Ring Shaped Structure
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Forests ◽  
2021 ◽  
Vol 12 (9) ◽  
pp. 1258
Author(s):  
Adrian Patrut ◽  
Roxana Teodora Patrut ◽  
Jean-Michel Leong Pock-Tsy ◽  
Pascal Danthu ◽  
Stephan Woodborne ◽  
...  

Over the past years, our research on baobabs mainly focused on the largest Malagasy species, namely the Reniala or Grandidier baobab (Adansonia grandidieri Baill.). The biggest A. grandidieri are located in the Morombe area, especially in the so-called Andombiry Forest. This giant forest of Reniala hosts well over 6000 mature individuals, out of which more than 30 have very large sizes, i.e., circumferences over 20 m. We investigated, measured and dated by AMS radiocarbon the largest specimens. We found that all large Grandidier baobabs are multi-stemmed. They mostly exhibit a closed ring-shaped structure, with a false cavity inside. In this architecture, which enables Grandidier baobabs to reach very large sizes, the stems that build the ring typically have similar ages. Here we present the AMS radiocarbon investigation of two large baobabs, A 215 (girth 21.50 m) and A 257 (girth 25.70 m). According to dating results, the baobab A 215 has an age of only 375 years. It consists of four fused stems and has a closed ring-shaped structure. The baobab A 257 has the second largest trunk of all known live Reniala trees. It also exhibits a closed ring-shaped structure, with five fused stems around a false cavity, which has an opening toward the exterior. The dating results indicate that A 257 is around 900 years old.


2020 ◽  
Author(s):  
Marie-Eve Charbonneau ◽  
Vedhika Raghunathan ◽  
Mary X.D. O’Riordan

ABSTRACTMacrophages adopt a pro-inflammatory phenotype in response to environmental challenges in a process that often coincides with the formation of transient cytosolic p62/SQSTM1 inclusions containing ubiquitinated proteins in structures known as aggresome-like induced structures (ALIS). Although described as stress-induced inclusions that accumulate aggregated proteins, little direct evidence supports their hypothesized structural role in the context of immune stimulation. Here, we showed that these structures in primary macrophages are induced by multiple microbialbased ligands, including exposure to cytosolic double-stranded DNA. Rather than accumulating aggregated proteins, we observed that ubiquitinated proteins form a ring-shaped structure around the perimeter of these circular foci. We identified that different microbial stimuli induced the formation of ubiquitin-positive foci with distinct characteristics and we observed selective recruitment of context-dependent immune regulators. Our findings are consistent with a model where these ubiquitin-containing structures act as adaptable organizing centers for innate immune signaling.SUMMARYCharbonneau et al. demonstrate that ubiquitin- and p62-containing cytosolic ring-shaped structures induced by bacterial infections, microbial ligands and cytosolic double-stranded DNA contain context-dependent immune regulators, revealing an important insight on the cellular architecture required to coordinate signal transduction in macrophage.


2020 ◽  
Vol 203 (2) ◽  
pp. e00463-20
Author(s):  
Amit Bhambhani ◽  
Isabella Iadicicco ◽  
Jules Lee ◽  
Syed Ahmed ◽  
Max Belfatto ◽  
...  

ABSTRACTPrevious work identified gene product 56 (gp56), encoded by the lytic bacteriophage SP01, as being responsible for inhibition of Bacillus subtilis cell division during its infection. Assembly of the essential tubulin-like protein FtsZ into a ring-shaped structure at the nascent site of cytokinesis determines the timing and position of division in most bacteria. This FtsZ ring serves as a scaffold for recruitment of other proteins into a mature division-competent structure permitting membrane constriction and septal cell wall synthesis. Here, we show that expression of the predicted 9.3-kDa gp56 of SP01 inhibits later stages of B. subtilis cell division without altering FtsZ ring assembly. Green fluorescent protein-tagged gp56 localizes to the membrane at the site of division. While its localization does not interfere with recruitment of early division proteins, gp56 interferes with the recruitment of late division proteins, including Pbp2b and FtsW. Imaging of cells with specific division components deleted or depleted and two-hybrid analyses suggest that gp56 localization and activity depend on its interaction with FtsL. Together, these data support a model in which gp56 interacts with a central part of the division machinery to disrupt late recruitment of the division proteins involved in septal cell wall synthesis.IMPORTANCE Studies over the past decades have identified bacteriophage-encoded factors that interfere with host cell shape or cytokinesis during viral infection. The phage factors causing cell filamentation that have been investigated to date all act by targeting FtsZ, the conserved prokaryotic tubulin homolog that composes the cytokinetic ring in most bacteria and some groups of archaea. However, the mechanisms of several phage factors that inhibit cytokinesis, including gp56 of bacteriophage SP01 of Bacillus subtilis, remain unexplored. Here, we show that, unlike other published examples of phage inhibition of cytokinesis, gp56 blocks B. subtilis cell division without targeting FtsZ. Rather, it utilizes the assembled FtsZ cytokinetic ring to localize to the division machinery and to block recruitment of proteins needed for septal cell wall synthesis.


2020 ◽  
Vol 19 (12) ◽  
pp. 1997-2014
Author(s):  
Yadong Yu ◽  
Haichuan Liu ◽  
Zanlin Yu ◽  
H. Ewa Witkowska ◽  
Yifan Cheng

AAA+ ATPases constitute a large family of proteins that are involved in a plethora of cellular processes including DNA disassembly, protein degradation and protein complex disassembly. They typically form a hexametric ring-shaped structure with six subunits in a (pseudo) 6-fold symmetry. In a subset of AAA+ ATPases that facilitate protein unfolding and degradation, six subunits cooperate to translocate protein substrates through a central pore in the ring. The number and type of nucleotides in an AAA+ ATPase hexamer is inherently linked to the mechanism that underlies cooperation among subunits and couples ATP hydrolysis with substrate translocation. We conducted a native MS study of a monodispersed form of PAN, an archaeal proteasome AAA+ ATPase, to determine the number of nucleotides bound to each hexamer of the WT protein. We utilized ADP and its analogs (TNP-ADP and mant-ADP), and a nonhydrolyzable ATP analog (AMP-PNP) to study nucleotide site occupancy within the PAN hexamer in ADP- and ATP-binding states, respectively. Throughout all experiments we used a Walker A mutant (PANK217A) that is impaired in nucleotide binding as an internal standard to mitigate the effects of residual solvation on mass measurement accuracy and to serve as a reference protein to control for nonspecific nucleotide binding. This approach led to the unambiguous finding that a WT PAN hexamer carried – from expression host – six tightly bound ADP molecules that could be exchanged for ADP and ATP analogs. Although the Walker A mutant did not bind ADP analogs, it did bind AMP-PNP, albeit at multiple stoichiometries. We observed variable levels of hexamer dissociation and an appearance of multimeric species with the over-charged molecular ion distributions across repeated experiments. We posit that these phenomena originated during ESI process at the final stages of ESI droplet evolution.


Author(s):  
Umair Rafique ◽  
Sami ud Din ◽  
Hisham Khalil

Abstract A compact co-planar waveguide (CPW) fed planar elliptical antenna has been designed and presented for super wideband (SWB) characteristics. The designed antenna has an overall size of 30 × 30 × 1.57 mm3, and it consists of an elliptical patch radiator fed using a modified 50 Ω CPW-fed tapered microstrip feed line. By using a semi-ring shaped structure with a tapered feed line, an impedance bandwidth of 180.66% has been observed from 1.27 to 25 GHz with a ratio bandwidth of 19.68:1. To validate simulation results, the designed antenna has been fabricated and measured, and a reasonable agreement has been observed between simulated and measured results. It has also been observed that the designed antenna offers good radiation properties over the entire operating bandwidth. The simulated average gain and radiation efficiency of the proposed SWB antenna is noted to be 4.3 dBi and 95.77%, respectively; while the measured average gain and radiation efficiency is 3.8 dBi and 94.69%, respectively.


2020 ◽  
Author(s):  
Abdullah F.U.H. Saeed ◽  
Chun Chan ◽  
Hongxin Guan ◽  
Bing Gong ◽  
Peixuan Guo ◽  
...  

ABSTRACTBiological motors, ubiquitous in living systems, convert chemical energy into different kinds of mechanical motions critical to cellular functions. Most of these biomotors belong to a group of enzymes known as ATPases, which adopt a multi-subunit ring-shaped structure and hydrolyze adenosine triphosphate (ATP) to generate forces. The gene product 16 (gp16), an ATPase in bacteriophage □29, is among the most powerful biomotors known. It can overcome substantial resisting forces from entropic, electrostatic, and DNA bending sources to package double-stranded DNA (dsDNA) into a preformed protein shell (procapsid). Despite numerous studies of the □29 packaging mechanism, a structure of the full-length gp16 is still lacking, let alone that of the packaging motor complex that includes two additional molecular components: a connector gp10 protein and a prohead RNA (pRNA). Here we report the crystal structure of the C-terminal domain of gp16 (gp16-CTD). Structure-based alignment of gp16-CTD with related RNase H-like nuclease domains revealed a nucleic acid binding surface in gp16-CTD, whereas no nuclease activity has been detected for gp16. Subsequent molecular dynamics (MD) simulations showed that this nucleic acid binding surface is likely essential for pRNA binding. Furthermore, our simulations of a full-length gp16 structural model highlighted a dynamic interplay between the N-terminal domain (NTD) and CTD of gp16, which may play a role in driving DNA movement into the procapsid, providing structural support to the previously proposed inchworm model. Lastly, we assembled an atomic structural model of the complete □29 dsDNA packaging motor complex by integrating structural and experimental data from multiple sources. Collectively, our findings provided a refined inchworm-revolution model for dsDNA translocation in bacteriophage □29 and suggested how the individual domains of gp16 work together to power such translocation.ABSTRACT (SHORT)Biological motors, ubiquitous in living systems, convert chemical energy into different kinds of mechanical motions critical to cellular functions. The gene product 16 (gp16) in bacteriophage □29 is among the most powerful biomotors known, which adopts a multi-subunit ring-shaped structure and hydrolyzes ATP to package double-stranded DNA (dsDNA) into a preformed procapsid. Here we report the crystal structure of the C-terminal domain of gp16 (gp16-CTD). Structure-based alignment and molecular dynamics (MD) simulations revealed an essential binding surface of gp16-CTD for prohead RNA (pRNA), a unique component of the motor complex. Furthermore, our simulations highlighted a dynamic interplay between the N-terminal domain (NTD) and CTD of gp16, which may play a role in driving DNA movement into the procapsid. Lastly, we assembled an atomic structural model of the complete □29 dsDNA packaging motor complex by integrating structural and experimental data from multiple sources. Collectively, our findings provided a refined inchworm-revolution model for dsDNA translocation in bacteriophage □29 and suggested how the individual domains of gp16 work together to power such translocation.


Cells ◽  
2020 ◽  
Vol 9 (6) ◽  
pp. 1497 ◽  
Author(s):  
Irina Bogolyubova ◽  
Dmitry Bogolyubov

During the period of oocyte growth, chromatin undergoes global rearrangements at both morphological and molecular levels. An intriguing feature of oogenesis in some mammalian species is the formation of a heterochromatin ring-shaped structure, called the karyosphere or surrounded “nucleolus”, which is associated with the periphery of the nucleolus-like bodies (NLBs). Morphologically similar heterochromatin structures also form around the nucleolus-precursor bodies (NPBs) in zygotes and persist for several first cleavage divisions in blastomeres. Despite recent progress in our understanding the regulation of gene silencing/expression during early mammalian development, as well as the molecular mechanisms that underlie chromatin condensation and heterochromatin structure, the biological significance of the karyosphere and its counterparts in early embryos is still elusive. We pay attention to both the changes of heterochromatin morphology and to the molecular mechanisms that can affect the configuration and functional activity of chromatin. We briefly discuss how DNA methylation, post-translational histone modifications, alternative histone variants, and some chromatin-associated non-histone proteins may be involved in the formation of peculiar heterochromatin structures intimately associated with NLBs and NPBs, the unique nuclear bodies of oocytes and early embryos.


2020 ◽  
Vol 1 (1) ◽  
pp. 33-47 ◽  
Author(s):  
Adrian Patrut ◽  
Roxana T. Patrut ◽  
Laszlo Rakosy ◽  
Karl F. Von Reden

The volcanic Comoro Islands, located in the Indian Ocean in between mainland Africa and Madagascar, host several thousand African baobabs (Adansonia digitata). Most of them are found in Mayotte, which currently belongs to France, as an overseas department. Baobabs constitute a reliable archive for climate change and millennial specimens were recently used as proxies for paleoclimate reconstructions in southern Africa. We report the investigation of the largest two baobabs of Mayotte, the Big baobab of Musical Plage and the largest baobab of Plage N’Gouja. The Big baobab of Musical Plage exhibits a cluster structure and consists of 5 fused stems, out of which 4 are common stems and one is a false stem. The baobab of Plage N’Gouja has an open ring-shaped structure and consists of 7 partially fused stems, out of which 3 stems are large and old, while 4 are young. Several wood samples were collected from both baobabs and analyzed via radiocarbon dating. The oldest dated sample from the baobab of Musical Plage has a radiocarbon date of 275 ± 25 BP, which corresponds to a calibrated calendar age of 365 ± 15 yr. On its turn, the oldest sample from Plage N’Gouja has a radiocarbon date of 231 ± 20 BP, corresponding to a calibrated age of 265 ± 15 yr. These results indicate that the Big baobab of Musical Plage is around 420 years old, while the baobab of Plage N’Gouja has an age close to 330 years. In present, both baobabs are in a general state of deterioration with many broken or damaged branches, and the Baobab of Plage N’Gouja has several missing stems. These observations suggest that the two baobabs are in decline and, most likely, close to the end of their life cycle.


2020 ◽  
Author(s):  
Adrian Patrut ◽  
Roxana Patrut ◽  
Laszlo Rakosy ◽  
Karl von Reden

The volcanic Comoro Islands, located in the Indian Ocean in between mainland Africa and Madagascar, host several thousand African baobabs (Adansonia digitata). Most of them are found in Mayotte, which currently belongs to France, as an overseas department. We report the investigation of the largest two baobabs of Mayotte, the Big baobab of Musical Plage and the largest baobab of Plage N’Gouja. The Big baobab of Musical Plage exhibits a cluster structure and consists of 5 fused stems, out of which 4 are common stems and one is a false stem. The baobab of Plage N’Gouja has an open ring-shaped structure and consists of 7 partially fused stems, out of which 3 stems are large and old, while 4 are young. Several wood samples were collected from both baobabs and analyzed via radiocarbon dating. The oldest dated sample from the baobab of Musical Plage has a radiocarbon date of 275 ± 25 BP, which corresponds to a calibrated calendar age of 365 ± 15 yr. On its turn, the oldest sample from Plage N’Gouja has a radiocarbon date of 231 ± 20 BP, which translates into a calibrated age of 265 ± 15 yr. These results indicate that the Big baobab of Musical Plage is around 420 years old, while the baobab of Plage N’Gouja has an age close to 330 years. In present, both baobabs are in a general state of deterioration with many broken or damaged branches, and the Baobab of Plage N’Gouja has several missing stems. These observations suggest that the two baobabs are in decline and, most likely, close to the end of their life cycle.


2020 ◽  
Author(s):  
Amit Bhambhani ◽  
Isabella Iadicicco ◽  
Jules Lee ◽  
Syed Ahmed ◽  
Max Belfatto ◽  
...  

ABSTRACTPrevious work identified gp56, encoded by the lytic bacteriophage SP01, as responsible for inhibition of Bacillus subtilis cell division during its infection. Assembly of the essential tubulin-like protein FtsZ into a ring-shaped structure at the nascent site of cytokinesis determines the timing and position of division in most bacteria. This FtsZ ring serves as a scaffold for recruitment of other proteins into a mature division-competent structure permitting membrane constriction and septal cell wall synthesis. Here we show that expression of the predicted 9.3-kDa gene product 56 (gp56) of SP01 inhibits latter stages of B. subtilis cell division without altering FtsZ ring assembly. GFP-tagged gp56 localizes to the membrane at the site of division. While its localization permits recruitment of early division proteins, gp56 interferes with the recruitment of late division proteins, including Pbp2b and FtsW. Imaging of cells with specific division components deleted or depleted and two-hybrid analysis suggest that gp56 localization and activity depends on its interaction with mid-recruited proteins DivIC and/or FtsL. Together these data support a model where gp56 interacts with a central part of the division machinery to disrupt late recruitment of the division proteins involved in septal cell wall synthesis.IMPORTANCEResearch over the past decades has uncovered bacteriophage-encoded factors that interfere with host cell shape or cytokinesis during viral infection. Phage factors that cause cell filamentation that have been investigated to date all act by targeting FtsZ, the conserved prokaryotic tubulin homolog that composes the cytokinetic ring in most bacteria and some groups of archaea. However, the mechanism of several identified phage factors that inhibit cytokinesis remain unexplored, including gp56 of bacteriophage SP01 of Bacillus subtilis. Here, we show that unlike related published examples of phage inhibition of cyotkinesis, gp56 blocks B. subtilis cell division without targeting FtsZ. Rather, it utilizes the assembled FtsZ cytokinetic ring to localize to the division machinery and block recruitment of proteins needed for the septal cell wall synthesis.


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