Cytochrome c oxidase (CcO) reduces O2 to water, coupled with a proton-pumping process. The structure of the O2-reduction site of CcO contains two reducing equivalents, Fea32+ and CuB1+, and suggests that a peroxide-bound state (Fea33+–O−–O−–CuB2+) rather than an O2-bound state (Fea32+–O2) is the initial catalytic intermediate. Unexpectedly, however, resonance Raman spectroscopy results have shown that the initial intermediate is Fea32+–O2, whereas Fea33+–O−–O−–CuB2+ is undetectable. Based on X-ray structures of static noncatalytic CcO forms and mutation analyses for bovine CcO, a proton-pumping mechanism has been proposed. It involves a proton-conducting pathway (the H-pathway) comprising a tandem hydrogen-bond network and a water channel located between the N- and P-side surfaces. However, a system for unidirectional proton-transport has not been experimentally identified. Here, an essentially identical X-ray structure for the two catalytic intermediates (P and F) of bovine CcO was determined at 1.8 Å resolution. A 1.70 Å Fe–O distance of the ferryl center could best be described as Fea34+ = O2−, not as Fea34+–OH−. The distance suggests an ∼800-cm−1 Raman stretching band. We found an interstitial water molecule that could trigger a rapid proton-coupled electron transfer from tyrosine-OH to the slowly forming Fea33+–O−–O−–CuB2+ state, preventing its detection, consistent with the unexpected Raman results. The H-pathway structures of both intermediates indicated that during proton-pumping from the hydrogen-bond network to the P-side, a transmembrane helix closes the water channel connecting the N-side with the hydrogen-bond network, facilitating unidirectional proton-pumping during the P-to-F transition.

Optic atrophy 1 (OPA1) is a dynamin protein that mediates mitochondrial fusion at the inner membrane. OPA1 is also necessary for maintaining the cristae and thus essential for supporting cellular energetics. OPA1 exists as membrane-anchored long form (L-OPA1) and short form (S-OPA1) that lacks the transmembrane region and is generated by cleavage of L-OPA1. Mitochondrial dysfunction and cellular stresses activate the inner membrane–associated zinc metallopeptidase OMA1 that cleaves L-OPA1, causing S-OPA1 accumulation. The prevailing notion has been that L-OPA1 is the functional form, whereas S-OPA1 is an inactive cleavage product in mammals, and that stress-induced OPA1 cleavage causes mitochondrial fragmentation and sensitizes cells to death. However, S-OPA1 contains all functional domains of dynamin proteins, suggesting that it has a physiological role. Indeed, we recently demonstrated that S-OPA1 can maintain cristae and energetics through its GTPase activity, despite lacking fusion activity. Here, applying oxidant insult that induces OPA1 cleavage, we show that cells unable to generate S-OPA1 are more sensitive to this stress under obligatory respiratory conditions, leading to necrotic death. These findings indicate that L-OPA1 and S-OPA1 differ in maintaining mitochondrial function. Mechanistically, we found that cells that exclusively express L-OPA1 generate more superoxide and are more sensitive to Ca2+-induced mitochondrial permeability transition, suggesting that S-OPA1, and not L-OPA1, protects against cellular stress. Importantly, silencing of OMA1 expression increased oxidant-induced cell death, indicating that stress-induced OPA1 cleavage supports cell survival. Our findings suggest that S-OPA1 generation by OPA1 cleavage is a survival mechanism in stressed cells.

pncRNA-D is an irradiation-induced 602-nt long noncoding RNA transcribed from the promoter region of the cyclin D1 (CCND1) gene. CCND1 expression is predicted to be inhibited through an interplay between pncRNA-D and RNA-binding protein TLS/FUS. Because the pncRNA-D–TLS interaction is essential for pncRNA-D–stimulated CCND1 inhibition, here we studied the possible role of RNA modification in this interaction in HeLa cells. We found that osmotic stress induces pncRNA-D by recruiting RNA polymerase II to its promoter. pncRNA-D was highly m6A-methylated in control cells, but osmotic stress reduced the methylation and also arginine methylation of TLS in the nucleus. Knockdown of the m6A modification enzyme methyltransferase-like 3 (METTL3) prolonged the half-life of pncRNA-D, and among the known m6A recognition proteins, YTH domain-containing 1 (YTHDC1) was responsible for binding m6A of pncRNA-D. Knockdown of METTL3 or YTHDC1 also enhanced the interaction of pncRNA-D with TLS, and results from RNA pulldown assays implicated YTHDC1 in the inhibitory effect on the TLS–pncRNA-D interaction. CRISPR/Cas9-mediated deletion of candidate m6A site decreased the m6A level in pncRNA-D and altered its interaction with the RNA-binding proteins. Of note, a reduction in the m6A modification arrested the cell cycle at the G0/G1 phase, and pncRNA-D knockdown partially reversed this arrest. Moreover, pncRNA-D induction in HeLa cells significantly suppressed cell growth. Collectively, these findings suggest that m6A modification of the long noncoding RNA pncRNA-D plays a role in the regulation of CCND1 gene expression and cell cycle progression.

tRNAs universally carry a CCA nucleotide triplet at their 3'-ends. In eukaryotes, the CCA is added post-transcriptionally by the CCA-adding enzyme (CAE). The mitochondrion of the parasitic protozoan Trypanosoma brucei lacks tRNA genes and therefore imports all of its tRNAs from the cytosol. This has generated interest in the tRNA modifications and their distribution in this organism, including how CCA is added to tRNAs. Here, using a BLAST search for genes encoding putative CAE proteins in T. brucei, we identified a single ORF, Tb927.9.8780, as a potential candidate. Knockdown of this putative protein, termed TbCAE, resulted in the accumulation of truncated tRNAs, abolished translation, and inhibited both total and mitochondrial CCA-adding activities, indicating that TbCAE is located both in the cytosol and mitochondrion. However, mitochondrially localized tRNAs were much less affected by the TbCAE ablation than the other tRNAs. Complementation assays revealed that the N-terminal 10 amino acids of TbCAE are dispensable for its activity and mitochondrial localization and that deletion of 10 further amino acids abolishes both. A growth arrest caused by the TbCAE knockdown was rescued by the expression of the cytosolic isoform of yeast CAE, even though it was not imported into mitochondria. This finding indicated that the yeast enzyme complements the essential function of TbCAE by adding CCA to the primary tRNA transcripts. Of note, ablation of the mitochondrial TbCAE activity, which likely has a repair function, only marginally affected growth.

The ribosome biogenesis factor Las1 is an essential endoribonuclease that is well-conserved across eukaryotes and a newly established member of the higher eukaryotes and prokaryotes nucleotide-binding (HEPN) domain-containing nuclease family. HEPN nucleases participate in diverse RNA cleavage pathways and share a short HEPN nuclease motif (RφXXXH) important for RNA cleavage. Most HEPN nucleases participate in stress-activated RNA cleavage pathways; Las1 plays a fundamental role in processing pre-rRNA. Underscoring the significance of Las1 function in the cell, mutations in the human LAS1L (LAS1-like) gene have been associated with neurological dysfunction. Two juxtaposed HEPN nuclease motifs create Las1's composite nuclease active site, but the roles of the individual HEPN motif residues are poorly defined. Here using a combination of in vivo experiments in Saccharomyces cerevisiae and in vitro assays, we show that both HEPN nuclease motifs are required for Las1 nuclease activity and fidelity. Through in-depth sequence analysis and systematic mutagenesis, we determined the consensus HEPN motif in the Las1 subfamily and uncovered its canonical and specialized elements. Using reconstituted Las1 HEPN-HEPN' chimeras, we defined the molecular requirements for RNA cleavage. Intriguingly, both copies of the Las1 HEPN motif were important for nuclease function, revealing that both HEPN motifs participate in coordinating the RNA within the Las1 active site. We also established that conformational flexibility of the two HEPN domains is important for proper nuclease function. The results of our work reveal critical information about how dual HEPN domains come together to drive Las1-mediated RNA cleavage.

Site-specific arrest of RNA polymerases (RNAPs) is fundamental to several technologies that assess RNA structure and function. Current in vitro transcription “roadblocking” approaches inhibit transcription elongation by blocking RNAP with a protein bound to the DNA template. One limitation of protein-mediated transcription roadblocking is that it requires inclusion of a protein factor extrinsic to the minimal in vitro transcription reaction. In this work, we developed a chemical approach for halting transcription by Escherichia coli RNAP. We first established a sequence-independent method for site-specific incorporation of chemical lesions into dsDNA templates by sequential PCR and translesion synthesis. We then show that interrupting the transcribed DNA strand with an internal desthiobiotin-triethylene glycol modification or 1,N6-etheno-2'-deoxyadenosine base efficiently and stably halts Escherichia coli RNAP transcription. By encoding an intrinsic stall site within the template DNA, our chemical transcription roadblocking approach enables display of nascent RNA molecules from RNAP in a minimal in vitro transcription reaction.

The arrangement of functionally-related genes in operons is a fundamental element of how genetic information is organized in prokaryotes. This organization ensures coordinated gene expression by co-transcription. Often, however, alternative genetic responses to specific stress conditions demand the discoordination of operon expression. During cold temperature stress, accumulation of the gene encoding the sole Asp–Glu–Ala–Asp (DEAD)-box RNA helicase in Synechocystis sp. PCC 6803, crhR (slr0083), increases 15-fold. Here, we show that crhR is expressed from a dicistronic operon with the methylthiotransferase rimO/miaB (slr0082) gene, followed by rapid processing of the operon transcript into two monocistronic mRNAs. This cleavage event is required for and results in destabilization of the rimO transcript. Results from secondary structure modeling and analysis of RNase E cleavage of the rimO–crhR transcript in vitro suggested that CrhR plays a role in enhancing the rate of the processing in an auto-regulatory manner. Moreover, two putative small RNAs are generated from additional processing, degradation, or both of the rimO transcript. These results suggest a role for the bacterial RNA helicase CrhR in RNase E-dependent mRNA processing in Synechocystis and expand the known range of organisms possessing small RNAs derived from processing of mRNA transcripts.

Kainate and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptors are two major, closely related receptor subtypes in the glutamate ion channel family. Excessive activities of these receptors have been implicated in a number of central nervous system diseases. Designing potent and selective antagonists of these receptors, especially of kainate receptors, is useful for developing potential treatment strategies for these neurological diseases. Here, we report on two RNA aptamers designed to individually inhibit kainate and AMPA receptors. To improve the biostability of these aptamers, we also chemically modified these aptamers by substituting their 2'-OH group with 2'-fluorine. These 2'-fluoro aptamers, FB9s-b and FB9s-r, were markedly resistant to RNase-catalyzed degradation, with a half-life of ∼5 days in rat cerebrospinal fluid or serum-containing medium. Furthermore, FB9s-r blocked AMPA receptor activity. Aptamer FB9s-b selectively inhibited GluK1 and GluK2 kainate receptor subunits, and also GluK1/GluK5 and GluK2/GluK5 heteromeric kainate receptors with equal potency. This inhibitory profile makes FB9s-b a powerful template for developing tool molecules and drug candidates for treatment of neurological diseases involving excessive activities of the GluK1 and GluK2 subunits.

A. M. Savchuk and I. V. Sadovnichaya
Trans. Moscow Math. Soc. 80 (2020), 235-250.
Abstract, references and article information

V. V. Vlasov and N. A. Rautian
Trans. Moscow Math. Soc. 80 (2020), 169-188.
Abstract, references and article information

K. A. Mirzoev and T. A. Safonova
Trans. Moscow Math. Soc. 80 (2020), 133-151.
Abstract, references and article information

V. A. Sadovnichii, Ya. T. Sultanaev and A. M. Akhtyamov
Trans. Moscow Math. Soc. 80 (2020), 123-131.
Abstract, references and article information

Trans. Moscow Math. Soc. 80 (2020), 113-122.
Abstract, references and article information

A. G. Sergeev and Kh. A. Khachatryan
Trans. Moscow Math. Soc. 80 (2020), 95-111.
Abstract, references and article information

V. V. Ryzhikov
Trans. Moscow Math. Soc. 80 (2020), 83-94.
Abstract, references and article information

S. Yu. Orevkov
Trans. Moscow Math. Soc. 80 (2020), 73-81.
Abstract, references and article information

S. A. Kashchenko
Trans. Moscow Math. Soc. 80 (2020), 53-71.
Abstract, references and article information

S. A. Nazarov
Trans. Moscow Math. Soc. 80 (2020), 1-51.
Abstract, references and article information

Publication Date: Apr 10 2020 ETFs that meet the definition of “Exchange Traded Fund” in Nasdaq Rule 5704(a)(1)(A) are eligible to be considered for listing pursuant to Nasdaq Rule 5704. ETFs that are excluded from operating pursuant to Rule 6c-11 under the Investment Company Act of 1940 are not eligible to list under Nasdaq Rule 5704....

Publication Date: May 4 2020 On May 1, 2020, Nasdaq adopted Rule 5636T, operative through, and including, June 30, 2020, to provide listed companies with a temporary exception from certain shareholder approval requirements. A Company must submit an application to Nasdaq’s Listing Qualifications Department demonstrating that the transaction satisfies the requirements in Rule 5636T and must provide the Notification Form: Listing of Additional Shares (“LAS Form”) required by...

Web hosting behemoth GoDaddy just filed a data breach notification with the US state of California.

Researchers have poked another small hole in air gapped security by showing how the electronics inside computer power supply units (PSUs) can be turned into covert data transmission devices.

Firefox's latest version is out, with new password management features and a raft of security fixes.

Five alleged members of hacking group InfinityBlack got some unexpected visitors last week when Polish law enforcement arrested them.

Get the latest cybersecurity news, opinion and advice.

Here's a ransomware story with a difference. Some of your files can be recovered without paying, while others get wiped out forever.

Google deleted more malicious extensions from the Chrome Web Store after they were found to be phishing cryptocurrency users.

If you enjoy what you read, hear and see from the Naked Security team, please vote for us - it means a lot!

1 November 2019

The 'Security and Prosperity in Asia' conference looked at the impact of international law in the Asia-Pacific with a focus on regional economic and security issues such as the South China Sea disputes.

6 November 2019 , Volume 95, Number 6

Research Event

Event participants

Charu Lata Hogg, Associate Fellow, Asia-Pacific Programme, Chatham House
Hameed Hakimi, Research Associate, Asia-Pacific Programme and Europe Programme, Chatham House
Chair: Champa Patel, Head of Asia-Pacific Programme, Chatham House

8 January 2020 , Volume 96, Number 1

8 January 2020 , Volume 96, Number 1

8 January 2020 , Volume 96, Number 1

8 January 2020 , Volume 96, Number 1

8 January 2020 , Volume 96, Number 1

6 November 2019 , Volume 96, Number 1

The first issue of International Affairs in 2020 explores the geopolitics of the 'Indo-Pacific' region.

Research Event

Event participants

Thant Myint-U, Conservationist; Author, The Hidden History of Burma: Race, Capitalism, and the Crisis of Democracy in the 21st Century
Chair: Champa Patel, Head of Asia-Pacific Programme, Chatham House

24 January 2020

Corporate Members Event

Event participants

Dr Yu Jie, Senior Research Fellow on China, Asia-Pacific Programme, Chatham House
David Lubin, Associate Fellow, Global Economy and Finance Programme, Chatham House; Managing Director and Head of Emerging Markets Economics, Citi
Jinny Yan, Managing Director and Chief China Economist, ICBC Standard
Chair: Creon Butler, Director, Global Economy and Finance Programme, Chatham House

Research Event

Event participants

K. Anis Ahmed, Publisher, Dhaka Tribune and Bangla Tribune; Author of Good Night, Mr. Kissinger, Co-director, Dhaka Literary Festival
Meenakshi Ganguly, South Asia Director, Human Rights Watch
Chair: Ed Cumming, Writer, The Independent

8 April 2020

Mathematics is not just numbers and brute force calculation there is considerable art and elegance to the subject. So it is natural that mathematics is now being used to analyze artists. styles and to help determine the identities of the creators of disputed works. Attempts at measuring style began with literature based on statistics of word use and have successfully identified disputed works such as some of The Federalist Papers. But drawings and paintings resisted quantification until very recently. In the case of Jackson Pollock, his paintings have a demonstrated complexity to them (corresponding to a fractal dimension between 1 and 2) that distinguishes them from simple random drips. A team examining digital photos of drawings used modern mathematical transforms known as wavelets to quantify attributes of a collection of 16th century master.s drawings. The analysis revealed measurable differences between authentic drawings and imitations, clustering the former away from the latter. This is an impressive feat for the non-experts and their model, yet the team agrees that its work, like mathematics itself, is not designed to replace humans, but to assist them. For More Information: The Style of Numbers Behind a Number of Styles, Dan Rockmore, The Chronicle of Higher Education, June 9, 2006.

The racing team is just as important to a car.s finish as the driver is. With little to separate competitors over hundreds of laps, teams search for any technological edge that will propel them to Victory Lane. Of special use today is computational fluid dynamics, which is used to predict airflow over a car, both alone and in relation to other cars (for example, when drafting). Engineers also rely on more basic subjects, such as calculus and geometry, to improve their cars. In fact, one racing team engineer said of his calculus and physics teachers, the classes they taught to this day were the most important classes I.ve ever taken.(1) Mathematics helps the performance and efficiency of non-NASCAR vehicles, as well. To improve engine performance, data must be collected and processed very rapidly so that control devices can make adjustments to significant quantities such as air/fuel ratios. Innovative sampling techniques make this real-time data collection and processing possible. This makes for lower emissions and improved fuel economy goals worthy of a checkered flag. For More Information: The Physics of NASCAR, Diandra Leslie-Pelecky, 2008.

The music of most hit songs is pretty well known, but sometimes there are mysteries. One question that remained unanswered for over forty years is: What instrumentation and notes make up the opening chord of the Beatles. "A Hard Day.s Night"? Mathematician Jason Brown - a big Beatles fan - recently solved the puzzle using his musical knowledge and discrete Fourier transforms, mathematical transformations that help decompose signals into their basic parts. These transformations simplify applications ranging from signal processing to multiplying large numbers, so that a researcher doesn.t have to be "working like a dog" to get an answer. Brown is also using mathematics, specifically graph theory, to discover who wrote "In My Life," which both Lennon and McCartney claimed to have written. In his graphs, chords are represented by points that are connected when one chord immediately follows another. When all songs with known authorship are diagrammed, Brown will see which collection of graphs - McCartney.s or Lennon.s - is a better fit for "In My Life." Although it may seem a bit counterintuitive to use mathematics to learn more about a revolutionary band, these analytical methods identify and uncover compositional principles inherent in some of the best Beatles. music. Thus it.s completely natural and rewarding to apply mathematics to the Fab 4 For More Information: Professor Uses Mathematics to Decode Beatles Tunes, "The Wall Street Journal", January 30, 2009..

With 468 stops served by 26 lines, the New York subway system can make visitors feel lucky when they successfully negotiate one planned trip in a day. Yet these two New Yorkers, Chris Solarz and Matt Ferrisi, took on the task of breaking a world record by visiting every stop in the system in less than 24 hours. They used mathematics, especially graph theory, to narrow down the possible routes to a manageable number and subdivided the problem to find the best routes in smaller groups of stations. Then they paired their mathematical work with practice runs and crucial observations (the next-to-last car stops closest to the stairs) to shatter the world record by more than two hours!

Although Chris and Matt.s success may not have huge ramifications in other fields, their work does have a lot in common with how people do modern mathematics research

* They worked together, frequently using computers and often asking experts for advice;
* They devoted considerable time and effort to meet their goal; and
* They continually refined their algorithm until arriving at a solution that was nearly optimal.
Finally, they also experienced the same feeling that researchers do that despite all the hours and intense preparation, the project .felt more like fun than work.
For More Information: Math whizzes shoot to set record for traversing subway system,. Sergey Kadinsky and Rich Schapiro, New York Daily News, January 22, 2009.
Photo by Elizabeth Ferrisi.
Map New York Metropolitan Transit Authority.
The Mathematical Moments program promotes appreciation and understanding of the role mathematics plays in science, nature, technology, and human culture.

A person needing a kidney transplant may have a friend or relative who volunteers to be a living donor, but whose kidney is incompatible, forcing the person to wait for a transplant from a deceased donor. In the U.S. alone, thousands of people die each year without ever finding a suitable kidney. A new technique applies graph theory to groups of incompatible patient-donor pairs to create the largest possible number of paired-donation exchanges. These exchanges, in which a donor paired with Patient A gives a kidney to Patient B while a donor paired with Patient B gives to Patient A, will dramatically increase transplants from living donors. Since transplantation is less expensive than dialysis, this mathematical algorithm, in addition to saving lives, will also save hundreds of millions of dollars annually. Naturally there can be more transplants if matches along longer patient-donor cycles are considered (e.g., A.s donor to B, B.s donor to C, and C.s donor to A). The problem is that the possible number of longer cycles grows so fast hundreds of millions of A >B>C>A matches in just 5000 donor-patient pairs that to search through all the possibilities is impossible. An ingenious use of random walks and integer programming now makes searching through all three-way matches feasible, even in a database large enough to include all incompatible patient-donor pairs. For More Information: Matchmaking for Kidneys, Dana Mackenzie, SIAM News, December 2008. Image of suboptimal two-way matching (in purple) and an optimal matching (in green), courtesy of Sommer Gentry.

It.s often a challenge to get from Point A to Point B in normal circumstances, but after a disaster it can be almost impossible to transport food, water, and clothing from the usual supply points to the people in desperate need. A new mathematical model employs probability and nonlinear programming to design supply chains that have the best chance of functioning after a disaster. For each region or country, the model generates a robust chain of supply and delivery points that can respond to the combination of disruptions in the network and increased needs of the population. Math also helps medical agencies operate more efficiently during emergencies, such as an infectious outbreak. Fluid dynamics and combinatorial optimization are applied to facility layout and epidemiological models to allocate resources and improve operations while minimizing total infection within dispensing facilities. This helps ensure fast, effective administering of vaccines and other medicines. Furthermore, solution times are fast enough that officials can input up-to-the-minute data specific to their situation and make any necessary redistribution of supplies or staff in real time. For More Information: Supply Chain Network Economics: Dynamics of Prices, Flows, and Profits, Anna Nagurney, 2006.

Once a problem only in the developed world, obesity is now a worldwide epidemic. The overwhelming cause of the epidemic is a dramatic increase in the food supply and in food consumption not a surprise. Yet there are still many mysteries about weight change that can.t be answered either inside the lab, because of the impracticality of keeping people isolated for long periods of time, or outside, because of the unreliability of dietary diaries. Mathematical models based on differential equations can help overcome this roadblock and allow detailed analysis of the relationship between food intake, metabolism, and weight change. The models. predictions fit existing data and explain such things as why it is hard to keep weight off and why obese people are more susceptible to further weight gain. Researchers are also investigating why dieters often plateau after a few months and slowly regain weight. A possible explanation is that metabolism slows to match the drop in food consumed, but models representing food intake and energy expenditure as a dynamical system show that such a weight plateau doesn.t take effect until much later. The likely culprit is a combination of slower metabolism and a lack of adherence to the diet. Most people are in approximate steady state, so that long-term changes are necessary to gain or lose weight. The good news is that each (enduring) drop of 10 calories a day translates into one pound of weight loss over three years, with about half the loss occurring in the first year. For More Information: Quantification of the effect of energy imbalance on bodyweight, Hall et al. Lancet, Vol. 378 (2011), pp. 826-837.