two Neotropical catfishes: baselines for conservation

Genetic diversity and structure of Pseudoplatystoma corruscans and P. reticulatum, large migratory South America catfishes, where overfishing and the construction of numerous dams in their feeding and reproducing areas are affecting their migratory processes negatively, were studied using microsatellites in samples from Paraguay (that comprises the Pantanal biome), and the upper and lower Paraná Basins. Genetic diversity was in accordance to that observed for other large migratory fishes, but the most geographically isolated populations of P. reticulatum and those P. corruscans subject to anthropogenic effects (stocking and dams) showed lower genetic diversity and evidences of bottlenecks compatible with low effective population size. Pseudoplatystoma reticulatum presented subtle genetic differentiation within the Paraguay area, especially between the edges of its distribution. Pseudoplatystoma corruscans, in this same area, presented a quite homogeneous but significant genetic break between the Paraguay and upper Paraná populations, apparently resulting from natural and historical isolation between the basins until recently. These data demonstrates that, although these Pseudoplatystoma spp. are abundant in the Pantanal area, anthropogenic events are leading to negative effects on their populations, particularly in the upper Paraná Basin. Genetic differentiation observed along each species distribution demands conservation actions to preserve each population's biodiversity. These results represent important genetic information using new microsatellite markers and the first genetic study of P. reticulatum covering this area of its native distribution. Data may also contribute to a better understanding of species migration patterns and to be used as a baseline for proper management.     

PDZ Ligand Binding-Induced Conformational Coupling of the PDZ–SH3–GK Tandems in PSD-95 Family MAGUKs

Discs large (DLG) MAGUKs are abundantly expressed in glutamatergic synapses, crucial for synaptic transmission, and plasticity by anchoring various postsynaptic components including glutamate receptors, downstream scaffold proteins and signaling enzymes. Different DLG members have shared structures and functions, but also contain unique features. How DLG family proteins function individually and cooperatively is largely unknown. Here, we report that PSD-95 PDZ3 directly couples with SH3–GK tandem in a PDZ ligand binding-dependent manner, and the coupling can promote PSD-95 dimerization and multimerization. Aided by sortase-mediated protein ligation and selectively labeling, we elucidated the PDZ3/SH3–GK conformational coupling mechanism using NMR spectroscopy. We further demonstrated that PSD-93, but not SAP102, can also undergo PDZ3 ligand binding-induced conformational coupling with SH3–GK and form homo-oligomers. Interestingly, PSD-95 and PSD-93 can also form ligand binding-induced hetero-oligomers, suggesting a cooperative assembly mechanism for the mega-N-methyl-d-aspartate receptor synaptic signaling complex. Finally, we provide evidence showing that ligand binding-induced conformational coupling between PDZ and SH3–GK is a common feature for other MAGUKs including CASK and PALS1.     

Assessing current genetic status of the Hainan gibbon using historical and demographic baselines: implications for conservation management of species of extreme rarity

Evidence‐based conservation planning is crucial for informing management decisions for species of extreme rarity, but collection of robust data on genetic status or other parameters can be extremely challenging for such species. The Hainan gibbon, possibly the world's rarest mammal, consists of a single population of ~25 individuals restricted to one protected area on Hainan Island, China, and has persisted for over 30 years at exceptionally low population size. Analysis of genotypes at 11 microsatellite loci from faecal samples for 36% of the current global population and tissue samples from 62% of existing historical museum specimens demonstrates limited current genetic diversity (Na = 2.27, Ar = 2.24, H_e = 0.43); diversity has declined since the 19th century and even further within the last 30 years, representing declines of ~30% from historical levels (Na = 3.36, Ar = 3.29, H_e = 0.63). Significant differentiation is seen between current and historical samples (F_ST = 0.156, P = 0.0315), and the current population exhibits extremely small N_e (current N_e = 2.16). There is evidence for both a recent population bottleneck and an earlier bottleneck, with population size already reasonably low by the late 19th century (historical N_e = 1162.96). Individuals in the current population are related at the level of half‐ to full‐siblings between social groups, and full‐siblings or parent–offspring within a social group, suggesting that inbreeding is likely to increase in the future. The species' current reduced genetic diversity must be considered during conservation planning, particularly for expectations of likely population recovery, indicating that intensive, carefully planned management is essential.     

Studying polyglutamine aggregation in Caenorhabditis elegans using an analytical ultracentrifuge equipped with fluorescence detection

This work explores the heterogeneity of aggregation of polyglutamine fusion constructs in crude extracts of transgenic Caenorhabditis elegans animals. The work takes advantage of the recent technical advances in fluorescence detection for the analytical ultracentrifuge. Further, new sedimentation velocity methods, such as the multi‐speed method for data capture and wide distribution analysis for data analysis, are applied to improve the resolution of the measures of heterogeneity over a wide range of sizes. The focus here is to test the ability to measure sedimentation of polyglutamine aggregates in complex mixtures as a prelude to future studies that will explore the effects of genetic manipulation and environment on aggregation and toxicity. Using sedimentation velocity methods, we can detect a wide range of aggregates, ranging from robust analysis of the monomer species through an intermediate and quite heterogeneous population of oligomeric species, and all the way up to detecting species that likely represent intact inclusion bodies based on comparison to an analysis of fluorescent puncta in living worms by confocal microscopy. Our results support the hypothesis that misfolding of expanded polyglutamine tracts into insoluble aggregates involves transitions through a number of stable intermediate structures, a model that accounts for how an aggregation pathway can lead to intermediates that can have varying toxic or protective attributes. An understanding of the details of intermediate and large‐scale aggregation for polyglutamine sequences, as found in neurodegenerative diseases such as Huntington's Disease, will help to more precisely identify which aggregated species may be involved in toxicity and disease.     

Effect of α-crystallin on thermal aggregation of glycogen phosphorylase <Emphasis Type="Italic">b</Emphasis> from rabbit skeletal muscle

Thermal aggregation of rabbit skeletal muscle glycogen phosphorylase b (Phb) has been investigated using dynamic light scattering under conditions of a constant rate of temperature increase (1 K/min). The linear behavior of the dependence of the hydrodynamic radius on temperature for Phb aggregation is consistent with the idea that thermal aggregation of proteins proceeds in the kinetic regime wherein the rate of aggregation is limited by diffusion of the interacting particles (the regime of "diffusion-limited cluster-cluster aggregation"). In the presence of alpha-crystallin, a protein exhibiting chaperone-like activity, the dependence of the hydrodynamic radius on temperature follows the exponential law; this suggests that the aggregation process proceeds in the kinetic regime where the sticking probability for colliding particles becomes lower than unity (the regime of "reaction-limited cluster-cluster aggregation"). Based on analysis of the ratio between the light scattering intensity and the hydrodynamic radius of Phb aggregates, it has been concluded that the addition of alpha-crystallin results in formation of smaller size starting aggregates. The data on differential scanning calorimetry indicate that alpha-crystallin interacts with the intermediates of the unfolding process of the Phb molecule. The proposed scheme of thermal denaturation and aggregation of Phb includes the stage of reversible dissociation of dimers of Phb into monomers, the stage of the formation of the starting aggregates from the denatured monomers of Phb, and the stage of the sticking of the starting aggregates and higher order aggregates. Dissociation of Phb dimer into monomers at elevated temperatures has been confirmed by analytical ultracentrifugation.     

Health-related monitoring and assessment of airborne particulate matter

Since 1992, the International Atomic Energy Agency (IAEA) has been promoting studies of air pollution using a standard design of air sampler that provides separation on filters into two size fractions with cutoffs of 2.5 and 10 Μm (approximately). These are the size ranges presently considered to have the most important health consequences. Such filter samples are highly amenable to analysis using nuclear and related techniques. After reviewing some of the health effects of airborne particulate matter and current air quality standards and guidelines, this article provides an overview of current and recent IAEA programs in this area, which involve collaborative activities with participants in more than 40 countries.     

Enantioselective determination of isradipine in human serum using chiral stationary phase liquid chromatography and gas chromatography with nitrogen selective detection

rac-Isradipine is a dihydropyridine type calcium antagonist. Its calcium entry blocking effect is due primarily to the (+)-(S)-enantiomer. This study describes a sensitive enantioselective method for the determination of isradipine in human serum. Following alkaline extraction into hexane, the enantiomers of isradipine are separated quantitatively by high-performance liquid chromatography on a Chiralcel OJ column at 39°C. The collected fractions were evaporated and assayed using capillary gas chromatography on a HP 50+ column with nitrogen selective detection. Using 2.0 ml of serum, 0.7 nmol/1 (0.26 ng/ml) of each enantiomer could be determined with acceptable precision. The method has successfully been used to measure (+)-(S)- and (−)-(R)-isradipine concentrations in samples from volunteers after intravenous and oral administration of isradipine. Chirality 10:808–812, 1998. © 1998 Wiley-Liss, Inc.     

Thermodynamics of an aminoglycoside modifying enzyme with low substrate promiscuity: The aminoglycoside N3 acetyltransferase‐VIa

Kinetic, thermodynamic, and structural properties of the aminoglycoside N3‐acetyltransferase‐VIa (AAC‐VIa) are determined. Among the aminoglycoside N3‐acetyltransferases, AAC‐VIa has one of the most limited substrate profiles. Kinetic studies showed that only five aminoglycosides are substrates for this enzyme with a range of fourfold difference in k_cat values. Larger differences in K_M (～40‐fold) resulted in ～30‐fold variation in k_cat/K_M. Binding of aminoglycosides to AAC‐VIa was enthalpically favored and entropically disfavored with a net result of favorable Gibbs energy (ΔG < 0). A net deprotonation of the enzyme, ligand, or both accompanied the formation of binary and ternary complexes. This is opposite of what was observed with several other aminoglycoside N3‐acetyltransferases, where ligand binding causes more protonation. The change in heat capacity (ΔCp) was different in H₂O and D₂O for the binary enzyme–sisomicin complex but remained the same in both solvents for the ternary enzyme–CoASH–sisomicin complex. Unlike, most other aminoglycoside‐modifying enzymes, the values of ΔCp were within the expected range of protein‐carbohydrate interactions. Solution behavior of AAC‐VIa was also different from the more promiscuous aminoglycoside N3‐acetyltransferases and showed a monomer‐dimer equilibrium as detected by analytical ultracentrifugation (AUC). Binding of ligands shifted the enzyme to monomeric state. Data also showed that polar interactions were the most dominant factor in dimer formation. Overall, thermodynamics of ligand‐protein interactions and differences in protein behavior in solution provide few clues on the limited substrate profile of this enzyme despite its >55% sequence similarity to the highly promiscuous aminoglycoside N3‐acetyltransferase. Proteins 2017; 85:1258–1265. © 2017 Wiley Periodicals, Inc.