M. Pinar and M. A. Penalva

TRAnsport Protein Particle (TRAPP) complexes regulate membrane traffic. TRAPPII and TRAPPIII share a core hetero-heptamer, also denoted TRAPPI. In fungi TRAPPIII and TRAPPII mediate GDP exchange on RAB1 and RAB11, respectively, regulating traffic across the Golgi, with TRAPPIII also activating RAB1 in autophagosomes. Our finding that Aspergillus nidulans TRAPPII can be assembled by addition of a TRAPPII-specific subcomplex onto core TRAPP prompted us to investigate the possibility that TRAPPI/TRAPPIII already residing in the Golgi matures into TRAPPII to determine a RAB1-to-RAB11 conversion as Golgi cisternae progress from early Golgi to TGN identity. By time-resolved microscopy we determine that the TRAPPII reporter Trs120/TRAPPC9 is recruited to existing TGN cisternae slightly before RAB11 arrives, and resides for~45 sec on them before cisternae tear off into RAB11 secretory carriers. Notably, the core TRAPP reporter Bet3/TRAPPC3 was not detectable in early Golgi cisternae, being instead recruited to TGN cisternae simultaneously with Trs120/TRAPPC9, indicating en bloc recruitment of TRAPPII to the Golgi and arguing strongly against the TRAPP maturation model.

Javad Fahanik-babaei, Bahareh Rezaee, Maryam Nazari, Nihad Torabi, Reza Saghiri, Remy Sauve, and Afsaneh Eliassi

We have determined the electropharmacological properties of a new potassium channel from brain mitochondrial membrane by planar lipid bilayer method. Our results showed the presence of a channel with a conductance of 150 pS at potentials between 0 and –60 mV in 200 cis/50 trans mM KCl solutions.

The channel was voltage-independent, with an open probability value ~0.6 at different voltages. ATP did not affect current amplitude and Po at positive and negative voltages. Notably, adding iberiotoxin, charybdotoxin, lidocaine, and margatoxin had no effect on the channel behavior. Similarly, no changes were observed by decreasing the cis-pH to 6. Interestingly, the channel was inhibited by adding sodium in a dose dependent manner. Our results also indicated a significant increase in mitochondrial complex IV activity and membrane potential and decrease in complex I activity and mitochondrial ROS production in the presence of sodium ions.

We propose that inhibition of mitochondrial K⁺ transport by Na ions on K⁺ channel opening may be important for cell protection and ATP synthesis.

Juan Martin D'Ambrosio, Veronique Albanese, Nicolas-Frederic Lipp, Lucile Fleuriot, Delphine Debayle, Guillaume Drin, and Alenka Copic

Osh6 and Osh7 are lipid transfer proteins (LTPs) that move phosphatidylserine (PS) from the endoplasmic reticulum (ER) to the plasma membrane (PM). High PS level at the PM is key for many cellular functions. Intriguingly, Osh6/7 localize to ER-PM contact sites, although they lack membrane-targeting motifs, in contrast to multidomain LTPs that both bridge membranes and convey lipids. We show that Osh6 localization to contact sites depends on its interaction with the cytosolic tail of the ER-PM tether Ist2, a homologue of TMEM16 proteins. We identify a motif in the Ist2 tail, conserved in yeasts, as the Osh6-binding region, and we map an Ist2-binding surface on Osh6. Mutations in the Ist2 tail phenocopy osh6 osh7 deletion: they decrease cellular PS levels, and block PS transport to the PM. Our study unveils an unexpected partnership between a TMEM16-like protein and a soluble LTP, which together mediate lipid transport at contact sites.

Julian Chollet, Alexander Dünkler, Anne Bäuerle, Laura Vivero-Pol, Medhanie A. Mulaw, Thomas Gronemeyer, and Nils Johnsson

Yeast cells select the position of their new bud at the beginning of each cell cycle. The recruitment of the septins to this prospective bud site is one of the critical events in a complex assembly pathway that culminates in the outgrowth of a new daughter cell. Hereby, the septin-rods follow the high concentration of Cdc42_GTP that is generated by the focused localization of its GEF Cdc24. We show that shortly before budding Cdc24 not only activates Cdc42 but also transiently interacts with Cdc11, the septin subunit that caps both ends of the septin rods. Mutations in Cdc24 reducing the affinity to Cdc11 impair septin recruitment and decrease the stability of the polarity patch. The interaction between septins and Cdc24 thus reinforces bud assembly at sites where septin structures are formed. Once the septins polymerize into the ring, Cdc24 is found at the cortex of the bud and directs its further outgrowth from this position.

Samantha-Su Z. Taylor, Nicole L. Jacobsen, Tasha K. Pontifex, Paul Langlais, and Janis M. Burt

Connexin 37 (Cx37) expression profoundly suppresses proliferation of rat insulinoma (Rin) cells in a manner dependent on gap junction channel (GJCh) functionality and the presence and phosphorylation status of its carboxyl-terminus (CT). In Rin cells growth arrested by induced Cx37 expression, serine 319 (S319) is frequently phosphorylated. Preventing phosphorylation at this site (alanine substitution; S319A) relieved Cx37 of its growth suppressive effect whereas mimicking phosphorylation at this site (aspartate substitution; S319D) enhanced Cx37's growth suppressive properties. Like Cx37-WT, -S319D GJChs and hemichannels (HChs) preferred the closed state, rarely opening fully, and gated slowly. In contrast, Cx37-S319A channels preferred open states, opened fully, and gated rapidly. These data indicate that phosphorylation-dependent conformational differences in Cx37 protein and channel function underlie Cx37-induced growth arrest vs. growth permissive phenotypes. That the closed state of -WT and Cx37-S319D GJChs and HChs favors growth arrest suggests that rather than specific permeants mediating cell cycle arrest, the closed conformation instead supports interaction of Cx37 with growth regulatory proteins that result in growth arrest.

Sanjeev Chavan Nayak and Vegesna Radha

C3G (RapGEF1) plays a role in cell differentiation and is essential for early embryonic development in mice. In this study, we identify C3G as a centrosomal protein colocalizing with cenexin at the mother centriole in interphase cells. C3G interacts through its catalytic domain with cenexin, and they show interdependence for localization to the centrosome. C3G depletion caused a decrease in cellular cenexin levels. Centrosomal localization is lost as myocytes differentiate to form myotubes. Stable clone of cells depleted of C3G by CRISPR/Cas9 showed the presence of supernumerary centrioles. Overexpression of C3G, or a catalytically active deletion construct inhibited centrosome duplication. Cilia length is longer in C3G knockout cells, and the phenotype could be reverted upon reintroduction of C3G or its catalytic domain. Association of C3G with the basal body is dynamic, decreasing upon serum starvation, and increasing upon reentry into the cell cycle. C3G inhibits cilia formation and length dependent on its catalytic activity. We conclude that C3G inhibits centrosome duplication and maintains ciliary homeostasis, properties that may be important for its role in embryonic development.

Thomas O'Loughlin, Antonina J. Kruppa, Andre L. R. Ribeiro, James R. Edgar, Abdulaziz Ghannam, Andrew M. Smith, and Folma Buss

Optineurin (OPTN) is a multifunctional protein involved in autophagy, secretion as well as NF-B and IRF3 signalling and OPTN mutations are associated with several human diseases. Here we show that, in response to viral RNA, OPTN translocates to foci in the perinuclear region, where it negatively regulates NF-B and IRF3 signalling pathways and downstream pro-inflammatory cytokine secretion. These OPTN foci consist of a tight cluster of small membrane vesicles, which are positive for ATG9A. Disease mutations linked to POAG cause aberrant foci formation in the absence of stimuli, which correlates with the ability of OPTN to inhibit signalling. Using proximity labelling proteomics, we identify the LUBAC complex, CYLD and TBK1 as part of the OPTN interactome and show that these proteins are recruited to this OPTN-positive perinuclear compartment. Our work uncovers a crucial role for OPTN in dampening NF-B and IRF3 signalling through the sequestration of LUBAC and other positive regulators in this viral RNA-induced compartment leading to altered pro-inflammatory cytokine secretion.

Mei Wang, Luping Yu, Shu Wang, Fan Yang, Min Wang, Lufan Li, and Xin Wu

RNA-binding protein LIN28A is required for maintaining tissue homeostasis, including the reproductive system, but the underlying mechanisms on how LIN28A regulates germline progenitors remain unclear. Here, we dissected LIN28A-binding targets using high-throughput sequencing of RNAs isolated by crosslinking immunoprecipitation (HITS-CLIP) in the mouse testes. LIN28A preferentially binds to CDS or 3'UTR regions through these sites with GGAG(A) sequences enriched within mRNAs. Further investigation of Lin28a null mouse testes indicated that meiosis-associated mRNAs mediated by LIN28A were differentially expressed. Next, ribosome profiling revealed that the mRNA levels of these targets were significantly reduced in polysome fractions, and their protein expression levels decreased in the Lin28a null mouse testes, even when meiotic arrest in null mouse testes was not apparent. Collectively, these findings provide a set of binding targets that are regulated by LIN28A, which may potentially be the mechanism for the prominent role of LIN28A in regulating mammalian undifferentiated spermatogonia fates and male fertility.

Mole

Mole is the JCS resident insectivore who shares his views on various aspects of life-science research. In this series, called The Corona Files, Mole talks about how the COVID-19 pandemic is changing the landscape for researchers.

The number and diversity of tectonic landforms in our solar system “is truly remarkable,” Watters and Schultz write. Photographs of these structures have stimulated a range of scholarly investigations.

The post Book Review: Planetary Tectonics examines otherworldly landforms appeared first on Smithsonian Insider.

The Smithsonian’s National Museum of Natural History recently acquired four remarkable gemstones and jewelry pieces for the Smithsonian’s National Gem Collection in celebration of the 100th anniversary of the museum.

The post National Museum of Natural History acquires gemstones in honor of its 100th anniversary appeared first on Smithsonian Insider.

The prehistoric Xenicibis used its wings like two clubs hinged at the wrist joint in order to swing at and attack one another.

The post Prehistoric bird able to yield extreme fighting force with club-like wings appeared first on Smithsonian Insider.

The Smithsonian Research Online program recently surpassed the mark of 10,000 publications in the Digital Repository. This collection of digital publications by Smithsonian staff represents a broad review of research done by researchers at the Institution.

The post Smithsonian Digital Repository Now Contains 10,000 Items appeared first on Smithsonian Insider.

The pendant took Grand Prize in the National Saul Bell Design Competition in 2008 and features a beautiful 3.76-ct pink tourmaline from Nigeria.

The post Pink tourmaline “Nautilus” pendant enters National Gem Collection appeared first on Smithsonian Insider.

During a press conference Friday, July 22 at the Smithsonian's National Air and Space Museum, NASA announced that Gale Crater will be the landing site for the Mars Science Laboratory. Scheduled to launch in late 2011 and arrive at Mars in August 2012, the Mars Science Laboratory is a rover that will assess the planet’s “habitability”—if it ever was, or is today, an environment able to support microbial life.

The post Gale Crater to be landing site for NASA’s Mars Science Laboratory appeared first on Smithsonian Insider.

More than 500 carats of rough diamonds were recently donated to the Department of Mineral Sciences of the Smithsonian’s Natural History Museum by Jewlers Mutual Insurance Co. of Neenah, Wis.

The post 500 carats of rough diamonds donated to Natural History Museum appeared first on Smithsonian Insider.

A mysterious cycle of booms and busts in marine biodiversity over the past 500 million years could be tied to a periodic uplifting of the world's continents, scientists report

The post Boom and bust cycle of marine biodiversity every 60 million years linked to uplifting of continents appeared first on Smithsonian Insider.

New images from NASA's Lunar Reconnaissance Orbiter (LRO) spacecraft show the moon's crust is being stretched, forming minute valleys in a few small areas on the lunar surface.

The post Photos reveal recent activity in moon’s crust appeared first on Smithsonian Insider.

The National Museum of Natural History will permanently display the Dom Pedro Aquamarine, which is the largest single piece of cut-gem aquamarine in the world, beginning Dec. 6.

The post Magnificent Dom Pedro aquamarine to go on view in the Smithsonian’s Natural History Museum appeared first on Smithsonian Insider.

Even tiny crustaceans scuttling across the deepest, darkest depths of the ocean floor will feel the effects of climate change, according to a new study […]

The post Climate change to impact even deep-ocean ecosystems appeared first on Smithsonian Insider.

Many traits unique to humans were long thought to have originated in the genus Homo between 2.4 and 1.8 million years ago in Africa. A […]

The post Human Evolution Rewritten: We owe our existence to our ancestor’s flexible response to climate change appeared first on Smithsonian Insider.

Left-handed snails, giant wombats, spiny trilobites, zombie ants, glyptodonts…these are a few of the fascinating animals and plants whose fossils spring to life across the […]

The post New Book: A History of Life in 100 Fossils appeared first on Smithsonian Insider.

A full 94 percent of the dead zones in the world’s oceans lie in regions expected to warm at least 2 degrees Celsius by the […]

The post Climate change expected to expand majority of ocean dead zones appeared first on Smithsonian Insider.

What was happening (geologically speaking) on Earth way back when it was a mere babe and being showered with meteorites? Until a time machine is […]

The post Beautiful meteorites hold clues to solar system’s violent start appeared first on Smithsonian Insider.

Everyone knows that the gravitational tugging of the moon makes earth’s oceans swell and recede. But did you know Earth’s tugging is causing the moon […]

The post Shrinking Moon Linked to Earth’s Tidal Forces appeared first on Smithsonian Insider.

Oysters are keystone organisms in estuaries around the world, influencing water quality, constructing habitat and providing food for humans and wildlife. Yet their populations in […]

The post Ancient Native-American methods may be key to sustainable oyster harvests appeared first on Smithsonian Insider.

Great white sharks, killer whales, sea lions, even polar bears—the ocean is full of giant predators. But one of the ocean’s worst enemies is not […]

The post Beautiful plastic sculptures tell ugly story of human garbage in the ocean appeared first on Smithsonian Insider.

Images obtained by NASA’s MErcury Surface, Space ENvironment, GEochemistry and Ranging (MESSENGER) spacecraft during the low-altitude orbital phase of the mission have revealed previously undetected […]

The post Mercury Joins Earth As Tectonically Active Planet appeared first on Smithsonian Insider.

The Pan-STARRS project at the University of Hawai’i Institute for Astronomy (UH IfA) is publicly releasing the world’s largest digital sky survey today from the […]

The post Pan-STARRS Releases Largest Digital Sky Survey to the World appeared first on Smithsonian Insider.

To the Hopewell Culture, ancient Native Americans who sought out the exotic from near and far, metal was a rare and precious resource. Copper, found […]

The post Ancient Native American beads traced to otherworldy source: an iron meteorite appeared first on Smithsonian Insider.

Monday, Aug. 21 was an unusual day across North America. Early in the morning, families, colleagues and tourists were searching for special solar glasses with […]

The post Crowds gather at Air and Space Museum to view solar eclipse appeared first on Smithsonian Insider.

As average annual temperatures increase, mosquitoes have also been on the move—up the mountains of the Hawaiian islands. Once a refuge for native birds susceptible […]

The post Scientists race to find genetic clues as malaria decimates rare Hawaiian honeycreepers appeared first on Smithsonian Insider.

A hunter touches an infected animal’s blood, a farmer breathes the moist air exhaled by sick cows, contaminated meat is served at an outdoor market—these […]

The post What causes disease outbreaks and how can we stop them? appeared first on Smithsonian Insider.

Structural investigations of amorphous and nanocrystalline phases forming in solution are historically challenging. Few methods are capable of in situ atomic structural analysis and rigorous control of the system. A mixed-flow reactor (MFR) is used for total X-ray scattering experiments to examine the short- and long-range structure of phases in situ with pair distribution function (PDF) analysis. The adaptable experimental setup enables data collection for a range of different system chemistries, initial supersaturations and residence times. The age of the sample during analysis is controlled by adjusting the flow rate. Faster rates allow for younger samples to be examined, but if flow is too fast not enough data are acquired to average out excess signal noise. Slower flow rates form older samples, but at very slow speeds particles settle and block flow, clogging the system. Proper background collection and subtraction is critical for data optimization. Overall, this MFR method is an ideal scheme for analyzing the in situ structures of phases that form during crystal growth in solution. As a proof of concept, high-resolution total X-ray scattering data of amorphous and crystalline calcium phosphates and amorphous calcium carbonate were collected for PDF analysis.

Appendices B4 and B5 of Cayron [Acta Cryst. (2019), A75, 411–437] contain equations involving the point group and the metric tensor in which the equality symbol should be substituted by the inclusion symbol.

Relativistic electron diffraction depends on linear and quadratic terms in the electric potential, the latter being neglected in the frequently used relativistically corrected Schrödinger equation. The quadratic electric potential term modifies atomic scattering amplitudes in particular for large-angle scattering and backscattering. The respective correction increases with increasing scattering angle, increasing atomic number and increasing kinetic energy. Conventional tabulations for electron scattering and its large-angle extrapolations can be amended in closed form by a universal correction based on the screened Coulomb potential squared.

A novel approach for finding and evaluating structural models of small metallic nanoparticles is presented. Rather than fitting a single model with many degrees of freedom, libraries of clusters from multiple structural motifs are built algorithmically and individually refined against experimental pair distribution functions. Each cluster fit is highly constrained. The approach, called cluster-mining, returns all candidate structure models that are consistent with the data as measured by a goodness of fit. It is highly automated, easy to use, and yields models that are more physically realistic and result in better agreement to the data than models based on cubic close-packed crystallographic cores, often reported in the literature for metallic nanoparticles.

The transformations from the primitive cells of the centered Bravais lattices to the corresponding centered cells have conventionally been listed as three-by-three matrices that transform three-space lattice vectors. Using those three-by-three matrices when working in the six-dimensional space of lattices represented as Selling scalars as used in Delone (Delaunay) reduction, one could transform to the three-space representation, apply the three-by-three matrices and then back-transform to the six-space representation, but it is much simpler to have the equivalent six-by-six matrices and apply them directly. The general form of the transformation from the three-space matrix to the corresponding matrix operating on Selling scalars (expressed in space S6) is derived, and the particular S6matrices for the centered Delone types are listed. (Note: in his later publications, Boris Delaunay used the Russian version of his surname, Delone.)

In this study, the atomic structure of the ternary icosahedral ZnMgTm quasicrystal (QC) is investigated by means of single-crystal X-ray diffraction. The structure is found to be a member of the Bergman QC family, frequently found in Zn–Mg–rare-earth systems. The ab initio structure solution was obtained by the use of the Superflip software. The infinite structure model was founded on the atomic decoration of two golden rhombohedra, with an edge length of 21.7 Å, constituting the Ammann–Kramer–Neri tiling. The refined structure converged well with the experimental diffraction diagram, with the crystallographic R factor equal to 9.8%. The Bergman clusters were found to be bonded by four possible linkages. Only two linkages, b and c, are detected in approximant crystals and are employed to model the icosahedral QCs in the cluster approach known for the CdYb Tsai-type QC. Additional short b and a linkages are found in this study. Short interatomic distances are not generated by those linkages due to the systematic absence of atoms and the formation of split atomic positions. The presence of four linkages allows the structure to be pictured as a complete covering by rhombic triacontahedral clusters and consequently there is no need to define the interstitial part of the structure (i.e. that outside the cluster). The 6D embedding of the solved structure is discussed for the final verification of the model.

Entangled embedded periodic nets and crystal frameworks are defined, along with their dimension type, homogeneity type, adjacency depth and periodic isotopy type. Periodic isotopy classifications are obtained for various families of embedded nets with small quotient graphs. The 25 periodic isotopy classes of depth-1 embedded nets with a single-vertex quotient graph are enumerated. Additionally, a classification is given of embeddings of n-fold copies of pcu with all connected components in a parallel orientation and n vertices in a repeat unit, as well as demonstrations of their maximal symmetry periodic isotopes. The methodology of linear graph knots on the flat 3-torus [0,1)3 is introduced. These graph knots, with linear edges, are spatial embeddings of the labelled quotient graphs of an embedded net which are associated with its periodicity bases.

A new approach is presented to obtain candidate structures from atomic pair distribution function (PDF) data in a highly automated way. It fetches, from web-based structural databases, all the structures meeting the experimenter's search criteria and performs structure refinements on them without human intervention. It supports both X-ray and neutron PDFs. Tests on various material systems show the effectiveness and robustness of the algorithm in finding the correct atomic crystal structure. It works on crystalline and nanocrystalline materials including complex oxide nanoparticles and nanowires, low-symmetry and locally distorted structures, and complicated doped and magnetic materials. This approach could greatly reduce the traditional structure searching work and enable the possibility of high-throughput real-time auto-analysis PDF experiments in the future.