scholarly journals Budding yeast chromatin is dispersed in a crowded nucleoplasm in vivo

2016 ◽  
Vol 27 (21) ◽  
pp. 3357-3368 ◽  
Author(s):  
Chen Chen ◽  
Hong Hwa Lim ◽  
Jian Shi ◽  
Sachiko Tamura ◽  
Kazuhiro Maeshima ◽  
...  

Chromatin organization has an important role in the regulation of eukaryotic systems. Although recent studies have refined the three-dimensional models of chromatin organization with high resolution at the genome sequence level, little is known about how the most fundamental units of chromatin—nucleosomes—are positioned in three dimensions in vivo. Here we use electron cryotomography to study chromatin organization in the budding yeast Saccharomyces cerevisiae. Direct visualization of yeast nuclear densities shows no evidence of 30-nm fibers. Aside from preribosomes and spindle microtubules, few nuclear structures are larger than a tetranucleosome. Yeast chromatin does not form compact structures in interphase or mitosis and is consistent with being in an “open” configuration that is conducive to high levels of transcription. From our study and those of others, we propose that yeast can regulate its transcription using local nucleosome–nucleosome associations.

2016 ◽  
Author(s):  
Chen Chen ◽  
Hong Hwa Lim ◽  
Jian Shi ◽  
Sachiko Tamura ◽  
Kazuhiro Maeshima ◽  
...  

AbstractChromatin organization has an important role in the regulation of eukaryotic systems. While recent studies have refined the 3-D models of chromatin organization with high resolution at the genome sequence level, little is known about how the most fundamental units of chromatin — nucleosomes — are positioned in 3-D in vivo. Here we have used electron cryotomography to study chromatin organization in the budding yeast S. cerevisiae. Direct visualization of yeast nuclear densities shows no evidence of 30-nm chromatin fibers. Aside from pre-ribosomes and spindle microtubules, few nuclear structures are larger than a tetranucleosome. Yeast chromatin does not form compact structures in interphase or mitosis and is consistent with being in an “open” configuration that is conducive to high levels of transcription. In the absence of higher-order chromatin packing, we propose that yeast can regulate its transcription using local nucleosome-nucleosome associations.


1987 ◽  
Vol 58 (4) ◽  
pp. 832-849 ◽  
Author(s):  
D. Tweed ◽  
T. Vilis

1. This paper develops three-dimensional models for the vestibuloocular reflex (VOR) and the internal feedback loop of the saccadic system. The models differ qualitatively from previous, one-dimensional versions, because the commutative algebra used in previous models does not apply to the three-dimensional rotations of the eye. 2. The hypothesis that eye position signals are generated by an eye velocity integrator in the indirect path of the VOR must be rejected because in three dimensions the integral of angular velocity does not specify angular position. Computer simulations using eye velocity integrators show large, cumulative gaze errors and post-VOR drift. We describe a simple velocity to position transformation that works in three dimensions. 3. In the feedback control of saccades, eye position error is not the vector difference between actual and desired eye positions. Subtractive feedback models must continuously adjust the axis of rotation throughout a saccade, and they generate meandering, dysmetric gaze saccades. We describe a multiplicative feedback system that solves these problems and generates fixed-axis saccades that accord with Listing's law. 4. We show that Listing's law requires that most saccades have their axes out of Listing's plane. A corollary is that if three pools of short-lead burst neurons code the eye velocity command during saccades, the three pools are not yoked, but function independently during visually triggered saccades. 5. In our three-dimensional models, we represent eye position using four-component rotational operators called quaternions. This is not the only algebraic system for describing rotations, but it is the one that best fits the needs of the oculomotor system, and it yields much simpler models than do rotation matrix or other representations. 6. Quaternion models predict that eye position is represented on four channels in the oculomotor system: three for the vector components of eye position and one inversely related to gaze eccentricity and torsion. 7. Many testable predictions made by quaternion models also turn up in models based on other mathematics. These predictions are therefore more fundamental than the specific models that generate them. Among these predictions are 1) to compute eye position in the indirect path of the VOR, eye or head velocity signals are multiplied by eye position feedback and then integrated; consequently 2) eye position signals and eye or head velocity signals converge on vestibular neurons, and their interaction is multiplicative.(ABSTRACT TRUNCATED AT 400 WORDS)


2019 ◽  
Author(s):  
Vlasta Lungova ◽  
Susan Thibeault

Abstract Development of treatments for vocal dysphonia has been inhibited by lack of human vocal fold (VF) mucosa models because of difficulty in procuring VF epithelial cells, epithelial cells’ limited proliferative capacity and absence of cell lines. We report development of engineered VF mucosae from hiPSC, transfected via TALEN constructs for green fluorescent protein, that mimic development of VF epithelial cells in utero. Modulation of FGF signaling achieves stratified squamous epithelium from definitive and anterior foregut derived cultures. Robust culturing of these cells on collagen-fibroblast constructs produces three-dimensional models comparable to in vivo VF mucosa.


Author(s):  
J. S. An ◽  
A. A. Espinoza Orías ◽  
H. S. An ◽  
G. B. J. Andersson ◽  
N. Inoue

To accurately quantify the anatomic parameters of the lumbar spinal bony canal using a novel three-dimensional imaging technique based on in vivo CT three-dimensional models.


Cells ◽  
2020 ◽  
Vol 9 (3) ◽  
pp. 672 ◽  
Author(s):  
Zain Akram ◽  
Ishtiaq Ahmed ◽  
Heike Mack ◽  
Ramandeep Kaur ◽  
Richard C. Silva ◽  
...  

The budding yeast Saccharomyces cerevisiae has an actin cytoskeleton that comprises a set of protein components analogous to those found in the actin cytoskeletons of higher eukaryotes. Furthermore, the actin cytoskeletons of S. cerevisiae and of higher eukaryotes have some similar physiological roles. The genetic tractability of budding yeast and the availability of a stable haploid cell type facilitates the application of molecular genetic approaches to assign functions to the various actin cytoskeleton components. This has provided information that is in general complementary to that provided by studies of the equivalent proteins of higher eukaryotes and hence has enabled a more complete view of the role of these proteins. Several human functional homologues of yeast actin effectors are implicated in diseases. A better understanding of the molecular mechanisms underpinning the functions of these proteins is critical to develop improved therapeutic strategies. In this article we chose as examples four evolutionarily conserved proteins that associate with the actin cytoskeleton: (1) yeast Hof1p/mammalian PSTPIP1, (2) yeast Rvs167p/mammalian BIN1, (3) yeast eEF1A/eEF1A1 and eEF1A2 and (4) yeast Yih1p/mammalian IMPACT. We compare the knowledge on the functions of these actin cytoskeleton-associated proteins that has arisen from studies of their homologues in yeast with information that has been obtained from in vivo studies using live animals or in vitro studies using cultured animal cell lines.


2004 ◽  
Vol 15 (4) ◽  
pp. 1519-1532 ◽  
Author(s):  
Jeffrey N. Molk ◽  
Scott C. Schuyler ◽  
Jenny Y. Liu ◽  
James G. Evans ◽  
E. D. Salmon ◽  
...  

In the budding yeast Saccharomyces cerevisiae the mitotic spindle must be positioned along the mother-bud axis to activate the mitotic exit network (MEN) in anaphase. To examine MEN proteins during mitotic exit, we imaged the MEN activators Tem1p and Cdc15p and the MEN regulator Bub2p in vivo. Quantitative live cell fluorescence microscopy demonstrated the spindle pole body that segregated into the daughter cell (dSPB) signaled mitotic exit upon penetration into the bud. Activation of mitotic exit was associated with an increased abundance of Tem1p-GFP and the localization of Cdc15p-GFP on the dSPB. In contrast, Bub2p-GFP fluorescence intensity decreased in mid-to-late anaphase on the dSPB. Therefore, MEN protein localization fluctuates to switch from Bub2p inhibition of mitotic exit to Cdc15p activation of mitotic exit. The mechanism that elevates Tem1p-GFP abundance in anaphase is specific to dSPB penetration into the bud and Dhc1p and Lte1p promote Tem1p-GFP localization. Finally, fluorescence recovery after photobleaching (FRAP) measurements revealed Tem1p-GFP is dynamic at the dSPB in late anaphase. These data suggest spindle pole penetration into the bud activates mitotic exit, resulting in Tem1p and Cdc15p persistence at the dSPB to initiate the MEN signal cascade.


2003 ◽  
Vol 14 (12) ◽  
pp. 4871-4884 ◽  
Author(s):  
Bo Huang ◽  
Guisheng Zeng ◽  
Alvin Y.J. Ng ◽  
Mingjie Cai

Prk1p is a serine/threonine kinase involved in the regulation of the actin cytoskeleton organization in the yeast Saccharomyces cerevisiae. Previously, we have identified LxxQxTG as the phosphorylation site of Prk1p. In this report, the recognition sequence for Prk1p is investigated more thoroughly. It is found that the presence of a hydrophobic residue at the position of P-5 is necessary for Prk1p phosphorylation and L, I, V, and M are all able to confer the phosphorylation at various efficiencies. The residue flexibility at P-2 has also been identified to include Q, N, T, and S. A homology-based three-dimensional model of the kinase domain of Prk1p provided some structural interpretations for these substrate specificities. The characterization of the [L/I/V/M]xx[Q/N/T/S]xTG motif led to the identification of a spectrum of potential targets for Prk1p from yeast genome. One of them, Scd5p, which contains three LxxTxTG motifs and is previously known to be important for endocytosis and actin organization, has been chosen to demonstrate its relationship with Prk1p. Phosphorylation of Scd5p by Prk1p at the three LxxTxTG motifs could be detected in vitro and in vivo, and deletion of PRK1 suppressed the defects in actin cytoskeleton and endocytosis in one of the scd5 mutants. These results allowed us to conclude that Scd5p is likely another regulatory target of Prk1p.


2016 ◽  
Author(s):  
François Serra ◽  
Davide Baù ◽  
Guillaume Filion ◽  
Marc A. Marti-Renom

The sequence of a genome is insufficient to understand all genomic processes carried out in the cell nucleus. To achieve this, the knowledge of its three- dimensional architecture is necessary. Advances in genomic technologies and the development of new analytical methods, such as Chromosome Conformation Capture (3C) and its derivatives, now permit to investigate the spatial organization of genomes. However, inferring structures from raw contact data is a tedious process for shortage of available tools. Here we present TADbit, a computational framework to analyze and model the chromatin fiber in three dimensions. To illustrate the use of TADbit, we automatically modeled 50 genomic domains from the fly genome revealing differential structural features of the previously defined chromatin colors, establishing a link between the conformation of the genome and the local chromatin composition. More generally, TADbit allows to obtain three-dimensional models ready for visualization from 3C-based experiments and to characterize their relation to gene expression and epigenetic states. TADbit is open-source and available for download from http://www.3DGenomes.org.


2020 ◽  
pp. 20190464
Author(s):  
Chien-Chih Chen ◽  
Cheng-Chung Lin ◽  
Hong-Po Hsieh ◽  
Yang-Chieh Fu ◽  
Yunn-Jy Chen ◽  
...  

Objectives: To measure in vivo three-dimensional kinematics of the mandible and associated end-point trajectories and to quantify their relationships during temporomandibular joint activities using 3D fluoroscopy. Methods: A novel fluoroscopy-based 3D measurement method was used to measure motions of the mandible and the associated end points (i.e. incisors and lateral poles of both condyles) during open close, lateral gliding and protrusion-retraction movements in healthy young individuals. The contributions of each of the rotational and translational components of the mandible to the end-point trajectories were quantified through experiment-based computer simulations. Results: The mandibular rotation was found to account for 91% of the maximal mouth-opening-capacity and 73% of the maximal lateral incisor movement, while the condylar translation contributed to 99% of the anterior protrusion distance. Incisor trajectories were nearly vertical within the first 60% of the maximal opening during the open-close movement. Conclusions: Similar condylar downward rotation paths but with bilaterally asymmetrical ranges were used to perform basic mandibular movements of different targeted TI trajectories in three dimensions, that is, open-close, lateral-gliding and protrusion-retraction. Mandibular rotations contributed to the majority of the principal displacement components of the incisor, that is, vertical during open-close and towards the working-side-during lateral-gliding, while mandibular translation contributed mainly to the forward movement of the incisor during protrusion-retraction. Owing to the anatomical constraints, the freedom of mandibular translation is limited and mainly in the anteroposterior direction, which is considered helpful for the control and stability of the TMJ during oral activities.


2020 ◽  
Vol 11 ◽  
pp. 204173142093340 ◽  
Author(s):  
Chengye Zhang ◽  
Zhaoting Yang ◽  
Da-Long Dong ◽  
Tae-Su Jang ◽  
Jonathan C. Knowles ◽  
...  

Cancer stem cells have been shown to be important in tumorigenesis processes, such as tumor growth, metastasis, and recurrence. As such, many three-dimensional models have been developed to establish an ex vivo microenvironment that cancer stem cells experience under in vivo conditions. Cancer stem cells propagating in three-dimensional culture systems show physiologically related signaling pathway profiles, gene expression, cell–matrix and cell–cell interactions, and drug resistance that reflect at least some of the tumor properties seen in vivo. Herein, we discussed the presently available Cancer stem cell three-dimensional culture models that use biomaterials and engineering tools and the biological implications of these models compared to the conventional ones.


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