Obtaining crystals and solving the phase problem remain major hurdles encountered by bio-crystallographers in their race to obtain new high-quality structures. Both issues can be overcome by the crystallophore, Tb-Xo4, a lanthanide-based molecular complex with unique nucleating and phasing properties. This article presents examples of new crystallization conditions induced by the presence of Tb-Xo4. These new crystalline forms bypass crystal defects often encountered by crystallographers, such as low-resolution diffracting samples or crystals with twinning. Thanks to Tb-Xo4's high phasing power, the structure determination process is greatly facilitated and can be extended to serial crystallography approaches.

The unique nucleating and phasing capabilities of the crystallophore, Tb-Xo4, are illustrated through challenging cases.

This paper reports on the two-scale fractal structure of chromatin organization in the nucleus of the HeLa cell.

The crystal structure of Pseudomonas aeruginosa Fis is composed of an N-terminal flexible loop and a C-terminal helix–turn–helix motif.

In a recent study of the mating behavior of these Asian spiders, researchers found that 87.5 percent of males had both palps amputated during copulation.

The post Don’t pick a fight with a eunuch spider. It has nothing to lose appeared first on Smithsonian Insider.

One problem in unraveling the mystery of quasars is that many (perhaps most) quasar nuclei seem to be surrounded by a torus of obscuring dust that makes them difficult to study.

The post The origins of a torus in a galactic nucleus appeared first on Smithsonian Insider.

Osiris Martinez-Guzman, Mathilda M. Willoughby, Arushi Saini, Jonathan V. Dietz, Iryna Bohovych, Amy E. Medlock, Oleh Khalimonchuk, and Amit R. Reddi

Heme is a cofactor and signaling molecule that is essential for much of aerobic life. All heme-dependent processes in eukaryotes require that heme is trafficked from its site of synthesis in the mitochondria to hemoproteins located throughout the cell. However, the mechanisms governing the mobilization of heme out of the mitochondria, and the spatio-temporal dynamics of these processes, are poorly understood. Herein, using genetically encoded fluorescent heme sensors, we developed a live cell assay to monitor heme distribution dynamics between the mitochondrial inner-membrane, where heme is synthesized, and the mitochondrial matrix, cytosol, and nucleus. Surprisingly, heme trafficking to the nucleus is ~25% faster than to the cytosol or mitochondrial matrix, which are nearly identical, potentially supporting a role for heme as a mitochondrial-nuclear retrograde signal. Moreover, we discovered that the heme synthetic enzyme, 5-aminolevulinic acid synthase (ALAS), and GTPases in control of the mitochondrial dynamics machinery, Mgm1 and Dnm1, and ER contact sites, Gem1, regulate the flow of heme between the mitochondria and nucleus. Overall, our results indicate that there are parallel pathways for the distribution of bioavailable heme.

Kasun Buddika, Ishara S. Ariyapala, Mary A. Hazuga, Derek Riffert, and Nicholas S. Sokol

Stressed cells downregulate translation initiation and assemble membrane-less foci termed stress granules (SGs). Extensively characterized in cultured cells, the existence of such structures in stressed adult stem cell pools remain poorly characterized. Here we report that Drosophila orthologs of mammalian SG components AGO1, ATX2, CAPRIN, eIF4E, FMRP, G3BP, LIN-28, PABP, and TIAR are enriched in adult intestinal progenitor cells where they accumulate in small cytoplasmic messenger ribonucleoprotein complexes (mRNPs). Treatment with sodium arsenite or rapamycin reorganized these mRNPs into large cytoplasmic granules. Formation of these intestinal progenitor stress granules (IPSGs) depended on polysome disassembly, led to translational downregulation, and was reversible. While canonical SG nucleators ATX2 and G3BP were sufficient for IPSG formation in the absence of stress, neither of them, nor TIAR, either individually or collectively, were required for stress-induced IPSG formation. This work therefore finds that IPSGs do not assemble via a canonical mechanism, raising the possibility that other stem cell populations employ a similar stress-response mechanism.

Kelly L. Dunlevy, Valentina Medvedeva, Jade E. Wilson, Mohammed Hoque, Trinity Pellegrin, Adam Maynard, Madison M. Kremp, Jason S. Wasserman, Andrey Poleshko, and Richard A. Katz

A large fraction of epigenetically silent heterochromatin is anchored to the nuclear periphery via "tethering proteins" that function to bridge heterochromatin and the nuclear membrane or nuclear lamina. We identified previously a human tethering protein, PRR14, that binds heterochromatin through an N-terminal domain, but the mechanism and regulation of nuclear lamina association remained to be investigated. Here we identify an evolutionarily conserved PRR14 nuclear lamina binding domain (LBD) that is both necessary and sufficient for positioning of PRR14 at the nuclear lamina. We also show that PRR14 associates dynamically with the nuclear lamina, and provide evidence that such dynamics are regulated through phosphorylation-dephosphorylation of the LBD. Furthermore, we identified a PP2A phosphatase recognition motif within the evolutionarily conserved PRR14 C-terminal Tantalus domain. Disruption of this motif affected PRR14 localization to the nuclear lamina. The overall findings demonstrate a heterochromatin anchoring mechanism whereby the PRR14 tether simultaneously binds heterochromatin and the nuclear lamina through two separable, modular domains. The findings also describe an optimal PRR14 LBD fragment that could be used for efficient targeting of fusion proteins to the nuclear lamina.

Isabella Guardamagna, Elisabetta Bassi, Monica Savio, Paola Perucca, Ornella Cazzalini, Ennio Prosperi, and Lucia A. Stivala

Assessing DNA repair is an important endpoint to study the DNA damage response for investigating the biochemical mechanisms of this process and the efficacy of chemotherapy, which often uses DNA damaging compounds. Numerous in vitro methods to biochemically characterize DNA repair mechanisms have been developed so far. However, they show some limitations mainly due to the lack of chromatin organization. Here we describe a functional cell-free system to study DNA repair synthesis in vitro, using G1-phase nuclei isolated from human cells treated with different genotoxic agents. Upon incubation in the correspondent damage-activated cytosolic extracts, containing biotin-16-dUTP, nuclei are able to initiate DNA repair synthesis. The use of specific DNA synthesis inhibitors markedly decreased biotinylated dUTP incorporation, indicating the specificity of the repair response. Exogenously added human recombinant PCNA protein, but not the sensors of UV-DNA damage DDB2 or DDB1, stimulated UVC induced dUTP incorporation. In contrast, a DDB2^PCNA- mutant protein, unable to associate with PCNA, interfered with DNA repair synthesis. Given its responsiveness to different type of DNA lesions, this system offers an additional tool to study DNA repair mechanisms.

The positional change of nitro­gen-7 of the RNA constituent guanosine to the bridgehead position-5 leads to the base-modified nucleoside 5-aza-7-de­aza­guanosine. Contrary to guanosine, this mol­ecule cannot form Hoogsteen base pairs and the Watson–Crick proton donor site N3—H becomes a proton-acceptor site. This causes changes in nucleobase recognition in nucleic acids and has been used to construct stable `all-purine' DNA and DNA with silver-mediated base pairs. The present work reports the single-crystal X-ray structure of 7-iodo-5-aza-7-de­aza­guanosine, C10H12IN5O5 (1). The iodinated nucleoside shows an anti conformation at the glycosylic bond and an N conformation (O4'-endo) for the ribose moiety, with an anti­periplanar orientation of the 5'-hy­droxy group. Crystal packing is controlled by inter­actions between nucleobase and sugar moieties. The 7-iodo substituent forms a contact to oxygen-2' of the ribose moiety. Self-pairing of the nucleobases does not take place. A Hirshfeld surface analysis of 1 highlights the contacts of the nucleobase and sugar moiety (O—H⋯O and N—H⋯O). The concept of pK-value differences to evaluate base-pair stability was applied to purine–purine base pairing and stable base pairs were predicted for the construction of `all-purine' RNA. Furthermore, the 7-iodo substituent of 1 was functionalized with benzo­furan to detect motional constraints by fluorescence spectroscopy.

Simon L. Bullock
Apr 6, 2020; 133:jcs245134-jcs245134
Meeting Report

Focused attention by world leaders is needed to address the substantial challenges posed by disposal of spent nuclear fuel from reactors and high-level radioactive waste from processing such fuel for military or energy purposes.

The 2011 Fukushima Daiichi nuclear accident should serve as a wake-up call to nuclear plant operators and regulators on the critical importance of measuring, maintaining, and restoring cooling in spent fuel pools during severe accidents and terrorist attacks, says a new report from the National Academies of Sciences, Engineering, and Medicine.

The science questions that could be answered by an electron ion collider (EIC) – a very large-scale particle accelerator – are significant to advancing our understanding of the atomic nuclei that make up all visible matter in the universe, says a new report by the National Academies of Sciences, Engineering, and Medicine.

A new report from the National Academies of Sciences, Engineering, and Medicine recommends changes in the way that the U.S. Department of Energy manages science and technology (S&T) development in order to accelerate the cleanup of radioactive waste and contaminated soil, groundwater, and facilities at U.S. nuclear weapons sites.

A new report from the National Academies of Sciences, Engineering, and Medicine – which reviews a separate report by a federally funded laboratory that examines options for treating low-activity radioactive waste at the Hanford Nuclear Reservation -- is available for public comment until Oct. 31.

In 1943, the town of Hanford in Washington State was selected by the Manhattan Project to be home to the first full-scale plutonium production reactor in the world.

A recent study has assessed the sustainability of different nuclear cycle scenarios in Europe, and suggests trade-offs are required between reducing the amount of uranium fuel needed, costs and proliferation risks.

The Fukushima accident in Japan has sparked international debate on nuclear energy. A new study has identified five factors which may have influenced the contrasting energy policy responses to the incident in the UK and Germany. Following the disaster, the UK is continuing to back nuclear power generation, whilst Germany is withdrawing support.

The greenhouse gas (GHG) emissions produced during the decommissioning phase of nuclear power plants may have been underestimated in previous assessments, new research suggests. The study estimated that the decommissioning process for a German plant resulted in 1 651 265 tonnes of CO₂ (or equivalent) emissions, or 0.825 tonnes of CO2 equivalent per tonne of waste. While the researchers acknowledge that impact is highly dependent on the unique characteristics of each decommissioning project, these results raise questions as to whether this phase has been accurately assessed in earlier research.

A case study in Sweden has shown that critically endangered European eels are being lost when they are sucked into the local nuclear power station???s cooling system. A process to pump the eels back into the sea could be beneficial to this species, the researchers conclude.

Leakage of radioactive material from the wreck of the nuclear submarine K-159 in the Barents Sea could increase levels of radioactivity in local populations of cod by a hundred times, new research suggests. However, this level remains well below ‘safe’ standards set by the Norwegian government.

A star from a distant galaxy produced the most intense X-ray blast ever.

There are 104 nuclear power plants in the continental United States, two of which operate in quake-prone areas and others that are in need of major upgrades.

More questions are being raised about nuclear power — in the United States, Europe, Asia and Africa.

If countries continue to slow the use of nuclear power can green energy be a viable alternative, and at what cost?

Robots need to be tailored made for their nuclear plants, and the Fukushima plant was built prior to the adoption of robots.

The future looks uncertain for an industry on the brink of making huge gains in Washington this year.

These maps, graphs and charts will answer your questions about radiation exposure and nuclear energy.

The state wants to expand a nuclear-waste storage facility inside an ancient salt bed to play a bigger role in handling spent fuel from U.S. reactors.

New study finds that nuclear radiation from bomb tests and power plant accidents leads to the birth of more boys than girls.

In the nuke-crazed 1950s, Ford wanted to put mini reactors in cars. That didn't fly, but now we're hearing of radioactive thorium lasers that could power a car

For some opponents of nuclear power, no amount of planning or patching is enough. Among those critics is actor Alec Baldwin, whose thoughts on the subject carry

A historic moment for the energy industry — leading technology company Siemens abandons its nuclear division in favor of growing wind market.

Next-gen nuclear plants could provide carbon-free energy, but the painfully slow process of approving better, safer reactors — not to mention real anxiety ove

The plant's operator found substances in a reactor which could be a result of nuclear fission, a possible setback in safely shutting down the plant.

The nuclear meltdowns at the Fukushima power plant after the Japanese tsunami a year ago has made Americans more leery of nuclear power, according to a Yale Uni

A well-placed nuclear explosion could actually save humanity from a big asteroid hurtling toward Earth, just like in the movies, a new study suggests.

A new report reveals that the Kodak industrial facility in upstate New York was home to a small nuclear reactor filled with weapons-grade uranium for more than

To mark the release of “The Chernobyl Diaries,” we’ve rounded up nine notable nuclear horror films that span over 50 years of murder, mayhem and reactor m

Scientists reexamine and reverse a 1955 study that claimed beer and soda would be safe to drink after a nuclear bomb drops and explodes nearby.

The technique uses GPS and radio telescopes to detect underground nuclear tests using waves that travel from the blast into the upper atmosphere.

Nuclear fusion could one day propel rockets that allow humans to go to Mars and back in 30 days

Actors join other others in urging President Obama to stay true to his commitment to reduce nuclear weapons during this year's G8 summit.

If a dangerous asteroid pops onto the radar with no time to spare, nuclear bombs may be the best way to respond.

Even a relatively small regional nuclear war could trigger global cooling, damage the ozone layer and cause droughts for more than a decade.

The aurora may hold the secret of a magnetic phenomenon related to the nuclear fusion powering the sun.