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A new assembler for decoding genomes of microbial communities developed

Researchers from the Center for Algorithmic Biotechnology at St Petersburg University, as part of a group of Russian and American…

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Researchers from the Center for Algorithmic Biotechnology at St Petersburg University, as part of a group of Russian and American scientists, have developed the metaFlye assembler.

Researchers from the Center for Algorithmic Biotechnology at St Petersburg University, as part of a group of Russian and American scientists, have developed the metaFlye assembler. It is designed to assemble DNA samples from microbial communities. With its help, it is possible to solve a wide range of fundamental and applied problems, among which is the control of the process of treating patients and even the creation of new drugs.

At present, to study the DNA of any living organism, scientists around the world use complex biotechnological instruments – DNA sequencers. These special machines cannot ‘read’ the genome from start to finish (like people read books). They do it in separate short fragments – reads. Combining reads into longer fragments, and ideally into a single sequence of the original genome, is an extremely complex computational problem. It is like assembling a million-piece puzzle. The problem is complicated by the fact that genomes often contain a large number of identical repetitive sequences, which often exceed the length of reads. It is possible to cope with this challenging problem using specialised software – genome assemblers.

Several dozen different assemblers are being developed in leading bioinformatics laboratories around the world, and they are available to scientists. This diversity is because the algorithms that assemblers are based on need to be adapted to: different types of input data obtained on different types of DNA sequencers; and different organisms. For example, approaches for assembling bacterial genomes may not be suitable at all for assembling the human genome and vice versa. Additionally, the developers of genomic assemblers are constantly striving to improve their solutions so that: their programmes run faster and use less memory; and the resulting assemblies are longer and more accurate than those produced by the competing software.

The new metaFlye assembler is designed for assembling metagenomes. These are DNA samples from microbial communities obtained from various environments, such as the deep sea, soil in a park, or human gut. Having received an assembly of such a sample, it is possible to determine what kind of and how many organisms are presented in it. Using additional assembly analysis, it is often possible to find out: what these organisms can feed on; how they interact; and what substances they synthesise. All this information can be used in the future, for example: to search for new drugs of natural origin; to determine the reasons underlying the extreme soil fertility; when checking the course of treating patients; and in solving many other fundamental and applied problems.

The metaFlye assembler is designed for data obtained using the current state-of-the-art sequencing technology – long-read sequencing. There are already several metagenomic assemblers working with short-read sequencing, or next-generation sequencing (NGS) data generated on Illumina instruments. Among these assemblers there is the metaSPAdes assembler. It was developed at the Center for Algorithmic Biotechnology at St Petersburg University in 2016. There are also software for assembling isolate genomes from long reads. metaFlye makes it possible to take advantage of the new technology for complex metagenomic data. It is the first metagenome assembler specially designed to work with Oxford Nanopore and PacBio technologies.

‘The impetus to develop metaFlye was the absence of a specific metagenomic assembler for long-read technology,’ says Mikhail Rayko, one of the project’s authors, a senior research fellow at the Center for Algorithmic Biotechnology at St Petersburg University. ‘This technology has already changed dramatically the whole modern genomic science. We have learned to obtain much more complete assemblies. For example, with its help, many missing fragments of the human genome have recently been sequenced and localised. The original Flye tool was used for that, and the members of our laboratory also took part in this project. However, such data have just begun to appear for metagenomes, and, of course, special tools are needed for processing it.’

Work on metaFlye started about two years ago. It is four years if we count from the creation of its predecessor, the genomic assembler Flye, on the basis of which the new project was implemented.

‘In our study, published in the journal Nature Methods, we used metaFlye and other assemblers to analyse several simulated (i.e., computer generated, without real DNA sequencing) and real metagenomic samples from the gastrointestinal tract of a human, a cow and a sheep,’ says Alexey Gurevich, a co-author of the assembler and a senior research fellow at the Center for Algorithmic Biotechnology at St Petersburg University. ‘A sample of the sheep microbiome is perhaps of principal interest. It was first obtained and studied in this work, while the initial sequencing data for the other two samples were taken from the works of third-party authors. metaFlye made it possible to assemble an order of magnitude more viral genomes and one and a half times more plasmids in this sample than when using the best existing analogue programmes.’

Another intriguing result was that it was possible to assemble in the sample the genomes of not only bacteria and archaea, but also eukaryotes. At the same time, bioinformatics analysis revealed that almost half of eukaryotic genomic fragments belong to representatives of nematodes, or roundworms. This result fully complies with the autopsy report of the animal, which showed signs of parasitic infection.

‘The metaFlye assembler is a tool for solving a wide range of tasks. It will be available to all researchers working with such data. Of the specific projects carried out in our laboratory, we use the assembler to study the soil composition in Chernevaya taiga – a unique biocoenosis of Western Siberia with abnormally high fertility,’ says Alexey Gurevich.

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Source: https://bioengineer.org/a-new-assembler-for-decoding-genomes-of-microbial-communities-developed/

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Bioengineer

Solving the puzzle of polymers binding to ice for Cryopreservation

Credit: Credit: University of Warwick Cryoprotectants are used to protect biological material during frozen storage They have to be removed

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  • Cryoprotectants are used to protect biological material during frozen storage
  • They have to be removed when defrosting, and how much to use and how exactly they inhibit ice recrystallisation is poorly understood
  • The polymer poly(vinyl)alcohol (PVA) is arguably the most potent ice recrystallisation inhibitor and researchers from the University of Warwick have unravelled how exactly it works.
  • This newly acquired knowledge base provides novel guidelines to design the next generation of cryoprotectants

When biological material (cells, blood, tissues) is frozen, cryoprotectants are used to prevent the damage associated with the formation of ice during the freezing process. New polymeric cryoprotectants are emerging, alongside the established cryoprotectants, but how exactly they manage to control ice formation and growth is still largely unknown. This is especially true for PVA, a deceptively simple synthetic polymer that interacts with ice by means of mechanisms that have now been revealed at the atomistic level thanks to researchers from the University of Warwick.

Cryoprotectants are crucial when freezing biological material to lessen the cellular damage involved with the formation of ice. Ice re-crystallization, that is the process by which larger ice crystals grow at the expense of smaller ones, is one of the major issues affecting the current cryopreservation protocols and it is still poorly understood. Researchers from the University of Warwick have investigated how a rather popular polymer with the potential to be used in cryopreservation binds to the growing ice crystals.

In the paper, ‘The atomistic details of the ice recrystallisation inhibition activity of PVA’, published in the journal Nature Communications, researchers from the University of Warwick have found that, contrary to the emerging consensus, shorter or longer polymeric chains of poly(vinyl)alcohol (PVA) all bind to ice.

Up to now, the community has been working under the assumption that short polymers do not bind strongly enough to the ice crystals, but in this work Dr. Sosso and co-workers have demonstrated that it is the subtle balance between these binding interactions and the effective volume occupied by the polymers at the interface with ice that determine their effectiveness in hindering ice re-crystallization.

This work brings together experimental measurements of ice recrystallization inhibition and computer simulations. The latter are invaluable tools to gain microscopic insight into processes such as the formation of ice, as they are able to see what is happening in very fast or very small processes which are hard to see via even the most advanced experimental techniques.

This work sheds new light onto the fundamental principles at the heart of ice re-crystallization, pinpointing design principles that can be directly harnessed to design the next generation of cryoprotectants. This achievement is a testament to the strength of what is affectionately known as ‘Team Ice’ at Warwick, an ever-growing collaborative network with the potential to make a huge impact on many aspects of ice formation, from atmospheric science to medicinal chemistry.

Fabienne Bachtiger, a PhD student working in the research group of Dr. Sosso (Department of Chemistry) who has spearheaded this work, explains:
“We have found that even rather short chains of PVA, containing just ten polymeric units, do bind to ice, and that small block co-polymers of PVA bind too. It is important for the experimental community to know this, as they have been working under different assumptions up to now. In fact, this means we can successfully use much smaller polymers than previously thought. This is crucial information to aid the development of new more active cryoprotectants.”

Dr. Gabriele Sosso, from the Department of Chemistry at the University of Warwick, who is leading a substantial computational effort to investigate the formation of ice in biological matter, points out that:
“With this contribution we have added a crucial piece to the puzzle of how exactly polymeric cryoprotectants interact with growing ice crystals. This is part of a larger body of computational and theoretical work that my group is pursuing with the intent to understand how cryoprotectants work at the molecular level, so as to identify designing principles that can be directly probed by our experimental colleagues. Warwick is the perfect place to further our understanding of ice, and this work showcases the impact of the very exciting collaboration between my research group and the Gibson Group.”

Professor Matthew Gibson, from the Department of Chemistry and Warwick Medical School at the University of Warwick adds: “Ice re-crystallization is a real challenge in cryobiology, leading to damage to cells but also in frozen foods or infrastructure. Understanding how even this ‘simple’ polymer works to control ice re-crystallization is a major step forward to discover new cryoprotectants, and ultimately to use them in the real world.”

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15 MARCH 2021

  • This newly acquired knowledge base provides novel guidelines to design the next generation of cryoprotectants
  • Source: https://bioengineer.org/solving-the-puzzle-of-polymers-binding-to-ice-for-cryopreservation/

    solving-the-puzzle-of-polymers-binding-to-ice-for-cryopreservation

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    Debris of stellar explosion found at unusual location

    eROSITA space telescope finds largest supernova remnant ever discovered with X-raysCredit: eROSITA/MPE (X-ray), CHIPASS / SPASS / N. Hurley-Walker, ICRAR-Curtin

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    eROSITA space telescope finds largest supernova remnant ever discovered with X-rays

    Credit: eROSITA/MPE (X-ray), CHIPASS / SPASS / N. Hurley-Walker, ICRAR-Curtin (Radio)

    In the first all-sky survey by the eROSITA X-ray telescope onboard SRG, astronomers at the Max Planck Institute for Extraterrestrial Physics have identified a previously unknown supernova remnant, dubbed “Hoinga”. The finding was confirmed in archival radio data and marks the first discovery of a joint Australian-eROSITA partnership established to explore our Galaxy using multiple wavelengths, from low-frequency radio waves to energetic X-rays. The Hoinga supernova remnant is very large and located far from the galactic plane – a surprising first finding – implying that the next years might bring many more discoveries.

    Massive stars end their lives in gigantic supernova explosions when the fusion processes in their interiors no longer produce enough energy to counter their gravitational collapse. But even with hundreds of billions of stars in a galaxy, these events are pretty rare. In our Milky Way, astronomers estimate that a supernova should happen on average every 30 to 50 years. While the supernova itself is only observable on a timescale of months, their remnants can be detected for about 100 000 years. These remnants are composed of the material ejected by the exploding star at high velocities and forming shocks when hitting the surrounding interstellar medium.

    About 300 such supernova remnants are known today – much less than the estimated 1200 that should be observable throughout our home Galaxy. So, either astrophysicists have misunderstood the supernova rate or a large majority has been overlooked so far. An international team of astronomers are now using the all-sky scans of the eROSITA X-ray telescope to look for previously unknown supernova remnants. With temperatures of millions of the degrees, the debris of such supernovae emits high-energy radiation, i.e. they should show up in the high-quality X-ray survey data.

    “We were very surprised that the first supernova remnant popped up straight away,” says Werner Becker at the Max Planck Institute for Extraterrestrial Physics. Named after the first author’s hometown’s Roman name, “Hoinga” is the largest supernova remnant ever discovered in X-rays. With a diameter of about 4.4 degrees, it covers an area about 90 times bigger than the size of the full Moon. “Moreover, it lies very far off the galactic plane, which is very unusual,” he adds. Most previous searches for supernova remnants have concentrated on the disk of our galaxy, where star formation activity is highest and stellar remnants therefore should be more numerous, but it seems that many supernova remnants have been overlooked by this search strategy.

    After the astronomers found the object in the eROSITA all-sky data, they turned to other resources to confirm its nature. Hoinga is – although barely – visible also in data taken by the ROSAT X-ray telescope 30 years ago, but nobody noticed it before due to its faintness and its location at high galactic latitude. However, the real confirmation came from radio data, the spectral band where 90% of all known supernova remnants were found so far.

    “We went through archival radio data and it had been sitting there, just waiting to be discovered,” marvels Natasha Walker-Hurley, from the Curtin University node of the International Centre for Radio Astronomy Research in Australia. “The radio emission in 10-year-old surveys clearly confirmed that Hoinga is a supernova remnant, so there may be even more of these out there waiting for keen eyes.”

    The eROSITA X-ray telescope will perform a total of eight all-sky surveys and is about 25 times more sensitive than its predecessor ROSAT. Both observatories were designed, build and are operated by the Max Planck Institute for Extraterrestrial Physics. The astronomers expected to discover new supernova remnants in its X-ray data over the next few years, but they were surprised to identify one so early in the programme. Combined with the fact that the signal is already present in decades-old data, this implies that many supernova remnants might have been overlooked in the past due to low-surface brightness, being in unusual locations or because of other nearby emission from brighter sources. Together with upcoming radio surveys, the eROSITA X-ray survey shows great promise for finding many of the missing supernova remnants, helping to solve this long-standing astrophysical mystery.

    ###

    Original publication

    W. Becker, N. Hurley-Walker, Ch. Weinberger, L. Nicastro, M. G. F. Mayer, A. Merloni, J. Sanders
    Hoinga – A Supernova Remnant Discovered in the SRG/eROSITA All-Sky Survey eRASS1
    Astronomy & Astrophysics, accepted 12 February 2021

    https://www.mpg.de/16527751/0302-ext0-giant-cloud-found-at-unusual-location-151510-x

    Source: https://bioengineer.org/debris-of-stellar-explosion-found-at-unusual-location/

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    Security most important to retaining mobile banking customers, NTU-WeBank study finds

    Service quality and system quality rank second and thirdCredit: NTU Singapore A study by a research team from Nanyang Technological

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    A study by a research team from Nanyang Technological University, Singapore (NTU Singapore) and China’s first digital-only bank WeBank has found that security, service quality and system quality are the most important factors for customers who use mobile banking.

    Two in five respondents (40%) said that the security they felt while carrying out transactions on mobile applications was their most important consideration.

    This was followed by the level of service quality (25%), which referred to whether the banking applications could fulfil users’ needs, such as carrying out transactions and easy access to credit card services.

    System quality, which considers the performance of the application, including compatibility with different mobile phones and loading speeds, came in a close third (24%).

    The results of the study were published in the Journal of Retailing and Consumer Services, an academic publication by Elsevier, last December.

    The researchers said their study which ranked factors that are important in determining customer loyalty would be useful to financial institutions who are looking at improving their mobile banking applications.

    Already widely used in China prior to COVID-19, mobile banking applications have seen a sharp rise in uptake throughout Asia during the pandemic, as the touchless payment systems provided by most mobile banking applications have gained traction.

    The NTU-WeBank team obtained their results after surveying 224 mobile banking users of a large bank in China in 2019. Over three-quarters of the respondents (79%) were frequent users of mobile banking, meaning that they used it at least once a week.

    The researchers said that although the study was conducted in China, the results are applicable to other countries where mobile banking has a high level of adoption, such as Singapore, Thailand, and Vietnam.

    Associate Professor Xu Hong, from NTU’s School of Social Sciences who led the study, said: “It was already known that all these factors: security, service quality, system quality, and interface design had an impact on customers, and this study highlights implications for banks’ strategies for retaining their mobile banking users, as well as exploring how to capture new customers.”

    Assistant Professor Yu Han, from NTU’s School of Computer Science and Engineering, who co-led the research, said: “Our study has implications for banks’ strategies for retaining their mobile banking users, as well as exploring how to capture new customers.”

    Assoc Prof Xu and Asst Prof Yu are part of the team at the Joint NTU-WeBank Research Centre on Fintech which initiated this study. The joint centre was launched in early 2019 with the aim of developing new technologies to support Banking 4.0, where banking can be personalised and done anytime, anywhere.

    Mr Joe Chen, Executive Vice President of WeBank, said: “The findings are relevant to other banks who are increasingly rolling out more digital solutions, which include payment, lending, and wealth management applications. As mobile banking worldwide is becoming increasingly accepted as replacement for branch-based banking in many countries, it is important for banks to know the factors that affect and influence customer loyalty. In this regard, the Joint NTU-WeBank Research Centre will continue to generate research outcomes and innovations for the benefit of the Fintech industry.”

    NTU Senior Vice President (Research) Professor Lam Khin Yong, added: “The NTU-WeBank partnership is another example of the University’s strong links with the private sector. It also shows our strong support for industry collaborations that accelerates the translation of research into innovation and commercial adoption. This study also serves as a good example of interdisciplinary research involving faculty from the social sciences and computer science, as it solves a very important issue in today’s fintech industry.”

    A multi-pronged approach to build customer loyalty

    The team’s analysis of the results also showed that a mobile application’s interface design had a strong and positive impact on respondents’ evaluation of system and service quality.

    This is despite it scoring relatively low compared to other factors surveyed in the study. For example, the team found that respondents tended to associate good interface design, such as smooth transitions between pages, with optimal system quality and high security.

    The findings also outlined a larger correlation between several factors that were surveyed. For example, service and system quality and interface design were found to be important in sparking user loyalty, which the researchers defined as “the intention to continuously use the mobile banking product and recommend it to others.”

    After analysing the survey results, the team advised that mobile banking operators should focus on providing multi-level security features to increase the users’ sense of security when using the applications.

    Such features might include pop-up messages that alert users to the potential risks that could occur when using mobile banking services, as well as a well-documented policy statement from the financial institution.

    Besides providing users assurance of their security while using the applications, Assoc Prof Xu added: “The level of service quality, which encompasses factors such as the levels of reliability, responsiveness, and empathy from bank staff, could enhance users’ satisfaction and increase their usage of mobile banking services.”

    “By providing a stable and secure mobile banking system that boasts fast responses and efficient service, banks can encourage customers to continue using their mobile banking application, while ultimately strengthening user loyalty. The results can also help improve their overall mobile banking strategy and cater the functions of their apps to the needs of different age groups.”

    Next steps: overseas studies

    To further their research on loyalty intention in mobile banking, the NTU-WeBank team is looking to conduct studies in other countries and regions to identify other determinants that could affect customer loyalty.

    Assoc Prof Xu said the team will continue to leverage the computing platform which it has developed to collect and analyse user experience data for future studies.

    “We believe the large-scale immersive studies we will conduct using our computing platform powered by social computing and social media technologies will be able to help banks gain more insights into customers’ intentions,” said Assoc Prof Xu.

    ###

    http://news.ntu.edu.sg/pages/newsdetail.aspx?URL=http://news.ntu.edu.sg/news/Pages/NR2021_Mar15.aspx&Guid=5210e29e-b797-4bda-8866-df252ffc77cd&Category=News+Releases

    The results of the study were published in the Journal of Retailing and Consumer Services, an academic publication by Elsevier, last December.

    Source: https://bioengineer.org/security-most-important-to-retaining-mobile-banking-customers-ntu-webank-study-finds/

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