Tag Archives: Chen Chen

CRISPR/Cas9 used successfully to edit SIV (simian immunodeficiency virus, which is similar to HIV) out of monkey genome

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Before reading further please note, the research discussed in this posting is based on animal testing, which many people find highly disturbing.

CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9), or more familiarly CRISPR/Cas9, has been been used to edit simian immunodeficiency virus from infected monkeys’ cells according to a December 2, 2020 article by Matthew Rozsa for Salon.com (Note: Links have been removed),

With multiple coronavirus vaccines being produced as we speak, the COVID-19 pandemic appears to have an end in sight, though the HIV pandemic continues after more than 40 years. That might seem like a head-scratcher: why is HIV, a virus we’ve known about for decades, so much harder to cure than a virus discovered just last year? Part of the reason is that HIV, as a retrovirus, is a more complex virus to vaccinate against than SARS-CoV-2 — hence why a vaccine or other cure has eluded scientists for decades. 

Now, a surprising new study on a related retrovirus shows incredible promise for the potential to develop a cure for HIV, or human immunodeficiency virus. In an article published in the scientific journal Nature Communications, scientists revealed that they had used CRISPR – a genetic technology that can alter DNA and whose developers won the 2020 Nobel Prize in Chemistry [specifically, Jennifer Doudna and Emanuelle Charpentier received the Nobel for developing CRISPR-cas9 or CRISPR/Cas9 not CRISPR alone) — to successfully edit SIV (simian immunodeficiency virus), a virus similar to HIV, out of the genomes of non-human primates.  Specifically, the scientists were able to edit out the SIV genome from rhesus macaque monkeys’ infected cells.

For anyone who’s interested in how CRISPR was developed and the many contributions which have led to the current state-of-the-art for CRISPR gene editing, see the History subsection of Wikipedia’s CRISPR entry.

Getting back to Rozsa’s December 2, 2020 article,

“This study used the CRISPR CaS9 system, which has been described as molecular scissors,” Andrew G. MacLean, PhD, wrote to Salon. MacLean is an associate professor at the Tulane National Primate Research Center and the Department of Microbiology and Immunology at Tulane University School of Medicine and was a senior co-investigator of the study. “It uses a highly specific targeting system to cut out a specific portion of DNA that is necessary for HIV to be able to produce more virus.”

He added, “Our collaborators at in the Khalili Lab at Temple University have developed a method of ‘packaging’ this within a single so-called vector. A vector is a non-disease causing virus that is used as a carrier for the CRISPR CaS9 scissors to get it into the tissues of interest.”

The experiments with SIV are considered to be a gateway to understanding HIV, as HIV is believed to have evolved from SIV, and is genetically similar.

“The rhesus macaque model of HIV/AIDS is the most valuable model to test efficacy of new interventions or approaches for preventing or treating HIV infection, prior to human clinical trials,” Binhua Ling, PhD, associate professor at the Southwest National Primate Research Center, Texas Biomedical Research Institute, wrote to Salon. “This first proof-of-principal [emphasis mine] study on the rhesus macaque model indicates that this virus-vehicle-delivered-CRISPR system can reach many tissue sites of the body, and is able to effectively delete virus DNA in infected cells. This paves the way for applying the same technology to the human body, which could lead to a cure for HIV infection.”

Tricia H. Burdo, PhD, another senior co-investigator on the new study who works at the Lewis Katz School of Medicine at Temple University, explained to Salon by email that “HIV is in a class of viruses (retroviruses) that inserts itself into the DNA of the host, so you can really think of this now as a genetic disease” — in other words, the kind of thing that would be ripe for CRISPR’s scissors-like ability to remove errant or unwanted genetic material. Burdo notes that the CRISPR technology discussed in the article “cuts out this foreign viral gene.”

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The study was conducted on eight Rhesus macaque monkeys. That is a very small number to start with and not all of the monkeys received the CRISPR/Cas9 treatment. From the ‘Animals used in the study and ethical statement‘ subsection of the study, “Animals were sacrificed for tissue collection 3 weeks after … .” Leaving aside how anyone may feel about ‘sacrificing …’, three weeks is not a long time for observation.

Should you be interested, there is a November 30, 2020 Tulane University news release announcing the research.

If you want to read the whole study, here’s a link and a citation,

CRISPR based editing of SIV proviral DNA in ART treated non-human primates by Pietro Mancuso, Chen Chen, Rafal Kaminski, Jennifer Gordon, Shuren Liao, Jake A. Robinson, Mandy D. Smith, Hong Liu, Ilker K. Sariyer, Rahsan Sariyer, Tiffany A. Peterson, Martina Donadoni, Jaclyn B. Williams, Summer Siddiqui, Bruce A. Bunnell, Binhua Ling, Andrew G. MacLean, Tricia H. Burdo & Kamel Khalili. Nature Communications volume 11, Article number: 6065 (2020) DOI: https://doi.org/10.1038/s41467-020-19821-7 Published: 27 November 2020

This paper is open access.

As Rozsa notes in his December 2, 2020 article, the Joint United Nations Programme on HIV/AIDS estimates that 32.7 million [24.8 million–42.2 million] people have died from AIDS-related illnesses since the start (1981?) of the epidemic to the end of 2019.

Biodegradable films from cellulose nanofibrils

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A team at Purdue University (Indiana, US) has developed a new process for biodegradable films based on cellulose according to a June 8, 2016 news item on phys.org,

Purdue University researchers have developed tough, flexible, biodegradable films from cellulose, the main component of plant cell walls. The films could be used for products such as food packaging, agricultural groundcovers, bandages and capsules for medicine or bioactive compounds.

Food scientists Srinivas Janaswamy and Qin Xu engineered the cellophane-like material by solubilizing cellulose using zinc chloride, a common inorganic salt, and adding calcium ions to cause the cellulose chains to become tiny fibers known as nanofibrils, greatly increasing the material’s tensile strength. The zinc chloride and calcium ions work together to form a gel network, allowing the researchers to cast the material into a transparent, food-grade film.

A June 7, 2016 Purdue University news release by Natalie van Hoose, which originated the news item, discusses the need for these films and provides a few more technical details about the work (Note: A link has been removed),

“We’re looking for innovative ways to adapt and use cellulose – an inexpensive and widely available material – for a range of food, biomedical and pharmaceutical applications,” said Janaswamy, research assistant professor of food science and principal author of the study. “Though plastics have a wide variety of applications, their detrimental impact on the environment raises a critical need for alternative materials. Cellulose stands out as a viable option, and our process lays a strong foundation for developing new biodegradable plastics.”

Cellulose’s abundance, renewability and ability to biodegrade make it a promising substitute for petroleum-based products. While a variety of products such as paper, cellophane and rayon are made from cellulose, its tightly interlinked structure and insolubility – qualities that give plants strength and protection – make it a challenging material to work with.

Janaswamy and Xu loosened the cellulose network by adding zinc chloride, which helps push cellulose’s closely packed sheets apart, allowing water to penetrate and solubilize it. Adding calcium ions spurs the formation of nanofibrils through strong bonds between the solubilized cellulose sheets. The calcium ions boost the tensile strength of the films by about 250 percent.

The production process preserves the strength and biodegradability of cellulose while rendering it transparent and flexible.

Because the zinc chloride can be recycled to repeat the process, the method offers an environmentally friendly alternative to conventional means of breaking down cellulose, which tend to rely on toxic chemicals and extreme temperatures.

“Products based on this film can have a no-waste lifecycle,” said Xu, research assistant professor of food science and first author of the study. “This process allows us to create a valuable product from natural materials – including low-value or waste materials such as corn stover or wood chips- that can eventually be returned to the Earth.”

The methodology could be adapted to mass-produce cellulose films, the researchers said.

The next step in the project is to find ways of making the cellulose film insoluble to water while maintaining its ability to biodegrade.

Here’s a link to and a citation for the paper,

A facile route to prepare cellulose-based films by Qin Xu, Chen Chen, Katelyn Rosswurm, Tianming Yao, Srinivas Janaswamy. Carbohydrate Polymers Volume 149, 20 September 2016, Pages 274–281 doi:10.1016/j.carbpol.2016.04.114

This paper is behind a paywall.

PlasCarb: producing graphene and renewable hydrogen from food waster

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I have two tidbits about PlasCarb the first being an announcement of its existence and the second an announcement of its recently published research. A Jan. 13, 2015 news item on Nanowerk describes the PlasCarb project (Note: A link has been removed),

The Centre for Process Innovation (CPI) is leading a European collaborative project that aims to transform food waste into a sustainable source of significant economic added value, namely graphene and renewable hydrogen.

The project titled PlasCarb will transform biogas generated by the anaerobic digestion of food waste using an innovative low energy microwave plasma process to split biogas (methane and carbon dioxide) into high value graphitic carbon and renewable hydrogen.

A Jan. 13, 2015 CPI press release, which originated the news item, describes the project and its organization in greater detail,

CPI  as the coordinator of the project is responsible for the technical aspects in the separation of biogas into methane and carbon dioxide, and separating of the graphitic carbon produced from the renewable hydrogen. The infrastructure at CPI allows for the microwave plasma process to be trialled and optimised at pilot production scale, with a future technology roadmap devised for commercial scale manufacturing.

Graphene is one of the most interesting inventions of modern times. Stronger than steel, yet light, the material conducts electricity and heat. It has been used for a wide variety of applications, from strengthening tennis rackets, spray on radiators, to building semiconductors, electric circuits and solar cells.

The sustainable creation of graphene and renewable hydrogen from food waste in provides a sustainable method towards dealing with food waste problem that the European Union faces. It is estimated that 90 million tonnes of food is wasted each year, a figure which could rise to approximately 126 million tonnes by 2020. In the UK alone, food waste equates to a financial loss to business of at least £5 billion per year.

Dr Keith Robson, Director of Formulation and Flexible Manufacturing at CPI said, “PlasCarb will provide an innovative solution to the problems associated with food waste, which is one of the biggest challenges that the European Union faces in the strive towards a low carbon economy.  The project will not only seek to reduce food waste but also use new technological methods to turn it into renewable energy resources which themselves are of economic value, and all within a sustainable manner.”

PlasCarb will utilise quality research and specialist industrial process engineering to optimise the quality and economic value of the Graphene and hydrogen, further enhancing the sustainability of the process life cycle.

Graphitic carbon has been identified as one of Europe’s economically critical raw materials and of strategic performance in the development of future emerging technologies. The global market for graphite, either mined or synthetic is worth over €10 billion per annum. Hydrogen is already used in significant quantities by industry and recognised with great potential as a future transport fuel for a low carbon economy. The ability to produce renewable hydrogen also has added benefits as currently 95% of hydrogen is produced from fossil fuels. Moreover, it is currently projected that increasing demand of raw materials from fossil sources will lead to price volatility, accelerated environmental degradation and rising political tensions over resource access.

Therefore, the latter stages of the project will be dedicated to the market uptake of the PlasCarb process and the output products, through the development of an economically sustainable business strategy, a financial risk assessment of the project results and a flexible financial model that is able to act as a primary screen of economic viability. Based on this, an economic analysis of the process will be determined. Through the development of a decentralised business model for widespread trans-European implementation, the valorisation of food waste will have the potential to be undertaken for the benefit of local economies and employment. More specifically, three interrelated post project exploitation markets have been defined: food waste management, high value graphite and RH2 sales.

PlasCarb is a 3-year collaborative project, co-funded under the European Union’s Seventh Framework Programme (FP7) and will further reinforce Europe’s leading position in environmental technologies and innovation in high value Carbon. The consortium is composed of eight partners led by CPI from five European countries, whose complimentary research and industrial expertise will enable the required results to be successfully delivered. The project partners are; The Centre for Process Innovation (UK), GasPlas AS (NO), CNRS (FR), Fraunhofer IBP (DE), Uvasol Ltd (UK), GAP Waste Management (UK), Geonardo Ltd. (HU), Abalonyx AS (NO).

You can find PlasCarb here.

The second announcement can be found in a PlasCarb Jan. 14, 2015 press release announcing the publication of research on heterostructures of graphene ribbons,

Few materials have received as much attention from the scientific world or have raised so many hopes with a view to their potential deployment in new applications as graphene has. This is largely due to its superlative properties: it is the thinnest material in existence, almost transparent, the strongest, the stiffest and at the same time the most strechable, the best thermal conductor, the one with the highest intrinsic charge carrier mobility, plus many more fascinating features. Specifically, its electronic properties can vary enormously through its confinement inside nanostructured systems, for example. That is why ribbons or rows of graphene with nanometric widths are emerging as tremendously interesting electronic components. On the other hand, due to the great variability of electronic properties upon minimal changes in the structure of these nanoribbons, exact control on an atomic level is an indispensable requirement to make the most of all their potential.

The lithographic techniques used in conventional nanotechnology do not yet have such resolution and precision. In the year 2010, however, a way was found to synthesise nanoribbons with atomic precision by means of the so-called molecular self-assembly. Molecules designed for this purpose are deposited onto a surface in such a way that they react with each other and give rise to perfectly specified graphene nanoribbons by means of a highly reproducible process and without any other external mediation than heating to the required temperature. In 2013 a team of scientists from the University of Berkeley and the Centre for Materials Physics (CFM), a mixed CSIC (Spanish National Research Council) and UPV/EHU (University of the Basque Country) centre, extended this very concept to new molecules that were forming wider graphene nanoribbons and therefore with new electronic properties. This same group has now managed to go a step further by creating, through this self-assembly, heterostructures that blend segments of graphene nanoribbons of two different widths.

The forming of heterostructures with different materials has been a concept widely used in electronic engineering and has enabled huge advances to be made in conventional electronics. “We have now managed for the first time to form heterostructures of graphene nanoribbons modulating their width on a molecular level with atomic precision. What is more, their subsequent characterisation by means of scanning tunnelling microscopy and spectroscopy, complemented with first principles theoretical calculations, has shown that it gives rise to a system with very interesting electronic properties which include, for example, the creation of what are known as quantum wells,” pointed out the scientist Dimas de Oteyza, who has participated in this project. This work, the results of which are being published this very week in the journal Nature Nanotechnology, therefore constitutes a significant success towards the desired deployment of graphene in commercial electronic applications.

Here’s a link to and a citation for the paper,

Molecular bandgap engineering of bottom-up synthesized graphene nanoribbon heterojunctions by Yen-Chia Chen, Ting Cao, Chen Chen, Zahra Pedramrazi, Danny Haberer, Dimas G. de Oteyza, Felix R. Fischer, Steven G. Louie, & Michael F. Crommie. Nature Nanotechnology (2015) doi:10.1038/nnano.2014.307 Published online 12 January 2015

This article is behind a paywall but there is a free preview available via ReadCube access.