Complex I (NADH:ubiquinone oxidoreductase) is central to cellular NAD + recycling and accounts for approximately 40% of mitochondrial ATP production. To understand how complex I function impacts respiration and plant development, we isolated Arabidopsis (Arabidopsis thaliana) lines that lack complex I activity due to the absence of the catalytic subunit NDUFV1 (for NADH:ubiquinone oxidoreductase flavoprotein1) and compared these plants with ndufs4 (for NADH:ubiquinone oxidoreductase Fe-S protein4) mutants possessing trace amounts of complex I. Unlike ndufs4 plants, ndufv1 lines were largely unable to establish seedlings in the absence of externally supplied sucrose. Measurements of mitochondrial respiration and ATP synthesis revealed that compared with ndufv1, the complex I amounts retained by ndufs4 did not increase mitochondrial respiration and oxidative phosphorylation capacities. No major differences were seen in the mitochondrial proteomes, cellular metabolomes, or transcriptomes between ndufv1 and ndufs4. The analysis of fluxes through the respiratory pathway revealed that in ndufv1, fluxes through glycolysis and the tricarboxylic acid cycle were dramatically increased compared with ndufs4, which showed near wild-type-like fluxes. This indicates that the strong growth defects seen for plants lacking complex I originate from a switch in the metabolic mode of mitochondria and an up-regulation of respiratory fluxes. Partial reversion of these phenotypes when traces of active complex I are present suggests that complex I is essential for plant development and likely acts as a negative regulator of respiratory fluxes.In most eukaryotic organisms, energy is mainly provided by cellular respiration, which is composed of three main pathways. Glycolysis in the cytosol, and additionally in the plastids of plants, degrades sugars into pyruvate. The tricarboxylic acid (TCA) cycle, which largely resides in the mitochondrial matrix, further dissimilates pyruvate into CO 2 . These two pathways generate reduced cofactors, mostly NADH. The oxidative phosphorylation (OXPHOS) system couples cofactor recycling with ATP production. The electron transfer chain (ETC) located in the mitochondrial inner membrane (IM) uses the redox energy of the reduced cofactors to create an electrochemical gradient across the IM. This gradient is then used by the ATP synthase to convert ADP to ATP, which is subsequently exported from the mitochondria to fuel cellular metabolism and sustain housekeeping functions and growth.The ETC is composed of four large multiprotein complexes. The first of these complexes is the NADHubiquinone oxidoreductase, also called complex I. It plays a crucial role in recycling NAD + for the TCA cycle, and its activity is responsible for about 40% of the total proton pumping across the IM (Wikström, 1984;Galkin et al., 2006). In plants, additional NADH dehydrogenases located on both sides of the IM are present (for review, see Rasmusson et al., 2008). These enzymes can recycle NAD + for use in glycolysis and the TCA cyc...

Single-molecule localization microscopy (SMLM) has the potential to quantify the diversity in spatial arrangements of molecules in intact cells. However, this requires that the single-molecule emitters are localized with ultrahigh precision irrespective of the sample format and the length of the data acquisition. We advance SMLM to enable direct distance measurements between molecules in intact cells on the scale between 1 and 20 nm. Our actively stabilized microscope combines three-dimensional real-time drift corrections and achieves a stabilization of <1 nm and localization precision of ~1 nm. To demonstrate the biological applicability of the new microscope, we show a 4-to 7-nm difference in spatial separations between signaling T cell receptors and phosphatases (CD45) in active and resting T cells. In summary, by overcoming the major bottlenecks in SMLM imaging, it is possible to generate molecular images with nanometer accuracy and conduct distance measurements on the biological relevant length scales. Ultraprecise single-molecule localization microscopy enables in situ distance measurements in intact cells. Sci. Adv. 6, eaay8271 (2020).

A well-defined scale calibration in flow cytometry can improve many aspects of data acquisition such as cytometer setup, instrument comparison and sample comparison. The theory for scale calibration was proposed by Steen over two decades ago, but it has never been put into regular use due to the lack of a widely available precision light source. The introduction of such a light source, the quantiFlash , gave this possibility. Here, we describe how this light source can be used to characterize a cytometer's PMT performance. We, therefore, characterized the instrument's response over the entire PMT voltage range. As a consequence, we propose a practical method to characterize a cytometer's signal-to-noise ratio (SNR) and dynamic range (DNR). This allows the selection of a voltage/gain corresponding to a PMT's maximum efficiency and hence the lowest electronic noise, which can help with experiment design. We further introduced a decibel (dB) scale for the presentation of SNR and DNR values. SNR and DNR are stand-alone values that allow the direct comparison of different instruments. Finally, with this method, it becomes clear that increased SNR comes at the expense of DNR and thus the limiting factor of modern cytometers is the DNR. © 2017 International Society for Advancement of Cytometry.

Heterosis, the greater vigor of hybrids compared to their parents, has been exploited in maize breeding for more than 100 years to produce ever better performing elite hybrids of increased yield. Despite extensive research, the underlying mechanisms shaping the extent of heterosis are not well understood, rendering the process of selecting an optimal set of parental lines tedious. This study is based on a dataset consisting of 112 metabolite levels in young roots of four parental maize inbred lines and their corresponding twelve hybrids, along with the roots' biomass as a heterotic trait. Because the parental biomass is a poor predictor for hybrid biomass, we established a model framework to deduce the biomass of the hybrid from metabolite profiles of its parental lines. In the proposed framework, the hybrid metabolite levels are expressed relative to the parental levels by incorporating the standard concept of additivity/dominance, which we name the Combined Relative Level (CRL). Our modeling strategy includes a feature selection step on the parental levels which are demonstrated to be predictive of CRL across many hybrid metabolites. We demonstrate that these selected parental metabolites are further predictive of hybrid biomass. Our approach directly employs the diallel structure in a multivariate fashion, whereby we attempt to not only predict macroscopic phenotype (biomass), but also molecular phenotype (metabolite profiles). Therefore, our study provides the first steps for further investigations of the genetic determinants to metabolism and, ultimately, growth. Finally, our success on the small-scale experiments implies a valid strategy for large-scale experiments, where parental metabolite profiles may be used together with profiles of selected hybrids as a training set to predict biomass of all possible hybrids.

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In recent years, multispectral flow cytometry systems have come to attention. They differ from conventional flow cytometers in two key ways: a multispectral flow cytometer collects the full spectral information at the single cell level and the detector configuration is fixed and not explicitly tuned to a particular staining panel. This brings about clear hardware advantages, as a closed system should be highly stable, and ease-of-use should be improved if used in conjunction with custom unmixing software. An open question remains: what are the benefits of multispectral over conventional flow cytometry in terms of sensitivity and resolution? To probe this, we use Q (detection efficiency) and B (background) values and develop a novel "multivariate population overlap factor" to characterize the cytometer performance. To verify the usefulness of our factor, we perform representative experiments and compare our overlap factor to Q and B. Finally, we conclude that the increased light collection of multispectral flow cytometry does indeed lead to increased sensitivity, an improved detection limit, and a higher resolution.

R scripts are available via https://fccf.mpiib-berlin.mpg.de/daten/drfz/bioinformatics/with{username,password}={bioinformatics,Sar=Gac4}.

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