Subunit organization in cytoplasmic dynein subcomplexes

Because cytoplasmic dynein plays numerous critical roles in eukaryotic cells, determining the subunit composition and the organization and functions of the subunits within dynein are important goals. This has been difficult partly because of accessory polypeptide heterogeneity of dynein populations. The motor domain containing heavy chains of cytoplasmic dynein are associated with multiple intermediate, light intermediate, and light chain accessory polypeptides. We examined the organization of these subunits within cytoplasmic dynein by separating the molecule into two distinct subcomplexes. These subcomplexes were competent to reassemble into a molecule with dynein-like properties. One subcomplex was composed of the dynein heavy and light intermediate chains whereas the other subcomplex was composed of the intermediate and light chains. The intermediate and light chain subcomplex could be further separated into two pools, only one of which contained dynein light chains. The two pools had distinct intermediate chain compositions, suggesting that intermediate chain isoforms have different light chain-binding properties. When the two intermediate chain pools were characterized by analytical velocity sedimentation, at least four molecular components were seen: intermediate chain monomers, intermediate chain dimers, intermediate chain monomers with bound light chains, and a mixture of intermediate chain dimers with assorted bound light chains. These data provide new insights into the compositional heterogeneity and assembly of the cytoplasmic dynein complex and suggest that individual dynein molecules have distinct molecular compositions in vivo.     

Automated, High Productivity Purification and Analysis of Synthetic Peptides

Methods for peptide assembly consist of techniques that allow for construction of complex sequences. The advantage of solid-phase methodologies is automation of the repetitive processes of deprotecting, washing, and coupling protected amino acids (acylation). However, for difficult sequences the crude product contains a variety of side products that must be removed to provide the desired target peptide in sufficient concentration and purity. This paper illustrates that high efficiency purification method-development can be achieved by combining purification and analysis on a single platform. Incorporation of fast LC-based assays using polystyrene-based POROS® Perfusion Chromatography media permitted rapid overall processing times from crude peptide purification through fraction pooling and product verification. Application of these technologies to the purification of peptides at scales of 100 mg is demonstrated.     

Changes in iodine mapping in rat thyroid during the course of iodine deficiency: imaging and relative quantitation by analytical ion microscope

The analytical ion microscope (AIM) makes possible imaging and relative quantitation of multiple stable or labeled elements on an even tissue section, according to their mass. The purpose of this work was to follow at the rat thyroid follicle level the changes in 127I mapping during low iodine diet (LID) in relation to the ability of thyroid to pick up radioiodine (129I) and to synthesize Tg from its precursor, 2H-labeled leucine. The overall picture of images and countings of 127I shows a progressive decrease of the luminal iodine concentration which on day 80 was 10-fold lower than that of control value. In control rat thyroid cell, concentration was 10-fold lower than that of follicular lumina and was unchanged until 35 days, but the size of the cytoplasmic compartment increased, suggesting a redistribution of iodine stores between thyroid cells and follicular lumina. 129I was always found in colloid as well as in cells at all stages. After 35 days of LID, cytoplasmic and luminal radioiodine concentrations decreased. In control rats, [2H]leucine was found mainly in the cells. During LID its localization was evidenced progressively in most of the lumina. The most striking fact was the presence up to 35 days of some large residual follicles with high 127I concentration and low 129I and 2H incorporation. These data demonstrate the follicular heterogeneity of thyroid response to progressive chronic TSH stimulation induced by LID.     

Direct Measurement of the Thermodynamics of Chiral Recognition in Bile Salt Micelles

Isothermal titration calorimetry (ITC) is shown to be a sensitive reporter of bile salt micellization and chiral recognition. Detailed ITC characterization of bile micelle formation as well as the chiral recognition capabilities of sodium cholate (NaC), deoxycholate (NaDC), and taurodeoxycholate (NaTDC) micelle systems are reported. The ΔH_demic of these bile salt micelle systems is directly observable and is strongly temperature‐dependent, allowing also for the determination of ΔCp_demic. Using the pseudo‐phase separation model, ΔG_demic and TΔS_demic were also calculated. Chirally selective guest–host binding of model racemic compounds 1,1’‐bi‐2‐napthol (BN) and 1,1’‐binaphthyl‐2,2’‐diylhydrogenphosphate (BNDHP) to bile salt micelles was then investigated. The S‐isomer was shown to bind more tightly to the bile salt micelles in all cases. A model was developed that allows for the quantitative determination of the enthalpic difference in binding affinity that corresponds to chiral selectivity, which is on the order of 1 kJ mol^‐1. Chirality 28:290–298, 2016. © 2016 Wiley Periodicals, Inc.     

Genomic signature of successful colonization of Eurasia by the allopolyploid shepherd's purse (Capsella bursa‐pastoris)

Polyploidization is a dominant feature of flowering plant evolution. However, detailed genomic analyses of the interpopulation diversification of polyploids following genome duplication are still in their infancy, mainly because of methodological limits, both in terms of sequencing and computational analyses. The shepherd's purse (Capsella bursa‐pastoris) is one of the most common weed species in the world. It is highly self‐fertilizing, and recent genomic data indicate that it is an allopolyploid, resulting from hybridization between the ancestors of the diploid species Capsella grandiflora and Capsella orientalis. Here, we investigated the genomic diversity of C. bursa‐pastoris, its population structure and demographic history, following allopolyploidization in Eurasia. To that end, we genotyped 261 C. bursa‐pastoris accessions spread across Europe, the Middle East and Asia, using genotyping‐by‐sequencing, leading to a total of 4274 SNPs after quality control. Bayesian clustering analyses revealed three distinct genetic clusters in Eurasia: one cluster grouping samples from Western Europe and Southeastern Siberia, the second one centred on Eastern Asia and the third one in the Middle East. Approximate Bayesian computation (ABC) supported the hypothesis that C. bursa‐pastoris underwent a typical colonization history involving low gene flow among colonizing populations, likely starting from the Middle East towards Europe and followed by successive human‐mediated expansions into Eastern Asia. Altogether, these findings bring new insights into the recent multistage colonization history of the allotetraploid C. bursa‐pastoris and highlight ABC and genotyping‐by‐sequencing data as promising but still challenging tools to infer demographic histories of selfing allopolyploids.     

Adult female Drosophila pseudoobscura survive and carry fertile sperm through long periods in the cold: populations are unlikely to suffer substantial bottlenecks in overwintering

To assess whether, while overwintering, natural populations of Drosophila pseudoobscura are likely to experience substantial bottlenecks in their numbers and genotypes, laboratory tests of the cold sensitivities of each stage of the life history and reproduction were undertaken. Three genetically distinctive lineages established from flies caught at high elevation were used for testing in temperatures likely to persist in protected pockets of fermenting deciduous leaf fall in overwintering sites. Sensitivities to cold of each stage in development were measured as frequencies of survival to adulthood following a period in 5 degrees C in a particular stage. The cold sensitivity of adults was measured as the survival in and following cold stays in adulthood. It was found that cold sensitivity decreases as development progresses, but that only adults (females more than males) are able to withstand long periods in the cold. The cold sensitivity of reproductive capacity of males was scored as their success in mating following a two-month cold stay, and of females as the numbers laying fertile eggs following periods of months in the cold. Both males and females maintain reproductive capacity. Of particular significance, however, is that even after six months in the cold females are able to restart production of eggs and these eggs may be fertilized by the sperm of matings prior to their cold stay. Thus, a substantial proportion of overwintering genomes must be those of adult females and those of the sperm carried by females from matings in the previous summer. This simple finding strongly suggests that populations are not likely to suffer substantial bottlenecks while overwintering. Further, it indicates how arrays of genetic variation may be maintained through winters and largely avoid winter selective pressures. Frequent migration between populations is therefore not required to maintain the variation commonly found in populations throughout the species range.     

Mitochondrial phylogeography of the Eurasian beaver Castor fiber L

Nucleotide variation in an approximately 490 bp fragment of the mitochondrial DNA control region (mtDNA CR) was used to describe the genetic variation and phylogeographical pattern in the Eurasian beaver (Castor fiber) over its entire range. The sampling effort was focused on the relict populations that survived a drastic population bottleneck, caused by overhunting, at the end of the 19th century. A total of 152 individuals grouped into eight populations representing all currently recognized subspecies were studied. Sixteen haplotypes were detected, none of them shared among populations. Intrapopulation sequence variation was very low, most likely a result of the severe bottleneck. Extreme genetic structure could result from human-mediated extinction of intermediate populations, but it could also be an effect of prior substantial structuring of the beaver populations with watersheds of major Eurasian rivers acting as barriers to gene flow. Phylogenetic analysis revealed the presence of two mtDNA lineages: eastern (Poland, Lithuania, Russia and Mongolia) and western (Germany, Norway and France), the former comprising more divergent haplotypes. The low level of sequence divergence of the entire cytochrome b gene among six individuals representing six subspecies suggests differentiation during the last glacial period and existence of multiple glacial refugia. At least two evolutionary significant units (ESU) can be identified, the western and the eastern haplogroup. The individual relict populations should be regarded as management units, the eastern subspecies possibly also as ESUs. Guidelines for future translocations and reintroductions are proposed.     

Retos y oportunidades en el estudio de vesículas extracelulares: contexto institucional a nivel mundial y situación actual en Colombia

In the last decade, the number of studies and publications on extracellular vesicles (EV) and exosomes has boomed. Colombia has displayed interest and progress in their study as shown in the increase of research project publications and products. However, this research field is still developing and has its own analytical challenges and technical limitations. For planning research projects and developing EV studies it is necessary to consider what is the state of the scientific field worldwide concerning EV nomenclature and classification, available techniques, resources, requirements and quality specifications, and the institutions that regulate the field. Answering this question will elicit EV studies that comply with international standards and respond to institutional demands and recommendations. However, the scientific information available is scattered and not all the aspects are considered in full.In this update, the available information is condensed and the official terms and currently defined nomenclature is presented, as well as the evolution of the field, the homogenization of the experimental parameters, the establishment of scientific authorities, institutions, and resources, and the recommendations generated worldwide for their development and research including their isolation, characterization, and functional studies. Finally, I analyzed the national context in a critical way, considering institutional strengths, common mistakes, and available analytical techniques and technologies.     

Structure and binding mechanism of vascular endothelial cadherin: a divergent classical cadherin

Vascular endothelial cadherin (VE-cadherin), a divergent member of the type II classical cadherin family of cell adhesion proteins, mediates homophilic adhesion in the vascular endothelium. Previous investigations with a bacterially produced protein suggested that VE-cadherin forms cell surface trimers that bind between apposed cells to form hexamers. Here we report studies of mammalian-produced VE-cadherin ectodomains suggesting that, like other classical cadherins, VE-cadherin forms adhesive trans dimers between monomers located on opposing cell surfaces. Trimerization of the bacterially produced protein appears to be an artifact that arises from a lack of glycosylation. We also present the 2.1-Å-resolution crystal structure of the VE-cadherin EC1-2 adhesive region, which reveals homodimerization via the strand-swap mechanism common to classical cadherins. In common with type II cadherins, strand-swap binding involves two tryptophan anchor residues, but the adhesive interface resembles type I cadherins in that VE-cadherin does not form a large nonswapped hydrophobic surface. Thus, VE-cadherin is an outlier among classical cadherins, with characteristics of both type I and type II subfamilies.