The Dynamics and Function of the Endolysosomal/Lysosomal System

Lysosomes are intracellular organelles that were considered for a long time to be simply an acidic and hydrolytically active end point of trafficking routes for degradation, in the last 20 years, light has been shed on their functional heterogeneity and striking role in signalling and nutrient homeostasis. While the dynamic nature and variety of lysosomal functions are now better appreciated, the mechanisms governing lysosomal fusion, reformation, signalling, and homeostasis remain to be fully elucidated, and are investigated here. In this study, endolysosomes which formed by fusion of late endosomes with lysosomes and are thought to be the predominant site of hydrolytic activity, were further characterised. Using live cell imaging and fluorescent labelling, the proportion of endolysosomes in the total pool of lysosomes was estimated using probes to their acidity and cathepsin activity, and their larger size compared to storage lysosomes was observed. The endolysosomal membrane was also shown to be marked by Rab7, Rab9, PI(3,5)P2 supporting the role of endolysosomes a highly active and dynamic principal site of hydrolase activity. The contributions of VAMP7 and VAMP8 to endolysosome fusion, measured by delivery of endocytosed cargo from late endosomes to endolysosomes, were analysed by CRISPR-Cas9 mediated knockout. Cells lacking VAMP7 and VAMP8 had no effect on delivery to endolysosomes, however at EM level, they displayed extensive tethering between late endocytic organelles, and accumulated small tethered vesicles. YKT6 knockdown impeded delivery to endolysosomes in VAMP7+VAMP8 knockout cells, which was rescued by VAMP7 expression, suggesting YKT6 substituted for VAMP7 in lysosome fusion. Following the hypothesis that reversible dissociation of V1 and Vo sectors of the V- ATPase may control the increase in pH of reforming storage lysosomes, cells expressing tagged V1G1 and Voa3 were generated. These markers of both sectors are present on endolysosomal membranes, and on the emerging endolysosomal tubules, suggesting the V1 and Vo sectors remain associated at this earliest stage of lysosome reformation, but these markers are still in development. IV Two assays were developed to give a readout of, and assess lysosomal stress. Firstly, an assay measuring TFEB-GFP translocation to the nucleus gave a robust and quantifiable readout of lysosomal perturbation. Secondly, a qPCR assay was developed to measure lysosomal gene upregulation as a downstream reporter of TFEB-activating lysosomal perturbations, however this assay, despite being more lysosome-specific, lacked the consistency and dynamic range of the TFEB translocation quantification. In summary, lysosomes are a heterogeneous collection of organelles, which have been better characterised primarily according to their acidity and hydrolytic capacity. Additionally, more SNAREs appear to be involved in lysosome fusion in cells than suggested by cell free assays, and I have developed tools to trace the V-ATPase during reformation of lysosomes after fusion to form endolysosomes. Lastly, I have developed a robust, reporter for a range of lysosomal stress-inducing conditions, providing a broad indication of their effects on lysosomal signalling and homeostasis.CASE Studentship co-funded by BBSRC and GS

Two Distinct Pathways Support Gene Correction by Single-Stranded Donors at DNA Nicks

SummaryNicks are the most common form of DNA damage. The mechanisms of their repair are fundamental to genomic stability and of practical importance for genome engineering. We define two pathways that support homology-directed repair by single-stranded DNA donors. One depends upon annealing-driven strand synthesis and acts at both nicks and double-strand breaks. The other depends upon annealing-driven heteroduplex correction and acts at nicks. Homology-directed repair via these pathways, as well as mutagenic end joining, are inhibited by RAD51 at nicks but largely independent of RAD51 at double-strand breaks. Guidelines for coordinated design of targets and donors for gene correction emerge from definition of these pathways. This analysis further suggests that naturally occurring nicks may have significant recombinogenic and mutagenic potential that is normally inhibited by RAD51 loading onto DNA, thereby identifying a function for RAD51 in maintenance of genomic stability

Religious Belief, Coping, and Mental Health in Seventh-day Adventists

The present study examines religious belief, coping style, and social support influences on psychological adjustment in 401 Seventh-day Adventists. Based on cross cultural psychology guidelines, Adventist Sabbath and eschatology belief measures were created and integrated into a religious coping framework. Sabbath and eschatology belief measures, the brief RCOPE, two social support scales, and the Medical Outcomes Study Mental Health Index II were administered. After controlling for demographics, religious coping, social support, and Adventist beliefs were significantly associated with psychological adjustment. Negative religious coping was the most powerful predictor of adjustment. Eschatology beliefs predicted adjustment after accounting for religious coping and social support effects. The findings highlight the importance of Adventist belief and religious coping in facilitating psychological adjustment among Seventh-day Adventists. vii

Endolysosomes Are the Principal Intracellular Sites of Acid Hydrolase Activity.

The endocytic delivery of macromolecules from the mammalian cell surface for degradation by lysosomal acid hydrolases requires traffic through early endosomes to late endosomes followed by transient (kissing) or complete fusions between late endosomes and lysosomes. Transient or complete fusion results in the formation of endolysosomes, which are hybrid organelles from which lysosomes are re-formed. We have used synthetic membrane-permeable cathepsin substrates, which liberate fluorescent reporters upon proteolytic cleavage, as well as acid phosphatase cytochemistry to identify which endocytic compartments are acid hydrolase active. We found that endolysosomes are the principal organelles in which acid hydrolase substrates are cleaved. Endolysosomes also accumulated acidotropic probes and could be distinguished from terminal storage lysosomes, which were acid hydrolase inactive and did not accumulate acidotropic probes. Using live-cell microscopy, we have demonstrated that fusion events, which form endolysosomes, precede the onset of acid hydrolase activity. By means of sucrose and invertase uptake experiments, we have also shown that acid-hydrolase-active endolysosomes and acid-hydrolase-inactive, terminal storage lysosomes exist in dynamic equilibrium. We conclude that the terminal endocytic compartment is composed of acid-hydrolase-active, acidic endolysosomes and acid hydrolase-inactive, non-acidic, terminal storage lysosomes, which are linked and function in a lysosome regeneration cycle.This work was supported by MRC research grant MR/M010007/1. The CIMR is supported by Wellcome Trust Strategic Award 100140. The Cellomics ArrayScan™ VTi High Content Screening Microscope, Zeiss LSM710 confocal microscope and FEI Tecnai G2 Spirit BioTWIN transmission EM were purchased with Wellcome Trust grants 079919 and 093026. LJD is supported by a BBSRC industrial CASE studentship with GSK Research and Development Ltd. We thank Sally Gray for preparing and sequencing pLXIN constructs and Matthew Gratian for help with light microscopy and analytical software.This is the final version of the article. It first appeared from Elsevier via https://doi.org/ 10.1016/j.cub.2016.06.04

An intein with genetically selectable markers provides a new approach to internally label proteins with GFP

<p>Abstract</p> <p>Background</p> <p>Inteins are proteins that catalyze their own removal from within larger precursor proteins. In the process they splice the flanking protein sequences, termed the N-and C-terminal exteins. Large inteins frequently have a homing endonuclease that is involved in maintaining the intein in the host. Splicing and nuclease activity are independent and distinct domains in the folded structure. We show here that other biochemical activities can be incorporated into an intein in place of the endonuclease without affecting splicing and that these activities can provide genetic selection for the intein. We have coupled such a genetically marked intein with GFP as the N-terminal extein to create a cassette to introduce GFP within the interior of a targeted protein.</p> <p>Results</p> <p>The <it>Pch </it>PRP8 mini-intein of <it>Penicillium chrysogenum </it>was modified to include: 1) aminoglycoside phosphotransferase; 2) imidazoleglycerol-phosphate dehydratase, His5 from <it>S. pombe </it>; 3) hygromycin B phosphotransferase; and 4) the transcriptional activator LexA-VP16. The proteins were inserted at the site of the lost endonuclease. When expressed in <it>E. coli</it>, all of the modified inteins spliced at high efficiency. Splicing efficiency was also greater than 96% when expressed from a plasmid in <it>S. cerevisiae</it>. In addition the inteins conferred either G418 or hygromycin resistance, or histidine or leucine prototropy, depending on the inserted marker and the yeast genetic background. DNA encoding the marked inteins coupled to GFP as the N-terminal extein was PCR amplified with ends homologous to an internal site in the yeast calmodulin gene <it>CMD1</it>. The DNA was transformed into yeast and integrants obtained by direct selection for the intein's marker. The His5-marked intein yielded a fully functional calmodulin that was tagged with GFP within its central linker.</p> <p>Conclusions</p> <p>Inteins continue to show their flexibility as tools in molecular biology. The <it>Pch </it>PRP8 intein can successfully tolerate a variety of genetic markers and still retain high splicing efficiency. We have shown that a genetically marked intein can be used to insert GFP in one-step within a target protein <it>in vivo</it>.</p

Interaction of vector solitons with a nonlinear interface

We develop the analytical method of field momenta for analyzing the dynamics of optical vector solitons in photorefractive nonlinear media. First, we derive the effective evolution equations for the parameters of multi-component solitons composed of incoherently coupled beams and investigate the soliton internal oscillations associated with the relative motion of the soliton components. Then, we apply this method for analyzing the vector soliton scattering by a nonlinear interface. In particular, we show that a vector soliton can be reflected, transmitted, captured, or split into separate components, depending on the initial energy of its internal degree of freedom. The results are verified by direct numerical simulations of spatial optical solitons in photorefractive nonlinear media

Examining Affect in Psychometric Schizotypy Using Behavioral Experience Sampling Methodology

poster abstractIn schizophrenia, patients often experience more negative emotions in the form of anger, sadness, and anxiety when compared to the general population. One unique way of measuring affect outside of the laboratory has been to use Experience Sampling Methods (ESM) to assess how individuals perceive current emotions in their daily life. However, these methods are still subject to self-report bias. In this study, we examined affect using traditional ESM methods while also implementing the Electronically Activated Recorder (EAR), a behaviorally-based ESM measure that provides real-world assessments of speech. To examine the EAR, we evaluated affect in schizotypy and non-schizotypy groups. Research shows that schizophrenia-like experiences, like increased negative affect, run along a continuum. Schizotypy is a category on the healthier end of the schizophrenia-spectrum; it applies to individuals who are thought to have a putative genetic liability for schizophrenia. Using the Linguistic Inquiry and Word Count (LIWC), we compared affective word usage among schizotypy and non-schizotypy groups to provide a real-world, behavioral ESM measure. When traditional ESM measures were used, we found individuals with schizotypy reported less negative emotions compared to the non-schizotypy group, but results did not reach the level of significance. We also observed that non-schizotypy individuals reported slightly higher positive emotions, and the schizotypy group reported slightly higher negative emotions. A similar pattern was observed when examining EAR data. Overall, results suggested that traditional and behavioral ESM measures of affect had significant overlap. In general, those with schizotypy demonstrated slightly more negative emotion and slightly less positive emotion than the non-schizotypy group. Findings did not reach the level of significance. This study demonstrates that the EAR provides behavioral ratings of affect that are on par with traditional ESM ratings. Future work should examine the EAR at different points on the schizophrenia-spectrum