1 November 2007 , Number 4

The world’s most populous democracy and its new economic engine are both busy modifying positions on Burma, their much smaller but troublesome neighbour. India and China have growing economic interests there, yet seem to have come to very different conclusions about how to protect them.

7 May 2020 , Volume 96, Number 3

Knowledge of the molecular events in mitochondrial DNA (mtDNA) replication is crucial to understanding the origins of human disorders arising from mitochondrial dysfunction. Twinkle helicase is an essential component of mtDNA replication. Here, we employed atomic force microscopy imaging in air and liquids to visualize ring assembly, DNA binding, and unwinding activity of individual Twinkle hexamers at the single-molecule level. We observed that the Twinkle subunits self-assemble into hexamers and higher-order complexes that can switch between open and closed-ring configurations in the absence of DNA. Our analyses helped visualize Twinkle loading onto and unloading from DNA in an open-ringed configuration. They also revealed that closed-ring conformers bind and unwind several hundred base pairs of duplex DNA at an average rate of ∼240 bp/min. We found that the addition of mitochondrial single-stranded (ss) DNA–binding protein both influences the ways Twinkle loads onto defined DNA substrates and stabilizes the unwound ssDNA product, resulting in a ∼5-fold stimulation of the apparent DNA-unwinding rate. Mitochondrial ssDNA-binding protein also increased the estimated translocation processivity from 1750 to >9000 bp before helicase disassociation, suggesting that more than half of the mitochondrial genome could be unwound by Twinkle during a single DNA-binding event. The strategies used in this work provide a new platform to examine Twinkle disease variants and the core mtDNA replication machinery. They also offer an enhanced framework to investigate molecular mechanisms underlying deletion and depletion of the mitochondrial genome as observed in mitochondrial diseases.

19 March 2020

K. D. Cherednichenko, Yu. Yu. Ershova, A. V. Kiselev and S. N. Naboko
Trans. Moscow Math. Soc. 80 (2020), 251-294.
Abstract, references and article information

17 January 2020

Muthu Alagappan explains how topology and analytics are bringing a new look to basketball.

Researcher: Norbert Stoop, MIT
Title: Adding a New Wrinkle
Description: Norbert Stoop talks about new research on the formation of wrinkles.

Researcher: Andy Andres, Boston University Moment: http://www.ams.org/samplings/mathmoments/mm136-baseball.pdf Andy Andres on baseball analytics.

Cathy Lloyd
Apr 1, 2005; 18:121-127
Feature Articles

Lens proteins become increasingly cross-linked through nondisulfide linkages during aging and cataract formation. One mechanism that has been implicated in this cross-linking is glycation through formation of advanced glycation end products (AGEs). Here, we found an age-associated increase in stiffness in human lenses that was directly correlated with levels of protein–cross-linking AGEs. α-Crystallin in the lens binds to other proteins and prevents their denaturation and aggregation through its chaperone-like activity. Using a FRET-based assay, we examined the stability of the αA-crystallin–γD-crystallin complex for up to 12 days and observed that this complex is stable in PBS and upon incubation with human lens–epithelial cell lysate or lens homogenate. Addition of 2 mm ATP to the lysate or homogenate did not decrease the stability of the complex. We also generated complexes of human αA-crystallin or αB-crystallin with alcohol dehydrogenase or citrate synthase by applying thermal stress. Upon glycation under physiological conditions, the chaperone–client complexes underwent greater extents of cross-linking than did uncomplexed protein mixtures. LC-MS/MS analyses revealed that the levels of cross-linking AGEs were significantly higher in the glycated chaperone–client complexes than in glycated but uncomplexed protein mixtures. Mouse lenses subjected to thermal stress followed by glycation lost resilience more extensively than lenses subjected to thermal stress or glycation alone, and this loss was accompanied by higher protein cross-linking and higher cross-linking AGE levels. These results uncover a protein cross-linking mechanism in the lens and suggest that AGE-mediated cross-linking of α-crystallin–client complexes could contribute to lens aging and presbyopia.

Knowledge of the molecular events in mitochondrial DNA (mtDNA) replication is crucial to understanding the origins of human disorders arising from mitochondrial dysfunction. Twinkle helicase is an essential component of mtDNA replication. Here, we employed atomic force microscopy imaging in air and liquids to visualize ring assembly, DNA binding, and unwinding activity of individual Twinkle hexamers at the single-molecule level. We observed that the Twinkle subunits self-assemble into hexamers and higher-order complexes that can switch between open and closed-ring configurations in the absence of DNA. Our analyses helped visualize Twinkle loading onto and unloading from DNA in an open-ringed configuration. They also revealed that closed-ring conformers bind and unwind several hundred base pairs of duplex DNA at an average rate of ∼240 bp/min. We found that the addition of mitochondrial single-stranded (ss) DNA–binding protein both influences the ways Twinkle loads onto defined DNA substrates and stabilizes the unwound ssDNA product, resulting in a ∼5-fold stimulation of the apparent DNA-unwinding rate. Mitochondrial ssDNA-binding protein also increased the estimated translocation processivity from 1750 to >9000 bp before helicase disassociation, suggesting that more than half of the mitochondrial genome could be unwound by Twinkle during a single DNA-binding event. The strategies used in this work provide a new platform to examine Twinkle disease variants and the core mtDNA replication machinery. They also offer an enhanced framework to investigate molecular mechanisms underlying deletion and depletion of the mitochondrial genome as observed in mitochondrial diseases.

(Institute for Operations Research and the Management Sciences) Job performance has long been understood to be the primary equalizing factor affecting promotions for men and women in the workplace, but research shows, women don't gain as much from the same performance improvements as men do. New research in the INFORMS journal Information Systems Research shows training plays an important part in promotions for women in the field of information technology.

(Anglia Ruskin University) A new study has found an association between low average levels of vitamin D and high numbers of COVID-19 cases and mortality rates across 20 European countries.

(Columbia University's Mailman School of Public Health) Researchers found that 92 percent of employers who responded to a survey on climate change and public health reported need for public health professionals with training in climate change will very likely increase in the next 5 to 10 years. While graduates of public health programs who focus on climate change are in demand in the current job market, these positions appear to be just a small proportion of the total number of jobs available in public health.

(Texas A&M University) Spoiling foods, souring wine and worsening wounds have a common culprit -- a process called oxidation. Although the ill effects of these chemical reactions can be curtailed by antioxidants, creating a sturdy platform capable of providing prolonged antioxidant activity is an ongoing challenge.

(Earth Institute at Columbia University) A uniquely resilient organism all but unheard of in the Arabian Sea 20 years ago has been proliferating and spreading at an alarming pace. New research describes how the continued loss of snow over the Himalayan-Tibetan Plateau region is fueling the expansion of this destructive algal bloom.

As businesses slowly reopen, experts warn that social distancing may need to be dialed back up: ‘It’s not an on-off switch’ * Coronavirus – latest US updates * Coronavirus – latest global updatesSome California businesses on Friday began opening their doors for business – at least partially.As states and counties across the nation contend with pressure to lift the stay-at-home measures that have destroyed local economies, California is taking an especially cautious approach, walking a fine line between political and economic pressure to reopen and the public health imperative to stop the spread of disease.Public health experts told the Guardian that while no US state was equipped with enough coronavirus testing and surveillance to feel fully confident reopening, California’s slow, piecemeal recovery plan – though far from perfect – seemed like the least risky option. The planSeven weeks after the governor, Gavin Newsom, ordered his 40 million constituents to shelter in place and all non-essential businesses to close, California on Friday entered phase two of its grand reopening plan.Some retail stores, including bookshops, florists, music stores, clothing and sporting goods retailers, can reopen if they organize curbside pickup. Some manufacturing and logistics in the retail supply chain can restart as well, as long as they follow safety and hygiene protocols. And local authorities are allowed to ease regulations further than the state guidelines if they meet certain testing and sanitation requirements.Phase three of the plan – potentially months away – could see salons, gyms, movie theaters and in-person church services resume. Phase four would end all restrictions. The timingFriday’s reopenings come as California has avoided the surge of infections states like New York have seen. And although California has seen more than 61,000 cases and 2,500 deaths, its hospitals have not been overwhelmed.Last week, state officials reported the first week-over-week decline in Covid-19 deaths.The new guidelines also follow small but sustained protests across the state to demand a relaxation of regulations to revive the state’s crippled economy, and some rural counties have partially reopened in defiance of the lockdown measures. The caveatsHowever, California still hasn’t seen the two weeks of declining cases that the White House suggested as a criterion for easing restrictions and that several European countries have used as a benchmark.The state also lacks the robust testing and tracking systems that countries such as Germany and South Korea have used.The state has ramped up its ability to administer and process tests, although for now, its rate of 29,414 tests a day is below the figure required by some analyses.Authorities are working to put a robust contact tracing effort in place to make sure those who test positive get the care they need and are able to isolate themselves until they recover. Although some counties and communities have spearheaded community-wide testing and tracing programs, overall, the state isn’t at the point where its system is as widespread or efficient as a country like Germany’s.Experts say California should also have a system in place to make sure vulnerable, unhoused populations have access to shelter and medical care – to prevent infection flare-ups in homeless shelters and encampments. Progress on those measures heavily varies county by county.And ideally, there would be a treatment or a vaccine before reopening, said Dr Richard Jackson, a professor emeritus at the UCLA Fielding School of Public Health and the former head of the California department of public health. While we await a cure, Jackson cautioned, “no one should feel completely safe as we remove restrictions.” The trade-offsCalifornia’s reopening strategy stands in sharp contrast to the approach of states like Georgia, which suddenly allowed gyms, barber shops, hair salons, tattoo parlors and bowling alleys to welcome customers last week.“What certain places have done, where they’ve just thrown open the doors and said, ‘OK, we don’t have to keep our distance any more,’ is a colossal mistake,” Jackson said. Reopening businesses that put lots of people into close contact and speed the spread of disease will reverse the success of shelter-in-place rules, he noted, and overwhelm hospitals as cases surge. “Doing it very cautiously and carefully does make sense at this point in time,” he said.“I get that governors have to balance the public health goals with the economic goals,” said Dr Robert Tsai, surgeon and health policy researcher at Brigham and Women’s hospital in Boston and the Harvard TH Chan School of Public Health. “But this stage of the pandemic is really all about trade-offs,” he noted. The weeks aheadIn the coming weeks, state and local leaders will have to watch closely and prepare to dial the distancing back up if the number of cases surges, said Tsai.“Social distancing isn’t an on-off switch. What it needs to be is a dial, which can be turned up or down depending on what the data show on the ground in terms of how the Covid-19 epidemic is progressing.“Reopening is going to be a very complicated process, and it should be complicated,” he added. “Because this is about making sure that people don’t end up in the hospital or dying.”That California’s plan allows for counties to maintain stricter distancing guidelines or ease up measures could be both a strength and a liability.The flexibility has allowed hotspots like the Bay Area and Los Angeles to take a more cautious approach, but it has also already caused confusion. In San Diego, where curbside shopping has already begun, business owners were unsure what, if anything, would change on Friday. In Bakersfield, restaurants allowed patrons to dine in on Monday and Tuesday, in defiance of the state’s guidelines.A hodgepodge reopening could cause surges in cases; Californians who travel between more lax and more strict counties could spread infections. Moreover, a rush to reopen fast in some areas could be counterproductive to economic recovery, said Alessandro Rebucci, an economist at the Johns Hopkins Carey School of Business.“If you reopen when the pandemic is still out there, people and businesses will not just go back to normal,” Rebucci noted. Based on research from China, it seems clear that fear of contracting the illness will keep businesses owners and patrons home until they feel it’s safe enough, he said.

Cathy Lloyd
Apr 1, 2005; 18:121-127
Feature Articles

Andreas Linden
Apr 24, 2020; 0:RA120.002028v1-mcp.RA120.002028
Research

Taewook Kang
Apr 7, 2020; 0:RA119.001882v1-mcp.RA119.001882
Research

Qingbo Shu
Apr 1, 2020; 19:672-689
Research

Karl A. T. Makepeace
Apr 1, 2020; 19:624-639
Research

Research Event

Event participants

Osamah Al Rawhani, Deputy Director, Sana’a Center for Strategic Studies
Moderator: Nadim Houry, Executive Director, Arab Reform Initiative

Protein-protein interactions play a vital role in nearly all cellular functions. Hence, understanding their interaction patterns and three-dimensional structural conformations can provide crucial insights about various biological processes and underlying molecular mechanisms for many disease phenotypes. Cross-linking mass spectrometry (XL-MS) has the unique capability to detect protein-protein interactions at a large scale along with spatial constraints between interaction partners. The inception of MS-cleavable cross-linkers enabled the MS2-MS3 XL-MS acquisition strategy that provides cross-link information from both MS2 and MS3 level. However, the current cross-link search algorithm available for MS2-MS3 strategy follows a "MS2-centric" approach and suffers from a high rate of mis-identified cross-links. We demonstrate the problem using two new quality assessment metrics ["fraction of mis-identifications" (FMI) and "fraction of interprotein cross-links from known interactions" (FKI)]. We then address this problem, by designing a novel "MS3-centric" approach for cross-link identification and implementing it as a search engine named MaXLinker. MaXLinker outperforms the currently popular search engine with a lower mis-identification rate, and higher sensitivity and specificity. Moreover, we performed human proteome-wide cross-linking mass spectrometry using K562 cells. Employing MaXLinker, we identified a comprehensive set of 9319 unique cross-links at 1% false discovery rate, comprising 8051 intraprotein and 1268 interprotein cross-links. Finally, we experimentally validated the quality of a large number of novel interactions identified in our study, providing a conclusive evidence for MaXLinker's robust performance.