Investigating centre of mass stabilisation as the goal of posture and movement coordination during human whole body reaching

In the light of experimental results showing significant forward centre of mass (CoM) displacements within the base of support, this study investigated if whole body reaching movements can be executed whilst keeping the CoM fixed in the horizontal axis. Using kinematic simulation techniques, angular configurations were recreated from experimental data imposing two constraints: a constant horizontal position of the CoM and an identical trajectory of the hand to grasp an object. The comparison between recorded and simulated trials showed that stabilisation of the CoM was associated with greater backward hip displacements, which became more marked with increasing object distance. This was in contrast to recorded trials showing reductions in backward hip displacements with increasing distance. Results also showed that modifications to angular displacements were necessary only at the shoulder and hip joints, but that these modifications were within the limits of joint mobility. The analysis of individual joint torques revealed that the pattern and timing of simulated trials were similar to those recorded experimentally. Peak joint torque values showed particularly that keeping the CoM at a constant horizontal position resulted in significantly smaller ankle peak flexor and extensor torques. It may be concluded from this study that `stabilising' the CoM during human whole body reaching represents a feasible strategy, but not the one chosen by subjects under experimental conditions. Our results also do not support the idea of the CoM as the stabilised reference value for the coordination between posture and goal-directed movements. Received: 22 September 1998 / Accepted in revised form: 2 June 1999     

Drivers of vegetative dormancy across herbaceous perennial plant species

Vegetative dormancy, that is the temporary absence of aboveground growth for ≥ 1 year, is paradoxical, because plants cannot photosynthesise or flower during dormant periods. We test ecological and evolutionary hypotheses for its widespread persistence. We show that dormancy has evolved numerous times. Most species displaying dormancy exhibit life‐history costs of sprouting, and of dormancy. Short‐lived and mycoheterotrophic species have higher proportions of dormant plants than long‐lived species and species with other nutritional modes. Foliage loss is associated with higher future dormancy levels, suggesting that carbon limitation promotes dormancy. Maximum dormancy duration is shorter under higher precipitation and at higher latitudes, the latter suggesting an important role for competition or herbivory. Study length affects estimates of some demographic parameters. Our results identify life historical and environmental drivers of dormancy. We also highlight the evolutionary importance of the little understood costs of sprouting and growth, latitudinal stress gradients and mixed nutritional modes.     

Integration of the Rosetta suite with the python software stack via reproducible packaging and core programming interfaces for distributed simulation

The Rosetta software suite for macromolecular modeling is a powerful computational toolbox for protein design, structure prediction, and protein structure analysis. The development of novel Rosetta‐based scientific tools requires two orthogonal skill sets: deep domain‐specific expertise in protein biochemistry and technical expertise in development, deployment, and analysis of molecular simulations. Furthermore, the computational demands of molecular simulation necessitate large scale cluster‐based or distributed solutions for nearly all scientifically relevant tasks. To reduce the technical barriers to entry for new development, we integrated Rosetta with modern, widely adopted computational infrastructure. This allows simplified deployment in large‐scale cluster and cloud computing environments, and effective reuse of common libraries for simulation execution and data analysis. To achieve this, we integrated Rosetta with the Conda package manager; this simplifies installation into existing computational environments and packaging as docker images for cloud deployment. Then, we developed programming interfaces to integrate Rosetta with the PyData stack for analysis and distributed computing, including the popular tools Jupyter, Pandas, and Dask. We demonstrate the utility of these components by generating a library of a thousand de novo disulfide‐rich miniproteins in a hybrid simulation that included cluster‐based design and interactive notebook‐based analyses. Our new tools enable users, who would otherwise not have access to the necessary computational infrastructure, to perform state‐of‐the‐art molecular simulation and design with Rosetta.     

The Protein Kinase CK2 Holoenzyme Structure Supports Proposed Models of Autoregulation and Trans-Autophosphorylation

Eukaryotic protein kinases are typically strictly controlled by second messenger binding, protein/protein interactions, dephosphorylations or similar processes. None of these regulatory mechanisms is known to work for protein kinase CK2 (former name “casein kinase 2”), an acidophilic and constitutively active eukaryotic protein kinase. CK2 predominantly exists as a heterotetrameric holoenzyme composed of two catalytic subunits (CK2α) complexed to a dimer of non-catalytic subunits (CK2β). One model of CK2 regulation was proposed several times independently by theoretical docking of the first CK2 holoenzyme structure. According to this model, the CK2 holoenzyme forms autoinhibitory aggregates correlated with trans-autophosphorylation and driven by the down-regulatory affinity between an acidic loop of CK2β and the positively charged substrate binding region of CK2α from a neighboring CK2 heterotetramer. Circular trimeric aggregates in which one-half of the CK2α chains show the predicted inhibitory proximity between those regions were detected within the crystal packing of the human CK2 holoenzyme. Here, we present further in vitro support of the “regulation-by-aggregation” model by an alternative crystal form in which CK2 tetramers are arranged as approximately linear aggregates coinciding essentially with the early predictions. In this assembly, the substrate binding region of every CK2α chain is blocked by a CK2β acidic loop from a neighboring tetramer. We found these crystals with CK2^Andante that contains a CK2β variant mutated in a CK2α-contact helix and described to be responsible for a prolonged circadian rhythm in Drosophila. The increased propensity of CK2^Andante to form aggregates with completely blocked active sites may contribute to this phenotype.     

Expression of TWISTED DWARF1 lacking its in‐plane membrane anchor leads to increased cell elongation and hypermorphic growth

Plant growth is achieved predominantly by cellular elongation, which is thought to be controlled on several levels by apoplastic auxin. Auxin export into the apoplast is achieved by plasma membrane efflux catalysts of the PIN‐FORMED (PIN) and ATP‐binding cassette protein subfamily B/phosphor‐glycoprotein (ABCB/PGP) classes; the latter were shown to depend on interaction with the FKBP42, TWISTED DWARF1 (TWD1). Here by using a transgenic approach in combination with phenotypical, biochemical and cell biological analyses we demonstrate the importance of a putative C‐terminal in‐plane membrane anchor of TWD1 in the regulation of ABCB‐mediated auxin transport. In contrast with dwarfed twd1 loss‐of‐function alleles, TWD1 gain‐of‐function lines that lack a putative in‐plane membrane anchor (HA–TWD1‐C_t) show hypermorphic plant architecture, characterized by enhanced stem length and leaf surface but reduced shoot branching. Greater hypocotyl length is the result of enhanced cell elongation that correlates with reduced polar auxin transport capacity for HA–TWD1‐C_t. As a consequence, HA–TWD1‐C_t displays higher hypocotyl auxin accumulation, which is shown to result in elevated auxin‐induced cell elongation rates. Our data highlight the importance of C‐terminal membrane anchoring for TWD1 action, which is required for specific regulation of ABCB‐mediated auxin transport. These data support a model in which TWD1 controls lateral ABCB1‐mediated export into the apoplast, which is required for auxin‐mediated cell elongation.     

CD36 initiates the secretory phenotype during the establishment of cellular senescence

Cellular senescence is a unique cell fate characterized by stable proliferative arrest and the extensive production and secretion of various inflammatory proteins, a phenomenon known as the senescence‐associated secretory phenotype (SASP). The molecular mechanisms responsible for generating a SASP in response to senescent stimuli remain largely obscure. Here, using unbiased gene expression profiling, we discover that the scavenger receptor CD36 is rapidly upregulated in multiple cell types in response to replicative, oncogenic, and chemical senescent stimuli. Moreover, ectopic CD36 expression in dividing mammalian cells is sufficient to initiate the production of a large subset of the known SASP components via activation of canonical Src–p38–NF‐κB signaling, resulting in the onset of a full senescent state. The secretome is further shown to be ligand‐dependent, as amyloid‐beta (Aβ) is sufficient to drive CD36‐dependent NF‐κB and SASP activation. Finally, loss‐of‐function experiments revealed a strict requirement for CD36 in secretory molecule production during conventional senescence reprogramming. Taken together, these results uncover the Aβ–CD36–NF‐κB signaling axis as an important regulator of the senescent cell fate via induction of the SASP.     

The açaí flavonoid velutin is a potent anti-inflammatory agent: blockade of LPS-mediated TNF-α and IL-6 production through inhibiting NF-κB activation and MAPK pathway

Recent studies have shown that some flavonoids are modulators of proinflammatory cytokine production. In this study, velutin, a unique flavone isolated from the pulp of açaí fruit (Euterpe oleracea Mart.), was examined for its effects in reducing lipopolysaccharide-induced proinflammatory cytokine tumor necrosis factor (TNF)-α and interleukin (IL)-6 production in RAW 264.7 peripheral macrophages and mice peritoneal macrophages. Three other structurally similar and well-studied flavones, luteolin, apigenin and chrysoeriol, were included as controls and for comparative purposes. Velutin exhibited the greatest potency among all flavones in reducing TNF-α and IL-6 production. Velutin also showed the strongest inhibitory effect in nuclear factor (NF)-κB activation (as assessed by secreted alkaline phosphatase reporter assay) and exhibited the greatest effects in blocking the degradation of inhibitor of NF-κB as well as in inhibiting mitogen-activated protein kinase p38 and JNK phosphorylation; all of these are important signaling pathways involved in production of TNF-α and IL-6. The present study led to the discovery of a strong anti-inflammatory flavone, velutin. This compound effectively inhibited the expression of proinflammatory cytokines TNF-α and IL-6 in low micromole levels by inhibiting NF-κB activation and p38 and JNK phosphorylation.     

Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements

Transfer RNAs (tRNAs) are present in all types of cells as well as in organelles. tRNAs of animal mitochondria show a low level of primary sequence conservation and exhibit 'bizarre' secondary structures, lacking complete domains of the common cloverleaf. Such sequences are hard to detect and hence frequently missed in computational analyses and mitochondrial genome annotation. Here, we introduce an automatic annotation procedure for mitochondrial tRNA genes in Metazoa based on sequence and structural information in manually curated covariance models. The method, applied to re-annotate 1876 available metazoan mitochondrial RefSeq genomes, allows to distinguish between remaining functional genes and degrading 'pseudogenes', even at early stages of divergence. The subsequent analysis of a comprehensive set of mitochondrial tRNA genes gives new insights into the evolution of structures of mitochondrial tRNA sequences as well as into the mechanisms of genome rearrangements. We find frequent losses of tRNA genes concentrated in basal Metazoa, frequent independent losses of individual parts of tRNA genes, particularly in Arthropoda, and wide-spread conserved overlaps of tRNAs in opposite reading direction. Direct evidence for several recent Tandem Duplication-Random Loss events is gained, demonstrating that this mechanism has an impact on the appearance of new mitochondrial gene orders.     

Segmental territories along the cardinal veins generate lymph sacs via a ballooning mechanism during embryonic lymphangiogenesis in mice

During lymphangiogenesis in the mammalian embryo, a subset of vascular endothelial cells in the cardinal veins is reprogrammed to adopt a lymphatic endothelial fate. The prevailing model of lymphangiogenesis contends that these lymphatic precursor cells migrate away from the cardinal veins and reassemble peripherally as lymph sacs from which a lymphatic vasculature is generated. However, this model fails to account for a number of observations that, as a result, have remained anecdotal. Here, we use optical projection tomography, confocal microscopy and in vivo live imaging to uncover three key stages of lymphatic vascular morphogenesis in the mouse embryo at high resolution. First, we define territories or "pre-lymphatic clusters" of Prox1-positive lymphatic endothelial progenitor cells along the antero-posterior axis of the cardinal veins. Second, these pre-lymphatic clusters undergo progressive extrusion ("ballooning") to generate primitive lymph sacs. Third, lymphatic vessels emerge by a combination of mechanisms including sprouting from the lymph sacs and direct delamination of streams of cells from the cardinal veins. Our data support a new model for lymphatic vascular patterning and morphogenesis, as a basis for identifying the molecular cues governing these processes.