Long wavelength fluorophores and cell-by-cell correction for autofluorescence significantly improves the accuracy of flow cytometric energy transfer measurements on a dual-laser benchtop flow cytometer

BACKGROUND: Flow cytometric fluorescence resonance energy transfer (FCET) is an efficient method to map associations between biomolecules because of its high sensitivity to changes in molecular distances in the range of 1-10 nm. However, the requirement for a dual-laser instrument and the need for a relatively high signal-to-noise system (i.e., high expression level of the molecules) pose limitations to a wide application of the method. METHODS: Antibodies conjugated to cyanines 3 and 5 (Cy3 and Cy5) were used to label membrane proteins on the cell surface. FCET measurements were made on a widely used benchtop dual-laser flow cytometer, the FACSCalibur, by using cell-by-cell analysis of energy transfer efficiency.ResultsTo increase the accuracy of FCET measurements, we applied a long wavelength donor-acceptor pair, Cy3 and Cy5, which beneficially affected the signal-to-noise ratio in comparison with the classic pair of fluorescein and rhodamine. A new algorithm for cell-by-cell correction of autofluorescence further improved the sensitivity of the technique; cell subpopulations with only slightly different FCET efficiencies could be identified. The new FCET technique was tested on various direct and indirect immunofluorescent labeling strategies. The highest FCET values could be measured when applying direct labeling on both (donor and acceptor) sides. Upon increasing the complexity of the labeling scheme by introducing secondary antibodies, we detected a decrease in the energy transfer efficiency. CONCLUSIONS: We developed a new FCET protocol by applying long wavelength excitation and detection of fluorescence and by refining autofluorescence correction. The increased accuracy of the new method makes cells with low receptor expression amenable to FCET investigation, and the new approach can be implemented easily on a commercially available dual-laser flow cytometer, such as a FACSCalibur.     

Fresh,frozen or fake: A comparison of predation rates measured by various types of sentinel prey

Arthropod predators and parasitoids support the health and functioning of the world's ecosystems, most notably by supplying biological control services to agricultural landscapes. Quantifying the impact that these organisms have on their prey can be challenging, as direct observation and measurement of arthropod predation is difficult. The use of sentinel prey is one method to measure predator impact; however, despite widespread use, few studies have compared predation on different prey types within a single experiment. This study evaluated the predation rates on four sentinel prey items in grass and wheat fields in south-east Queensland, Australia. Attack rates on live and dead Helicoverpa armigera eggs, and dead H. armigera larvae and artificial plasticine larvae, were compared and the predators that were attracted to each prey type were documented with the use of field cameras. There was no significant difference in predation rates between sentinel eggs, while dead larvae were significantly more attacked than artificial larvae. Prey were attacked by a diverse range of predators, including ants, beetles, various nymph and juvenile insects and small mammals. Different predators were active in grass and crop fields, with predator activity peaking around dawn and dusk. The same trends were observed within and between the two habitats studied, providing a measure of confidence in the sentinel prey method. A range of different sentinel prey types could be suitable for use in most comparative studies; however, each prey type has its own benefits and limitations, and these should be carefully evaluated to determine which is most suitable to address the research questions.     

Interaction of the HOPS complex with Syntaxin 17 mediates autophagosome clearance in Drosophila

Homotypic fusion and vacuole protein sorting (HOPS) is a tethering complex required for trafficking to the vacuole/lysosome in yeast. Specific interaction of HOPS with certain SNARE (soluble NSF attachment protein receptor) proteins ensures the fusion of appropriate vesicles. HOPS function is less well characterized in metazoans. We show that all six HOPS subunits (Vps11 [vacuolar protein sorting 11]/CG32350, Vps18/Dor, Vps16A, Vps33A/Car, Vps39/CG7146, and Vps41/Lt) are required for fusion of autophagosomes with lysosomes in Drosophila. Loss of these genes results in large-scale accumulation of autophagosomes and blocks autophagic degradation under basal, starvation-induced, and developmental conditions. We find that HOPS colocalizes and interacts with Syntaxin 17 (Syx17), the recently identified autophagosomal SNARE required for fusion in Drosophila and mammals, suggesting their association is critical during tethering and fusion of autophagosomes with lysosomes. HOPS, but not Syx17, is also required for endocytic down-regulation of Notch and Boss in developing eyes and for proper trafficking to lysosomes and eye pigment granules. We also show that the formation of autophagosomes and their fusion with lysosomes is largely unaffected in null mutants of Vps38/UVRAG (UV radiation resistance associated), a suggested binding partner of HOPS in mammals, while endocytic breakdown and lysosome biogenesis is perturbed. Our results establish the role of HOPS and its likely mechanism of action during autophagy in metazoans.     

Molecular systematics of racers, whipsnakes and relatives (Reptilia: Colubridae) using mitochondrial and nuclear markers

Four protein-encoding mitochondrial genes (cytochrome b , NADH-dehydrogenase subunits 1, 2 and 4) and one nuclear (c-mos) gene were sequenced to infer phylogenetic relationships among Old and New World representatives of racers and whipsnakes, Coluber (sensu lato). New World Coluber ( Coluber sensu stricto, including Masticophis ) and Salvadora proved to have affinities with the Old World non-racer colubrine genus Ptyas (and possibly Elaphe s.l. and Coronella ), whereas Old World ' Coluber ' form several basally related clades; these are (1) Hemorrhois -( Spalerosophis-Platyceps ); (2) Hierophis , with Eirenis nested within this paraphyletic genus and (3) ' Coluber ' dorri as the sister taxon to Macroprotodon cucullatus . The position of ' Coluber ' zebrinus along with Hemerophis socotrae located at the base of the Old World racer radiation forming the possible sister group to all remaining Palearctic racers and whipsnakes remains less well supported. Nevertheless, inter- and subgeneric relationships among many of the Old World racer groups have been resolved.     

Size reduction associated with brachymesophalangia-5: a possible selective advantage

The skin reflectance characteristics of a group of Quechua Indians have been described with an emphasis upon the effects of varying degrees of hybridization, sex and age. This group of Peruvian Indians occupied a reflectance range common to that of all other reported groups of South American Indians. Miscegenation with European Whites had a statistically significant although small influence upon skin color. In general males were consistently darker than females on the three body sites measured. A significant darkening on unexposed body areas occurred in both sexes during early adolescence which may have been caused by the high activity level of the pituitary gland at that stage of the growth cycle.     

Synergistic Cooperation between Two ClpB Isoforms in Aggregate Reactivation

Bacterial AAA⁺ ATPase ClpB cooperates with DnaK during reactivation of aggregated proteins. The ClpB-mediated disaggregation is linked to translocation of polypeptides through the channel in the oligomeric ClpB. Two isoforms of ClpB are produced in vivo: the full-length ClpB95 and ClpB80, which does not contain the substrate-interacting N-terminal domain. The biological role of the truncated isoform ClpB80 is unknown. We found that resolubilization of aggregated proteins in Escherichia coli after heat shock and reactivation of aggregated proteins in vitro and in vivo occurred at higher rates in the presence of ClpB95 with ClpB80 than with ClpB95 or ClpB80 alone. Combined amounts of ClpB95 and ClpB80 bound to aggregated substrates were similar to the amounts of either ClpB95 or ClpB80 bound to the substrates in the absence of another isoform. The ATP hydrolysis rate of ClpB95 with ClpB80, which is linked to the rate of substrate translocation, was not higher than the rates measured for the isolated ClpB95 or ClpB80. We postulate that a reaction step that takes place after substrate binding to ClpB and precedes substrate translocation is rate-limiting during aggregate reactivation, and its efficiency is enhanced in the presence of both ClpB isoforms. Moreover, we found that ClpB95 and ClpB80 form hetero-oligomers, which are similar in size to the homo-oligomers of ClpB95 or ClpB80. Thus, the mechanism of functional cooperation of the two isoforms of ClpB may be linked to their heteroassociation. Our results suggest that the functionality of other AAA⁺ ATPases may be also optimized by interaction and synergistic cooperation of their isoforms.     

Axial loading induces rotation of the proximal carpal row bones around unique screw-displacement axes

The changes in carpal bone alignment secondary to the aplication of an axial compressive load through the major wrist motor tendons while the wrist is kept in neutral position (isometric loading) have been investigated on 13 fresh cadaver specimens using a biplanar radiographic method of kinematic analysis. The scaphoid, lunate and triquetrum rotate an average of 5.1, 4.2 and 3.8°, respectively, around different ‘screw displacement axes’, all implying flexion, radial deviation and supination. Based on these findings, a new interpretation of the mechanism by which the wrist remains stable under physiologic loads is provided.     

Spectrally silent light induced conformation change in photosynthetic reaction centers

Spectrally silent conformation change after photoexcitation of photosynthetic reaction centers isolated from Rhodobacter sphaeroides R-26 was observed by the optical heterodyne transient grating technique. The signal showed spectrally silent structural change in photosynthetic reaction centers followed by the primary P+BPh- charge separation and this change remains even after the charge recombination. Without bound quinone to the RC, the conformation change relaxes with about 28micros lifetime. The presence of quinone at the primary quinone (QA) site may suppress this conformation change. However, a weak relaxation with 30-40micros lifetime is still observed under the presence of QA, which increases up to 40micros as a function of the occupancy of the secondary quinone (QB) site.     

Alternative splicing of SNAP-25 regulates secretion through nonconservative substitutions in the SNARE domain

The essential membrane fusion apparatus in mammalian cells, the soluble N-ethylmaleimide-sensitive factor attachment protein receptor (SNARE) complex, consists of four alpha-helices formed by three proteins: SNAP-25, syntaxin 1, and synaptobrevin 2. SNAP-25 contributes two helices to the complex and is targeted to the plasma membrane by palmitoylation of four cysteines in the linker region. It is alternatively spliced into two forms, SNAP-25a and SNAP-25b, differing by nine amino acids substitutions. When expressed in chromaffin cells from SNAP-25 null mice, the isoforms support different levels of secretion. Here, we investigated the basis of that different secretory phenotype. We found that two nonconservative substitutions in the N-terminal SNARE domain and not the different localization of one palmitoylated cysteine cause the functional difference between the isoforms. Biochemical and molecular dynamic simulation experiments revealed that the two substitutions do not regulate secretion by affecting the property of SNARE complex itself, but rather make the SNAP-25b-containing SNARE complex more available for the interaction with accessory factor(s).