A conserved mitochondrial outer membrane protein mediates kDNA maintenace in Trypanosoma brucei

Kinetoplastids are defined by the unique organization of their mitochondrial DNA (kDNA). It forms a highly concatenated DNA network that is linked to the basal body of the flagellum by the tripartite attachment complex (TAC). The TAC encompasses intra and extramitochondrial filaments and a highly differentiated region of the two mitochondrial membranes. Here we identify and characterize a mitochondrial outer membrane protein of Trypanosoma brucei that is predominantly localized in the TAC. The protein is essential for growth in both life cycle stages. Immunofluorescence shows that ablation of the protein does not affect kDNA replication but abolishes the segregation of the replicated kDNA network causing rapid loss of kDNA. Besides its role in kDNA maintenance in vivo and in vitro experiments show that the protein is involved in mitochondrial protein import and that it interacts with a recently discovered protein import factor. RNAi experiments in a T. brucei cell line in which the kDNA is dispensable suggest that the essential function is linked to kDNA maintenance. Bioinformatic analysis shows that the studied outer membrane protein has beta-barrel topology and that it belongs to the mitochondrial porin family comprising VDAC, Tom40 and Mdm10. Interestingly, Mdm10 has so far only been found in yeast. Its function in protein import and mitochondrial DNA maintenance suggests that the protein in our study is the functional homologue of Mdm10. Thus, the TAC – a defining structure of Kinetoplastids – contains a conserved protein which in yeast and trypanosomes performs the same function. Our study therefore provides an example that trypanosomal biology, rather than being unique, often simply represents a more extreme manifestation of a conserved biological concept.

On the Co-Occurrence of Warm Conveyor Belt Outflows and PV Streamers*

The co-occurrence of warm conveyor belts (WCBs), strongly ascending moist airstreams in extratropical cyclones, and stratospheric potential vorticity (PV) streamers, indicators for breaking Rossby waves on the tropopause, is investigated for a 21-yr period in the Northern Hemisphere using Interim European Centre for Medium-Range Weather Forecasts (ECMWF) Re-Analysis (ERA-Interim) data. WCB outflows and PV streamers are respectively identified as two- and three-dimensional objects and tracked during their life cycle. PV streamers are more frequent than WCB outflows and nearly 15% of all PV streamers co-occur with WCBs during their life cycle, whereas about 60% of all WCB outflows co-occur with PV streamers. Co-occurrences are most frequent over the North Atlantic and North Pacific in spring and winter. WCB outflows are often located upstream of the PV streamers and form earlier, indicating the importance of diabatic processes for downstream Rossby wave breaking. Less frequently, PV streamers occur first, leading to the formation of new WCBs.

Quantifying the turnover of transcriptional subclasses of HIV-1-infected cells

HIV-1-infected cells in peripheral blood can be grouped into different transcriptional subclasses. Quantifying the turnover of these cellular subclasses can provide important insights into the viral life cycle and the generation and maintenance of latently infected cells. We used previously published data from five patients chronically infected with HIV-1 that initiated combination antiretroviral therapy (cART). Patient-matched PCR for unspliced and multiply spliced viral RNAs combined with limiting dilution analysis provided measurements of transcriptional profiles at the single cell level. Furthermore, measurement of intracellular transcripts and extracellular virion-enclosed HIV-1 RNA allowed us to distinguish productive from non-productive cells. We developed a mathematical model describing the dynamics of plasma virus and the transcriptional subclasses of HIV-1-infected cells. Fitting the model to the data allowed us to better understand the phenotype of different transcriptional subclasses and their contribution to the overall turnover of HIV-1 before and during cART. The average number of virus-producing cells in peripheral blood is small during chronic infection. We find that a substantial fraction of cells can become defectively infected. Assuming that the infection is homogenous throughout the body, we estimate an average in vivo viral burst size on the order of 104 virions per cell. Our study provides novel quantitative insights into the turnover and development of different subclasses of HIV-1-infected cells, and indicates that cells containing solely unspliced viral RNA are a good marker for viral latency. The model illustrates how the pool of latently infected cells becomes rapidly established during the first months of acute infection and continues to increase slowly during the first years of chronic infection. Having a detailed understanding of this process will be useful for the evaluation of viral eradication strategies that aim to deplete the latent reservoir of HIV-1.

Functional proteomics and biochemsitry: working together to unravel mitochondrial phenomena of African trypansomes

Eukaryotic cells are compartmentalized into membrane-bound organelles in order to provide sheltered reaction rooms for various specific processes. Organelles are not randomly distributed in a cell or operate isolated from each other. At the contrary — some organelles are closely linked and their functions are tightly orchestrated. The most well-known example of two such organelles acting in concert are the ER and the mitochondrion that work together in order to coordinate cellular lipid biosynthesis, maintain Ca2+-homeostasis, regulate mitochondrial division and control mitochondrial/ER shape as well as to synchronize the movement of these organelles within a cell. To study the mitochondrion and its interface to the ER requires a simplified mitochondrial system. African trypanosomes represent such a system. The unicellular parasite that causes devastating diseases in humans and animals has only one large mitochondrion that does not undergo fission/fusion events except for the context of cell division. Moreover, mitochondrial functions and morphology are highly regulated throughout the life cycle of the protozoan. Central to the understanding of how mitochondria control their morphology, communicate with their surroundings and manage exchange of metabolites and transport of biopolymers (proteins, RNAs) is the mitochondrial outer membrane (MOM), as the MOM defines the boundary of the organelle. Recently, we have purified the MOM of T. brucei and characterized its proteome using label-free quantitative mass spectrometry for protein abundance profiling in combination with statistical analysis. Our results show that the trypanosomal MOM proteome consists of 82 proteins, two thirds of which have never been associated with mitochondria before. Among these, we identified novel factors required to regulate mitochondrial morphology and the long-elusive protein import machinery of T. brucei. A comparison with the MOM proteome of yeast defines a set of 17 common proteins that are likely present in the mitochondrial outer membrane of all eukaryotes. One of these is the Miro-GTPase Gem1. In yeast, this Ca2+-EF-Hand containing polypeptide is thought to be involved in a protein complex that physically tethers the mitochondrion to the ER. Interestingly, a putative tethering complex in mammalian cells was linked to the mitochondrial fusion/fission machinery. Thus, the concept of a protein complex-mediated connection seems to be a general and conserved feature. We are currently investigating, if such a protein complex exists in T. brucei and if the trypanosomal Gem1 protein is involved. This ER-subdomain associated with mitochondria has been termed mitochondria-associated ER-membranes or MAM. The MAM has recently been implicated to play a key role in Alzheimer’s disease. It is therefore of broad and general interest to establish other eukaryotic model systems in order to investigate the MAM-MOM connection in more detail.

Heterogeneity in the Relationship between Happiness and Age: Evidence from the German Socio-Economic Panel

This paper studies the evolution of life satisfaction over the life course in Germany. It clarifies the causal interpretation of the econometric model by discussing the choice of control variables and the underidentification between age, cohort and time effects. The empirical part analyzes the distribution of life satisfaction over the life course at the aggregated, subgroup and individual level. To the findings: On average, life satisfaction is mildly decreasing up to age 55 followed by a hump shape with a maximum at 70. The analysis at the lower levels suggests that people differ in their life satisfaction trends, whereas the hump shape after age 55 is robust. No important differences between men and women are found. In contrast, education groups differ in their trends: highly educated people become happier over the life cycle, where life satisfaction decreases for less-educated people.

The TIM translocase in T. brucei contains Rhomboid-like proteins that are essential for mitochondrial protein import

The parasitic protozoon Trypanosoma brucei is often considered as one of the earliest branching eukaryotes that have mitochondria capable of oxidative phosphorylation. Its protein import systems are therefore of great interest. Recently, it was shown that the outer mitochondrial membrane protein translocase is of similar complexity yet different composition than in other eukaryotes (1). In the inner membrane however, only a single orthologue of the pore forming Tim17/22/23 protein family was identified and termed TbTim17. Based on this finding it has been suggested that, instead of separate TIM22 and TIM23 complexes as in other eukaryotes, trypanosomes may have a single multifunctional translocase of the inner mitochondrial membrane (TIM) of reduced complexity. To elucidate the composition of the trypanosomal TIM complex we performed co-immunoprecipitations (CoIP) of epitope-tagged TbTim17 in combination with SILAC-based quantitative mass spectrometry. This led to the identification of 22 highly enriched TbTim17-interacting proteins. We tagged two of the top-scoring proteins for reciprocal CoIP analyses and recovered a set of ten proteins that are highly enriched in all three CoIPs. These proteins are excellent candidates for core subunits of the trypanosomal TIM complex. Eight of them were present in the previously determined inner membrane proteome and four show homology to small Tim chaperones. Three candidates, a novel trypanosomatid-specific 42 kDa protein, termed Tim42, and two putative orthologues of probably inactive rhomboid proteases were chosen for further analysis. All three proteins are essential in both life cycle stages and in a cell line that can grow in the absence of mitochondrial DNA. Additionally, their ablation by RNAi results in a strong protein import defect both in vivo and in vitro. Blue native PAGE reveals that Tim42, like TbTim17 is present in a high molecular weight complex. Moreover, ablation of either Tim42 or TbTim17 leads to a destabilization of the complex containing the other protein, suggesting a tight interaction of the two proteins. In summary our study shows that unlike anticipated trypanosomes have a highly complex TIM translocase that has extensively been redesigned. We have characterized three novel TIM subunits that have never been associated with mitochondrial protein import before. Two of them belong to the rhomboid protease family, a member of which recently has been implicated in the ERAD translocation system. Our study provides insight into mitochondrial evolution over large phylogenetic distances and suggests an exciting analogy between protein translocation systems of mitochondria and the ER.

Functional proteomics and biochemistry: working together to unravel mitochondrial phenomena of African trypanosomes

Eukaryotic cells are compartmentalized into membrane-bound organelles in order to provide sheltered reaction rooms for various specific processes. Organelles are not randomly distributed in a cell or operate isolated from each other. At the contrary — some organelles are closely linked and their functions are tightly orchestrated. The most well-known example of two such organelles acting in concert are the ER and the mitochondrion that work together in order to coordinate cellular lipid biosynthesis, maintain Ca2+-homeostasis, regulate mitochondrial division and control mitochondrial/ER shape as well as to synchronize the movement of these organelles within a cell. To study the mitochondrion and its interface to the ER requires a simplified mitochondrial system. African trypanosomes represent such a system. The unicellular parasite that causes devastating diseases in humans and animals has only one large mitochondrion that does not undergo fission/fusion events except for the context of cell division. Moreover, mitochondrial functions and morphology are highly regulated throughout the life cycle of the protozoan. Central to the understanding of how mitochondria control their morphology, communicate with their surroundings and manage exchange of metabolites and transport of biopolymers (proteins, RNAs) is the mitochondrial outer membrane (MOM), as the MOM defines the boundary of the organelle. Recently, we have purified the MOM of T. brucei and characterized its proteome using label-free quantitative mass spectrometry for protein abundance profiling in combination with statistical analysis. Our results show that the trypanosomal MOM proteome consists of 82 proteins, two thirds of which have never been associated with mitochondria before. Among these, we identified novel factors required to regulate mitochondrial morphology and the long-elusive protein import machinery of T. brucei. A comparison with the MOM proteome of yeast defines a set of 17 common proteins that are likely present in the mitochondrial outer membrane of all eukaryotes. One of these is the Miro-GTPase Gem1. In yeast, this Ca2+-EF-Hand containing polypeptide is thought to be involved in a protein complex that physically tethers the mitochondrion to the ER. Interestingly, a putative tethering complex in mammalian cells was linked to the mitochondrial fusion/fission machinery. Thus, the concept of a protein complex-mediated connection seems to be a general and conserved feature. We are currently investigating, if such a protein complex exists in T. brucei and if the trypanosomal Gem1 protein is involved. This ER-subdomain associated with mitochondria has been termed mitochondria-associated ER-membranes or MAM. The MAM has recently been implicated to play a key role in Alzheimer’s disease. It is therefore of broad and general interest to establish other eukaryotic model systems in order to investigate the MAM-MOM connection in more detail.

Cloning of a protease gene family of Fasciola hepatica by the polymerase chain reaction

Degenerate oligonucleotide primers derived from conserved cysteine protease sequences were used in the reverse transcription polymerase chain reaction to amplify seven different cysteine protease cDNA clones, Fcp1-7, from RNA isolated from adult Fasciola hepatica. Five of the amplified F. hepatica sequences showed homology to the cathepsin L type and two were more related to the cathepsin B type. Southern blot analysis suggests that some members of this protease gene family are present in multiple copies. Northern blot analysis revealed differences in the levels of steady state mRNA expression for some of these proteases. The 5' and the 3' regions of Fcp1 were amplified using the rapid amplification of cDNA ends PCR protocol (RACE-PCR) and an additional clone was obtained by screening a lambda gt10 cDNA library using Fcp1 as a probe. The Fcp1 cDNA fragment was also subcloned in the expression vector pGEX and expressed as a glutathione-S-transferase (GST) fusion protein in Escherichia coli. Antibodies, raised in rabbits against the GST:Fcp1 fusion protein, were used in western blot analysis to examine expression in different life-cycle stages of F. hepatica. In extracts from adult and immature parasites, the immune serum recognised predominantly two proteins of 30 kDa and 38 kDa. In other parasite stages, proteins of different molecular weight were recognised by the anti-GST:Fcp1 antiserum, indicating stage-specific gene expression or processing of Fcp1. In gelatine substrate gel analysis, strong proteolytic activity could be detected at 30 kDa, but not at 38 kDa, suggesting that the 30 kDa protein represents the mature enzyme and the 38 kDa protein the proenzyme.

The Secret Life of Mundane Transaction Costs

Transaction costs, one often hears, are the economic equivalent of friction in physical systems. Like physicists, economists can sometimes neglect friction in formulating theories; but like engineers, they can never neglect friction in studying how the system actually does let alone should work. Interestingly, however, the present-day economics of organization also ignores friction. That is, almost single-mindedly, the literature analyzes transactions from the point of view of misaligned incentives and (especially) transaction-specific assets. The costs involved are certainly costs of running the economic system in some sense, but they are not obviously frictions. Stories about frictions in trade are not nearly as intriguing as stories about guileful trading partners and expensive assets placed at risk. But I will argue that these seemingly dull categories of cost what Baldwin and Clark (2003) call mundane transaction costs actually have a secret life. They are at least as important as, and quite probably far more important than, the more glamorous costs of asset specificity in explaining the partition between firm and market. These costs also have a secret life in another sense: they have a secret life cycle. I will argue that these mundane transaction costs provide much better material for helping us understanding how the boundaries among firms, markets, and hybrid forms change over time.

HEAD OF HOUSEHOLD STRUCTURE: ITS INFLUENCE ON THE DIETARY QUALITY OF U.S. HOUSEHOLDS, 1977-78 (UNITED STATES, NATIONWIDE FOOD CONSUMPTION SURVEY)

Using analysis of variance, household data collected in the Spring portion of the 1977-78 Nationwide Food Consumption Survey conducted by the United States Department of Agriculture were analyzed to examine the relationship between household characteristics and dietary quality of the household food supply. Results indicated that head of household structure was a statistically significant variable, with female headed households having higher dietary quality.^ Further analysis indicated that neither race, degree of urbanization, regional location, the education level of the female head, nor her employment status were significant variables in influencing dietary quality. The influence of head of household structure remained significant when these variables were controlled. However, income, household size, and family life cycle stage had statistically significant effects on dietary quality, and when individually controlled, the influence of head of household structure disappeared. ^

Dominant pelagic amphipods collected as swimmers from a mooring time-series at AWI HAUSGARTEN

Time series length-frequency data are presented for Themisto amphipods collected as swimmers by moored sediment traps since 2000 at the AWI deep-sea observatory HAUSGARTEN (79°N/4°E) in the eastern Fram Strait. Amphipod occurrences increased significantly from 2000 to 2009 at 200-300 m depth, and the North Atlantic species Themisto compressa was continuously present in the samples starting in 2004. We present year-round records of large adult Themisto amphipods, including the appearance of Themisto libellula with a total body length of up to 56.7 mm and juveniles starting from 4.0 mm. The length of Themisto abyssorum ranged from 4.2 to 25.6 mm, whereas it varied for Themisto compressa from 8.8 to 24.4 mm. Length-frequency analysis indicated a life span of 2 years for T. abyssorum and at least 3 years for T. libellula. The absence of juveniles for T. compressa suggested its reproduction in southern subarctic areas and its occasional northward migration with warmer Atlantic water into the eastern Fram Strait. The seasonal and long-term size structures of the three pelagic species were consistent over the course of the study, indicating no changes occurred in cohort development due to increasing abundances or warming water temperatures.

Tab. 1: Geographical, temperature and chemical features of sites on Bear Island and Spitsbergen

In arctic populations of Macrothrix hirsuticornis life cycles are mainly governed by temperature. This was found by using laboratory cultures in combination with the analysis of population samples from waters in Svalbard. In arctic waters ex-ephippio-++ usually produce gamogenetic F1-++ together with a high percentage of oo, which have to fertilize the resting eggs. Temperatures around 14°C, which are very rare in waters of Svalbard, will induce parthenogenetic oo in the F1 and even the F2-generation, a mode of reproduction normally found in Macrothrix-populations of Central Europe. This was found in laboratory cultures of M. hirsuticornis from Bear Island, and there was evidence, that a similar cycle occurs in warm wells in Spitsbergen. The arctic distribution of M. hirsuticornis mainly depends on temperature, which regulates the speed of individual development. But this can only be understood together with the length of time, during which suitable life conditions are given. Physiological adaptations to life in waters in high latitudes could not be found, in spite of the extreme northern occurrence of M. hirsuticornis.

Seawater carbonate chemistry, Acropora digitifera growth and skeletal U/Ca ratios during experiments, 2011

The impact of ocean acidification caused by the increasing atmospheric CO2 has been studied in marine calcifiers, including hermatypic corals. However, the effect of elevated pCO2 on the early developmental life-cycle stage of corals has been little studied. In this study, we reared polyps of Acropora digitifera in seawater at pHT 6.55, 7.31, 7.64, 7.77, and 8.03, controlled by CO2 bubbling. We measured the dry weights of polyp skeletons after the 40-d experiment to investigate the relationship between the seawater aragonite saturation state and polyp growth. In addition, we measured skeletal U/Ca ratio to estimate their pH dependence. Skeletal weights of coral polyps increased with the aragonite saturation state and reached an apparent saturation plateau above pH 7.77. U/Ca ratios had a strong inverse relationship with pH and a negligible relationship with skeletal growth rate (polyp weight), suggesting that skeletal U/Ca could be useful for reconstructing paleo-pH.

Seawater carbonate chemistry and Strongylocentrotus droebachiensis larval and juvenile survival and reporductive processes, 2012

Anthropogenic CO2 emissions are acidifying the world's oceans. A growing body of evidence demonstrates that ocean acidification can impact survival, growth, development and physiology of marine invertebrates. Here we tested the impact of long term (up to 16 months) and trans life-cycle (adult, embryo/larvae and juvenile) exposure to elevated pCO2 (1200 µatm, compared to control 400 µatm) on the green sea urchin Strongylocentrotus droebachiensis. Female fecundity was decreased 4.5 fold when acclimated to elevated pCO2 for 4 months during reproductive conditioning while no difference was observed in females acclimated for 16 months. Moreover, adult pre-exposure for 4 months to elevated pCO2, had a direct negative impact on subsequent larval settlement success. Five to nine times fewer offspring reached the juvenile stage in cultures using gametes collected from adults previously acclimated to high pCO2 for 4 months. However, no difference in larval survival was observed when adults were pre-exposed for 16 months to elevated pCO2. pCO2 had no direct negative impact on juvenile survival except when both larvae and juveniles were raised in elevated pCO2. These negative effects on settlement success and juvenile survival can be attributed to carry-over effects from adults to larvae and from larvae to juveniles. Our results support the contention that adult sea urchins can acclimate to moderately elevated pCO2 in a matter of a few months and that carry-over effects can exacerbate the negative impact of ocean acidification on larvae and juveniles.

Seawater carbonate chemistry and giant kelp Macrocystis pyrifera reproduction processes during experiments, 2011

The worldwide effects of ocean acidification (OA) on marine species are a growing concern. In temperate coastal seas, seaweeds are dominant primary producers that create complex habitats and supply energy to higher trophic levels. Studies on OA and macroalgae have focused on calcifying species and adult stages but, critically, they have overlooked the microscopic stages of the reproductive life cycle, which, for other anthropogenic stress e.g. UV-B radiation, are the most susceptible life-history phase. Also, environmental cues and stressors can cause changes in the sex ratio which has implications for the mating system and recruitment success. Here, we report the effects of pH (7.59-8.50) on meiospore germination and sex determination for the giant kelp, Macrocystis pyrifera (Laminariales), in the presence and absence of additional dissolved inorganic carbon (DIC). Lowered pH (7.59-7.60, using HCl-only) caused a significant reduction in germination, while added DIC had the opposite effect, indicating that increased CO2 at lower pH ameliorates physiological stress. This finding also highlights the importance of appropriate manipulation of seawater carbonate chemistry when testing the effects of ocean acidification on photosynthetic organisms. The proportion of male to female gametophytes did not vary significantly between treatments suggesting that pH was not a primary environmental modulator of sex. Relative to the baseline (pH 8.19), gametophytes were 32% larger under moderate OA (pH 7.86) compared to their size (10% increase) under extreme OA (pH 7.61). This study suggests that metabolically-active cells can compensate for the acidification of seawater. This homeostatic function minimises the negative effects of lower pH (high H+ ions) on cellular activity. The 6-9% reduction in germination success under extreme OA suggests that meiospores of M.pyrifera may be resistant to future ocean acidification.