The Rab11-family interacting proteins reveal selective interaction of mammalian recycling endosomes with the Toxoplasma parasitophorous vacuole in a Rab11- and Arf6-dependent manner

After mammalian cell invasion, the parasite Toxoplasma multiplies in a self-made membrane-bound compartment, the parasitophorous vacuole (PV). We previously showed that Toxoplasma interacts with many host cell organelles, especially from recycling pathways, and sequestrates Rab11A and Rab11B vesicles into the PV. Here, we examine the specificity of host Rab11 vesicle interaction with the PV by focusing on the recruitment of subpopulations of Rab11 vesicles characterized by different effectors, for example, Rab11-family interacting roteins (FIPs) or Arf6. Our quantitative microscopic analysis illustrates the presence of intra-PV vesicles with FIPs from class I (FIP1C, FIP2, FIP5) and class II (FIP3, FIP4) but to various degrees. The intra-PV delivery of vesicles with class I, but not class II, FIPs is dependent on Rab11 binding. Cell depletion of Rab11A results in a significant decrease in intra-PV FIP5, but not FIP3 vesicles. Class II FIPs also bind to Arf6, and we observe vesicles associated with FIP3-Rab11A or FIP3-Arf6 complexes concomitantly within the PV. Abolishing FIP3 binding to both Rab11 and Arf6 reduces the number of intra-PV FIP3 vesicles. These data point to a selective process of mammalian Rab11 vesicle recognition and scavenging mediated by Toxoplasma, suggesting that specific parasite PV proteins may be involved in these processes.     

Process monitoring of virus-like particle reassembly by diafiltration with UV/Vis spectroscopy and light scattering

Virus-like particles (VLPs) have shown great potential as biopharmaceuticals in the market and in clinics. Nonenveloped, in vivo assembled VLPs are typically disassembled and reassembled in vitro to improve particle stability, homogeneity, and immunogenicity. At the industrial scale, cross-flow filtration (CFF) is the method of choice for performing reassembly by diafiltration. Here, we developed an experimental CFF setup with an on-line measurement loop for the implementation of process analytical technology (PAT). The measurement loop included an ultraviolet and visible (UV/Vis) spectrometer as well as a light scattering photometer. These sensors allowed for monitoring protein concentration, protein tertiary structure, and protein quaternary structure. The experimental setup was tested with three Hepatitis B core Antigen (HBcAg) variants. With each variant, three reassembly processes were performed at different transmembrane pressures (TMPs). While light scattering provided information on the assembly progress, UV/Vis allowed for monitoring the protein concentration and the rate of VLP assembly based on the microenvironment of Tyrosine-132. VLP formation was verified by off-line dynamic light scattering (DLS) and transmission electron microscopy (TEM). Furthermore, the experimental results provided evidence of aggregate-related assembly inhibition and showed that off-line size-exclusion chromatography does not provide a complete picture of the particle content. Finally, a Partial-Least Squares (PLS) model was calibrated to predict VLP concentrations in the process solution. values of 0.947–0.984 were reached for the three HBcAg variants. In summary, the proposed experimental setup provides a powerful platform for developing and monitoring VLP reassembly steps by CFF.     

Angling-induced cardiac disturbance of free-swimming largemouth bass (Micropterus salmoides) monitored with heart rate telemetry

The sub‐lethal effects of catch‐and‐release angling have been poorly studied because of the difficulties in monitoring physiological parameters in free‐swimming fish. Laboratory studies provide the opportunity to examine sub‐lethal effects in controlled environments, but do not incorporate site‐specific characteristics. In this study we angled free‐swimming largemouth bass (Micropterus salmoides) equipped with heart rate transmitters to exhaustion using rod and reel, and exposed fish to air for 30 s. Experiments were repeated at four water temperatures (13, 17, 21, and 25°C). These field data were compared with published findings from largemouth bass collected at the same water temperatures in a controlled laboratory setting using Doppler flow probes. Field collected heart rate data increased with increasing water temperatures (Q₁₀ values 1.30–1.37). Pre‐disturbance heart rates were ～30% higher for free‐swimming fish in the field than previously collected laboratory data at the same water temperatures. Fish angled in the field exhausted ～40% more rapidly than fish chased in the laboratory. Maximal heart rate was ～15% higher for free‐swimming fish in the field than for data collected from laboratory restrained fish, but scope for heart rate was reduced by up to 20% in the field, especially at higher water temperatures. Heart rate in free‐swimming fish was highly variable at all times, obscuring clear recovery patterns. Conversely, laboratory cardiac parameters exhibited less variable patterns, peaking clearly following disturbances and recovering in about 135 min, independent of water temperature. Based upon these findings, we suggest that comprehensive studies incorporating both laboratory and field experiments are needed for truly understanding the effect of catch‐and‐release angling on fish.     

Calibration-in-time versus calibration-in-space (transfer function) to quantitatively infer July air temperature using biological indicators (chironomids) preserved in lake sediments

Calibration-in-space (i.e. modern taxonomic assemblages of biota from many lakes located along a wide temperature gradient calibrated against meteorological data) is generally used to derive species-specific optima and tolerances. This results in transfer functions which then are applied to subfossil assemblages to quantitatively reconstruct environmental variables such as air/water temperature. Developing such transfer functions is time- and money-consuming, thus many biota-inferred temperature records are either based on transfer functions from other regions which might not take into account local characteristics or are only used qualitatively. In varved Lake Silvaplana (Engadine, Switzerland), another way of obtaining quantitative climate reconstructions from taxonomical assemblages preserved in lake sediments was assessed for the past 1000 years. A calibration-in-time (i.e. taxonomic-assemblage-of-biota time series calibrated against meteorological data covering the same time period) was developed for chironomids (non-biting midges) using a weighted-average-partial-least-square (WAPLS) model and compared with a calibration-in-space model. The calibration-in-time had a weaker correlation coefficient (r² = 0.71) than the calibration-in-space (r² = 0.86), but the error of prediction (RMSEP = 0.58 °C) and the maximum bias (Max Bias = 0.73 °C) outperformed the statistics of the calibration-in-space (RMSEP = 1.5 °C; Max Bias = 1.72). This result is probably due to the smaller temperature gradient of the calibration-in-time (6.5 °C) than the calibration-in-space (11.5 °C). For the last 150 years, the Pearson correlation coefficient was significant between the two reconstructions (r_Pearson = 0.52; p < 0.01) suggesting that both models recorded a similar pattern of temperature changes. On the millennium time-scale, both models showed a warm “Medieval Climate Anomaly”, a cold “Little Ice Age” and a warming through the present with significant correlations (rPearson corrected for autocorrelation (corr) = 0.61, p < 0.01) until ca. 1780 AD and between ca. 1937 and 2000 AD (r_{Pearson corr} = 0.90, p < 0.01). The reconstructions using both models significantly diverged between ca. 1780 and 1937 AD (r_{Pearson corr} = ?0.47, p < 0.01). The results of both reconstruction methods were compared with four independent local and regional records of early instrumental and documentary data during the period of divergence. Both reconstructions showed similarities with the early instrumental/documentary records, thus it was inconclusive which of the reconstruction models provides the better estimates. However, these results suggest that a calibration-in-time can be used to reconstruct climate over the last 1000 years when no calibration-in-space is available.     

LuTHy: a double‐readout bioluminescence‐based two‐hybrid technology for quantitative mapping of protein–protein interactions in mammalian cells

Information on protein–protein interactions (PPIs) is of critical importance for studying complex biological systems and developing therapeutic strategies. Here, we present a double‐readout bioluminescence‐based two‐hybrid technology, termed LuTHy, which provides two quantitative scores in one experimental procedure when testing binary interactions. PPIs are first monitored in cells by quantification of bioluminescence resonance energy transfer (BRET) and, following cell lysis, are again quantitatively assessed by luminescence‐based co‐precipitation (LuC). The double‐readout procedure detects interactions with higher sensitivity than traditional single‐readout methods and is broadly applicable, for example, for detecting the effects of small molecules or disease‐causing mutations on PPIs. Applying LuTHy in a focused screen, we identified 42 interactions for the presynaptic chaperone CSPα, causative to adult‐onset neuronal ceroid lipofuscinosis (ANCL), a progressive neurodegenerative disease. Nearly 50% of PPIs were found to be affected when studying the effect of the disease‐causing missense mutations L115R and ?L116 in CSPα with LuTHy. Our study presents a robust, sensitive research tool with high utility for investigating the molecular mechanisms by which disease‐associated mutations impair protein activity in biological systems.     

Systematic Identification of Rhythmic Genes Reveals camk1gb as a New Element in the Circadian Clockwork

A wide variety of biochemical, physiological, and molecular processes are known to have daily rhythms driven by an endogenous circadian clock. While extensive research has greatly improved our understanding of the molecular mechanisms that constitute the circadian clock, the links between this clock and dependent processes have remained elusive. To address this gap in our knowledge, we have used RNA sequencing (RNA–seq) and DNA microarrays to systematically identify clock-controlled genes in the zebrafish pineal gland. In addition to a comprehensive view of the expression pattern of known clock components within this master clock tissue, this approach has revealed novel potential elements of the circadian timing system. We have implicated one rhythmically expressed gene, camk1gb, in connecting the clock with downstream physiology of the pineal gland. Remarkably, knockdown of camk1gb disrupts locomotor activity in the whole larva, even though it is predominantly expressed within the pineal gland. Therefore, it appears that camk1gb plays a role in linking the pineal master clock with the periphery.     

A Systematic Approach for the Genetic Dissection of Protein Complexes in Living Cells

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Gene silencing with RNA interference in the human pathogenic fungus Aspergillus fumigatus

Aspergillus fumigatus is an opportunistic pathogenic fungus which causes fatal invasive aspergillosis among immunocompromised patients. To obtain a better understanding of the key elements involved in A. fumigatus virulence and to identify possible drug targets, it is necessary to be able to generate gene-deletion strains. Unfortunately, the molecular techniques available do not include a rapid method to disrupt and identify essential genes. RNA interference, a process in which the presence of double-stranded RNA homologous to a gene of interest results in specific degradation of the corresponding message, has been successfully tested on A. fumigatus. We have shown that expression of double stranded RNA corresponding to portions of the ALB1/PKSP and FKS1 genes results in reduced mRNA levels for those genes, with phenotypic consequences similar to that of gene disruption. The two genes could also be subjected to simultaneous interference through expression of chimeric double-stranded RNA. Use of RNA interference in Aspergillus will allow easier examination of the phenotypic consequences of reducing expression of a gene of interest, especially for essential genes.     

Beclin1-binding UVRAG targets the class C Vps complex to coordinate autophagosome maturation and endocytic trafficking

Autophagic and endocytic pathways are tightly regulated membrane rearrangement processes that are crucial for homeostasis, development and disease. Autophagic cargo is delivered from autophagosomes to lysosomes for degradation through a complex process that topologically resembles endosomal maturation. Here, we report that a Beclin1-binding autophagic tumour suppressor, UVRAG, interacts with the class C Vps complex, a key component of the endosomal fusion machinery. This interaction stimulates Rab7 GTPase activity and autophagosome fusion with late endosomes/lysosomes, thereby enhancing delivery and degradation of autophagic cargo. Furthermore, the UVRAG-class-C-Vps complex accelerates endosome-endosome fusion, resulting in rapid degradation of endocytic cargo. Remarkably, autophagosome/endosome maturation mediated by the UVRAG-class-C-Vps complex is genetically separable from UVRAG-Beclin1-mediated autophagosome formation. This result indicates that UVRAG functions as a multivalent trafficking effector that regulates not only two important steps of autophagy - autophagosome formation and maturation - but also endosomal fusion, which concomitantly promotes transport of autophagic and endocytic cargo to the degradative compartments.