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[
Methods Enzymol,
2008]
Apoptosome refers to the multimeric protein complex that mediates activation of an initiator caspase at the onset of apoptosis. This chapter describes the assembly of three related apoptosomes from mammals, fruit flies, and worms. The assembly of the mammalian apoptosome, which is responsible for the activation of caspase-9, involves Apaf-1 and requires cytochrome c and ATP/dATP binding. Assembly of the apoptosome in Drosophila melanogaster, which activates caspase-9 homologue Dronc, involves the Apaf-1 homologue known as Dark/Hac-1/Dapaf-1. In Caenorhabditis elegans, assembly of the CED-4 apoptosome requires EGL-1-mediated dissociation of CED-9 (a Bcl-2 homologue) from the CED-4-CED-9 complex and subsequent oligomerization of CED-4. Recent biochemical and structural investigation revealed insights into the assembly and function of the various apoptosomes.
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[
MicroPubl Biol,
2021]
Parkinson's disease (PD) patients have been shown to benefit greatly from intense physical activity (Schenkman et al. 2018). Recent studies have demonstrated that exercise causes changes in the levels of alpha-synuclein aggregate species, a hallmark of PD, in different mammalian animal models (Koo and Cho 2017; Shin et al. 2017; Zhou et al. 2017; Minakaki et al. 2019). However, questions still remain about how exercise affects specifically native alpha-synuclein protein species directly after the cessation of exercise and the longer-term downstream effects which exercise may have on organismal health. It was recently discovered that periods of thrashing in liquid solution, otherwise called swimming exercise, in C. elegans worms, induces many mechanisms invoked during mammalian exercise (Laranjeiro et al. 2017). This has provided an avenue for studying exercise conditions in various C. elegans models of neurodegeneration (Laranjeiro et al. 2019). In order to study the effect of exercise on native human alpha-synuclein protein species, we utilized the NL5901- pkIs2386 worm model of Parkinson's which contains human alpha-synuclein tagged to a yellow fluorescent protein (YFP) in the muscle cells (van Ham et al. 2008). We performed tissue analysis via Blue Native (BN) page westerns and confocal microscopy. In addition, because pharyngeal pumping is decreased while worms are swimming, we controlled for this effect by exposing worms in parallel to a period of food restriction (FR) conditions (Vidal-Gadea et al. 2012). We also performed thrashing assays to assess longer term downstream behavioral effects on the animals after either exercise or food restriction conditions.
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[
MicroPubl Biol,
2021]
RMD-1 was discovered as a cytoplasmic regulator of microtubule dynamics in C. elegans and several highly homologous proteins were inferred from the C. elegans and human genome sequences (Oishi et al., 2007). One of the human homologs, RMD-3/PTPIP51, has an N-terminal extension relative to other RMDs that targets it to the mitochondrial outer membrane and which binds the endoplasmic reticulum (ER) protein VAPB (De Vos et al., 2012). This interaction mediates tethering of mitochondria to the ER in human cells (Stoica et al., 2014). None of the C. elegans RMDs have sequence homology with the N-terminal extension found on human RMD-3/PTPIP51, however, C. elegans RMD-2 has an N-terminal extension relative to the other RMDs and this extension has potential to form a transmembrane helix as determined by TMpred release 25 (https://embnet.vital-it.ch/software/TMPRED_form.html). RMD-2 is present in sperm whereas RMD-3 and RMD-6 are highly enriched in sperm (Ma et al., 2014). Paternal mitochondria are eventually degraded in the embryo (Sato and Sato, 2011). However, they are maintained, along with other sperm contents, at the opposite end of the zygote from the female meiotic spindle during meiosis (Fig. 1). We hypothesized that RMD-2, 3 and 6 on paternal mitochondria bind to the VAPB homolog, VPR-1, on maternal ER at fertilization to tether the sperm contents at the future posterior end of the zygote.
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[
Ann N Y Acad Sci,
1993]
Excitation-contraction coupling is one of the interesting mechanisms to be elucidated from the point of view of calcium signal transduction in muscle contraction. Calcium channel genes were cloned and sequenced as the receptors of dihydropyridine and ryanodine receptor in mammals. Takeshima et al. confirmed that the ryanodine receptor has a molecular mass of 500,000 daltons with a large portion at the N-terminal, which was observed as a foot structure by electron microscopy, and the transmembrane domain at the C-terminal. The molecular architecture of the receptor was close to that of rabbit, mink, and human. The functional loss of the molecule causes malignant hyperthermia of swine. The ryanodine binding site and the channel-forming transmembrane structure were clarified by several other observations.
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[
Neuron,
2006]
Recent studies have begun to shed light on the molecular guidance cues controlling anterior-posterior axon guidance. Two recent studies in the current issue of Developmental Cell show that Wnts play critical roles in patterning processes and directing neuronal migration in C. elegans. Together with previous findings in vertebrates and flies, these new results establish conserved function of Wnts in A-P guidance.
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[
Bioinformatics,
2012]
MOTIVATION: Normal development of multicellular organisms is regulated by a highly complex process in which a set of precursor cells proliferate, differentiate and move, forming over time a functioning tissue. To handle their complexity, developmental systems can be studied over distinct scales. The dynamics of each scale is determined by the collective activity of entities at the scale below it. RESULTS: I describe a multi-scale computational approach for modeling developmental systems and detail the methodology through a synthetic example of a developmental system that retains key features of real developmental systems. I discuss the simulation of the system as it emerges from cross-scale and intra-scale interactions and describe how an in silico study can be carried out by modifying these interactions in a way that mimics in vivo experiments. I highlight biological features of the results through a comparison with findings in Caenorhabditis elegans germline development and finally discuss about the applications of the approach in real developmental systems and propose future extensions. AVAILABILITY AND IMPLEMENTATION: The source code of the model of the synthetic developmental system can be found in www.wisdom.weizmann.ac.il/~yaki/MultiScaleModel. CONTACT: yaki.setty@gmail.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
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[
Computer Applications in the Biosciences,
1994]
We present a dynamic programming algorithm for computing a best global alignment of two sequences. The proposed algorithm is robust in identifying any of several global relationships between two sequences. The algorithm delivers a best alignment of two sequences in linear space and quadratic time. We also describe a multiple alignment algorithm based on the pairwise algorithm. Both algorithms have been implemented as portable C programs. Experimental results indicate that for a commonly used set of gap penalties, the new programs produce more satisfactory alignments on sequences of various lengths than some existing pairwise and multiple programs based on the dynamic programming algorithm of Needleman and Wunsch.
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[
Tanpakushitsu Kakusan Koso,
1993]
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[
Cell Metab,
2010]
Does life span extension come with a reproductive trade-off? In a recent report published in Nature, Greer et al. (2010) show that in the nematode worm C. elegans, life span extension, as a consequence of deficiencies in histone methylation, requires an intact germline and ongoing fertility.
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Sun J, Pommier Y, SenGupta T, Su Y, Duncan LH, Murphy E, Glidewell M, Smith C, Rey-Suarez I, Bao L, Christensen R, Roy S, Fischer R, Combs C, Upadhyaya A, Wu X, Daniels JS, Patel A, Shi YB, Han X, Shroff H, La Riviere P, Colon-Ramos D, Liu J, Chen J, Sun Y, Wu Y
[
Nature,
2021]
Confocal microscopy<sup>1</sup> remains a major workhorse in biomedical optical microscopy owing to its reliability and flexibility in imaging various samples, but suffers from substantial point spread function anisotropy, diffraction-limited resolution, depth-dependent degradation in scattering samples and volumetric bleaching<sup>2</sup>. Here we address these problems, enhancing confocal microscopy performance from the sub-micrometre to millimetre spatial scale and the millisecond to hour temporal scale, improving both lateral and axial resolution more than twofold while simultaneously reducing phototoxicity. We achieve these gains using an integrated, four-pronged approach: (1) developing compact line scanners that enable sensitive, rapid, diffraction-limited imaging over large areas; (2) combining line-scanning with multiview imaging, developing reconstruction algorithms that improve resolution isotropy and recover signal otherwise lost to scattering; (3) adapting techniques from structured illumination microscopy, achieving super-resolution imaging in densely labelled, thick samples; (4) synergizing deep learning with these advances, further improving imaging speed, resolution and duration. We demonstrate these capabilities on more than 20 distinct fixed and live samples, including protein distributions in single cells; nuclei and developing neurons in Caenorhabditis elegans embryos, larvae and adults; myoblasts in imaginal disks of Drosophila wings; and mouse renal, oesophageal, cardiac and brain tissues.