Tag Archives: Poland

Keeping ancient rock art traditions alive

While I have a preference for the new and emerging, sometimes, I like to take a look backwards. This October 1, 2024 news item on phys.org explores how rock art links the Indigenous peoples of Central Asia and Canada to each other and how both are bringing the tradition into contemporary art,

A new project is assessing the influence of ancient rock art on the modern art of Indigenous peoples in Central Asia and Canada, revealing its importance to reclaiming cultural identities.

Rock art holds an important place in the cultures of many Indigenous peoples to this day, indicating their shared communal identities and ancient ties to the land on which they live. However, the influence of rock art on current artistic movements is still rarely recognized and poorly understood.

“The contemporary re-use of rock art is a growing phenomenon,” says author of the research, Professor Andrzej Rozwadowski from Adam Mickiewicz University, Poland. “However, to date, very little attention has been paid to how rock art inspires contemporary Indigenous artists, especially in such little known areas as Siberia or Central Asia.”

An October 3, 2024 article by Conny Waters for AncientPages.com delves further into the topic,

Numerous cultures around the globe are engaged in preserving their artistic legacies. This effort involves safeguarding these cultural treasures from being forgotten and emphasizing their significance to ensure they remain a vital part of their shared heritage.

“The contemporary re-use of rock art is a growing phenomenon,” says author of the research. However, to date, very little attention has been paid to how rock art inspires contemporary Indigenous artists, especially in such little known areas as Siberia or Central Asia,” said Professor Andrzej Rozwadowski from Adam Mickiewicz University, Poland.

In his project “Rock Art as a Source of Contemporary Cultural Identity,” Professor Rozwadowski focuses on exploring and understanding the cultural significance of rock art created by Indigenous artists in Central Asia, specifically in regions such as Siberia and Kazakhstan, as well as in Canada.

It is also important to investigate how the work of the artists in these regions, was inspired by rock art.

… As younger generations forget First Nations traditions, the application of ancient rock art to contemporary artistic expression is essential for the preservation of heritage.

Many Indigenous Canadian artists also consciously link rock art traditions to modern colonial injustice, for example, the residential schools system, acting as decolonizing symbols intended to heal some wounds in Indigenous history. Moreover, the way rock art motifs are incorporated into modern art is strikingly similar across thousands of kilometers.

“The most memorable thing for me was what Canadian artist from the Cree Nation, Jane Ash Poitras said when I met her in Edmonton. When I showed her the work of the Khakass artist Alexander Domozhakov, from southern Siberia,  she said: ‘

Isn’t it Norval Morrisseau?!’ (Canada’s most prominent Indigenous artist).”

Here’s an example of contemporary art influenced by rock art from Central Asian artist,t Alexander Domozhakov,

Spirit of the Night by Khakas artist Alexander Domozhakov, oil on canvas, 1.6 × 1.1m, 1991 (collection of Olga Akhrimchik). Photograph by Andrzej Rozwadowski; source – Antiquity. [downloaded from https://www.ancientpages.com/2024/10/03/the-indigenous-artists-keeping-ancient-rock-art-traditions-alive-for-future-generations/]

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

Giving rock art new life: combining past images, identity and contemporary art by Andrzej Rozwadowski. Antiquity DOI:10.15184/aqy.2024.135 Published online 2024:1-7.

This paper is open access and, as academic papers go, it’s written in an accessible style with a minimum of jargon.

You’ll find the information in the October 1, 2024 news item and Waters’ October 3, 2024 article to be close to identical but the Waters’ article highlights the embedded images more successfully than either the news item or the paper does.

Leiden, European City of Science 2022, hosts EuroScience Open Forum (ESOF) 2022

The 2022 EuroScience Open Forum (ESOF) runs from July 13 – 16, 2022 but the 2022 European City of Science programme runs for the entire year and a July 15, 2022 University of Leiden press release (received via email) announces a special anniversary date being celebrated by Europe’s current City of Science [Leiden, Netherlands]*,

The smallest statue in the world: Leiden physicists and sculptor build a
nano-Rembrandt

Researchers from Leiden University together with sculptor Jeroen Spijker
created a 3D-printed statue of Rembrandt van Rijn of 28 micrometers tall
– that’s a third of the thickness of a hair. The sculpture, that
isn’t visible to the naked eye, is on display at Museum De Lakenhal in
Leiden. Leiden is the birth town of the famous painter, and on his
birthday today, everyone can come and ‘see’ the statue for free.

To celebrate Leiden European City of Science 2022, Jeroen Spijker worked
with physicists Daniela Kraft and Rachel Doherty from Leiden University
on a micro-statue of Rembrandt made from polymer with a layer of
platinum. At just 28 micrometres tall, the statue, which was made with a
3D printer, is around a third of the thickness of a human hair. This
makes it the smallest work of art in the world, says Jeroen Spijker.

3D printed as small as possible
The work is based on a bronze sculpture of Rembrandt that Spijker had
previously made. This was scanned and printed as small as possible with
a 3D printer. This isn’t Leiden University’s first miniature work.

In 2020 Kraft and Doherty’s research group used the same 3D printer to
make the smallest boat in the world, which could even sail. At 30
micrometres, this was slightly larger than Rembrandt.

Discover the limits of scientific devices
Not only are such tiny creations fun challenges but they also help
scientific research. Kraft and Doherty are studying microswimmers:
microscopic particles that can move in a fluid environment. They print
these microswimmers themselves with a very accurate 3D printer. ‘The
Rembrandt project is helping us discover the limits of our devices,’
says Doherty. ‘How small can we print something?’

On display next to Rembrandt’s paintings
Visitors will see for themselves how this is invisible to the naked eye.
The statue will be in the same room as paintings by Rembrandt. There is
also a short film about the process. Jeroen Spijker: ‘I wanted to
create a statue that I could still accept as a work of art with my own
signature. Any smaller and there would have been too many
distortions.’

About Leiden2022 European City of Science
The nano-statue of Rembrandt was created as a project where art meets
science, one aspect of Leiden2022 European City of Science. The statue
will be on display at Museum De Lakenhal until 31 July.

Leiden is European City of Science in 2022: for a year Leiden is the
capital of European science. Leiden University is a proud partner of
Leiden2022. For an entire year Leiden2022 will be offering a programme
for anyone with an open and curious mind, a programme packed with
science, knowledge, art and expertise.

Here’s the statue,

A special photo of the Rembrandt, which cannot be seen with the naked eye. Courtesy: University of Leident

You can find more about Leiden 2022 European City of Science here. While it’s late for the 2022 EuroScience Open Forum, there’s a preview of the upcoming 2024 European City of Science to be held in Katowice, Poland, which will likely be the site of the 2024 EuroScience Open Forum (ESOF) as well.

*[Leiden, Netherlands] added July 15, 2022 at 1325 hours PT.

Gold glue?

If you’re hoping for gold flecks in your glue, this is not going to satisfy you, given that it’s all at the nanoscale. An August 7, 2019 news item on Nanowerk briefly describes this gold glue (Note: A link has been removed),

It has long been known that gold can be used to do things that philosophers have never even dreamed of. The Institute of Nuclear Physics of the Polish Academy of Sciences in Cracow has confirmed the existence of ‘gold glue’: bonds involving gold atoms, capable of permanently bonding protein rings. Skilfully used by an international team of scientists, the bonds have made it possible to construct molecular nanocages with a structure so far unparalleled in nature or even in mathematics (Nature, “An ultra-stable gold-coordinated protein cage displaying reversible assembly”).

Caption: The ‘impossible’ sphere, i.e. a molecular nanocage of 24 protein rings, each of which has an 11-sided structure. The rings are connected by bonds with the participation of gold atoms, here marked in yellow. Depending on their position in the structure, not all gold atoms have to be used to attach adjacent proteins (an unused gold atom is marked in red). Credit: Source: UJ, IFJ PAN

An August 6, 2019 Polish Academy of Sciences press release (also on EurekAlert but published August 7, 2019), which originated the news item, expands on the theme,

The world of science has been interested in molecular cages for years. Not without reason. Chemical molecules, including those that would under normal conditions enter into chemical reactions, can be enclosed within their empty interiors. The particles of the enclosed compound, separated by the walls of the cage from the environment, have nothing to bond with. These cages can be therefore be used, for example, to transport drugs safely into a cancer cell, only releasing the drug when they are inside it.

Molecular cages are polyhedra made up of smaller ‘bricks’, usually protein molecules. The bricks can’t be of any shape. For example, if we wanted to build a molecular polyhedron using only objects with the outline of an equilateral triangle, geometry would limit us to only three solid figures: a tetrahedron, an octahedron or an icosahedron. So far, there have been no other structural possibilities.

“Fortunately, Platonic idealism is not a dogma of the physical world. If you accept certain inaccuracies in the solid figure being constructed, you can create structures with shapes that are not found in nature, what’s more, with very interesting properties,” says Dr. Tomasz Wrobel from the Cracow Institute of Nuclear Physics of the Polish Academy of Sciences (IFJ PAN).

Dr. Wrobel is one of the members of an international team of researchers who have recently carried out the ‘impossible’: they built a cage similar in shape to a sphere out of eleven-walled proteins. The main authors of this spectacular success are scientists from the group of Prof. Jonathan Heddle from the Malopolska Biotechnology Centre of the Jagiellonian University in Cracow and the Japanese RIKEN Institute in Wako. The work described in Nature magazine took place with the participation of researchers from universities in Osaka and Tsukuba (Japan), Durham (Great Britain), Waterloo (Canada) and other research centres.

Each of the walls of the new nanocages was formed by a protein ring from which eleven cysteine molecules stuck out at regular intervals. It was to the sulphur atom found in each cysteine molecule that the ‘glue’, i.e. the gold atom, was planned to be attached. In the appropriate conditions, it could bind with one more sulphur atom, in the cysteine of a next ring. In this way a permanent chemical bond would be formed between the two rings. But would the gold atom under these conditions really be able to form a bond between the rings?

“In the Spectroscopic Imaging Laboratory of IFJ PAS we used Raman spectroscopy and X-ray photoelectron spectroscopy to show that in the samples provided to us with the test nanocages, the gold really did form bonds with sulphur atoms in cysteines. In other words, in a difficult, direct measurement, we proved that gold ‘glue’ for bonding protein rings in cages really does exist,” explains Dr. Wrobel.

Each gold atom can be treated as a stand-alone clip that makes it possible to attach another ring. The road to the ‘impossible’ begins when we realize that we don’t always have to use all of the clips! So, although all the rings of the new nanocages are physically the same, depending on their place in the structure they connect with their neighbours with a different number of gold atoms, and thus function as polygons with different numbers of vertices. 24 nanocage walls presented by the researchers were held together by 120 gold atoms. The outer diameter of the cages was 22 nanometres and the inner diameter was 16 nm.

Using gold atoms as a binder for nanocages is also important due to its possible applications. In earlier molecular structures, proteins were glued together using many weak chemical bonds. The complexity of the bonds and their similarity to the bonds responsible for the existence of the protein rings themselves did not allow for precise control over the decomposition of the cages. This is not the case in the new structures. On the one hand, gold-bonded nanocages are chemically and thermally stable (for example, they withstand hours of boiling in water). On the other hand, however, gold bonds are sensitive to an increase in acidity. By its increase, the nanocage can be decomposed in a controlled way and the contents can be released into the environment. Since the acidity within cells is greater than outside them, gold-bonded nanocages are ideal for biomedical applications.

The ‘impossible’ nanocage is the presentation of a qualitatively new approach to the construction of molecular cages, with gold atoms in the role of loose clips. The demonstrated flexibility of the gold bonds will make it possible in the future to create nanocages with sizes and features precisely tailored to specific needs.

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

An ultra-stable gold-coordinated protein cage displaying reversible assembly by Ali D. Malay, Naoyuki Miyazaki, Artur Biela, Soumyananda Chakraborti, Karolina Majsterkiewicz, Izabela Stupka, Craig S. Kaplan, Agnieszka Kowalczyk, Bernard M. A. G. Piette, Georg K. A. Hochberg, Di Wu, Tomasz P. Wrobel, Adam Fineberg, Manish S. Kushwah, Mitja Kelemen, Primož Vavpetič, Primož Pelicon, Philipp Kukura, Justin L. P. Benesch, Kenji Iwasaki & Jonathan G. Heddle Nature volume 569, pages438–442 (2019) Issue Date: 16 May 2019 DOI: https://doi.org/10.1038/s41586-019-1185-4 Published online: 08 May 2019

This paper is behind a paywall.

Entangling a single photon with a trillion atoms

Polish scientists have cast light on an eighty-year old ‘paradox’ according to a March 2, 2017 news item on plys.org,

A group of researchers from the Faculty of Physics at the University of Warsaw has shed new light on the famous paradox of Einstein, Podolsky and Rosen after 80 years. They created a multidimensional entangled state of a single photon and a trillion hot rubidium atoms, and stored this hybrid entanglement in the laboratory for several microseconds. …

In their famous Physical Review article, published in 1935, Einstein, Podolsky and Rosen considered the decay of a particle into two products. In their thought experiment, two products of decay were projected in exactly opposite directions—or more scientifically speaking, their momenta were anti-correlated. Though not be a mystery within the framework of classical physics, when applying the rules of quantum theory, the three researchers arrived at a paradox. The Heisenberg uncertainty principle, dictating that position and momentum of a particle cannot be measured at the same time, lies at the center of this paradox. In Einstein’s thought experiment, it is possible to measure the momentum of one particle and immediately know the momentum of the other without measurement, as it is exactly opposite. Then, by measuring the position of the second particle, the Heisenberg uncertainty principle is seemingly violated, an apparent paradox that seriously baffled the three physicists.

A March 2, 2017 University of Warsaw press release (also on EurekAlert), which originated the news item, expands on the topic,

Only today we know that this experiment is not, in fact, a paradox. The mistake of Einstein and co-workers was to use one-particle uncertainty principle to a system of two particles. If we treat these two particles as described by a single quantum state, we learn that the original uncertainty principle ceases to apply, especially if these particles are entangled.

In the Quantum Memories Laboratory at the University of Warsaw, the group of three physicists was first to create such an entangled state consisting of a macroscopic object – a group of about one trillion atoms, and a single photon – a particle of light. “Single photons, scattered during the interaction of a laser beam with atoms, are registered on a sensitive camera. A single registered photon carries information about the quantum state of the entire group of atoms. The atoms may be stored, and their state may be retrieved on demand.” – says Michal Dabrowski, PhD student and co-author of the article.

The results of the experiment confirm that the atoms and the single photon are in a joint, entangled state. By measuring position and momentum of the photon, we gain all information about the state of atoms. To confirm this, polish scientists convert the atomic state into another photon, which again is measured using the state-of-the-art camera developed in the Quantum Memories Laboratory. “We demonstrate the Einstein-Podolsky-Rosen apparent paradox in a very similar version as originally proposed in 1935, however we extend the experiment by adding storage of light within the large group of atoms. Atoms store the photon in a form of a wave made of atomic spins, containing one trillion atoms. Such a state is very robust against loss of a single atoms, as information is spread across so many particles.” – says Michal Parniak, PhD student taking part in the study.

The experiment performed by the group from the University of Warsaw is unique in one other way as well. The quantum memory storing the entangled state, created thanks to “PRELUDIUM” grant from the Poland’s National Science Centre and “Diamentowy Grant” from the Polish Ministry of Science and Higher Education, allows for storage of up to 12 photons at once. This enhanced capacity is promising in terms of applications in quantum information processing. “The multidimensional entanglement is stored in our device for several microseconds, which is roughly a thousand times longer than in any previous experiments, and at the same time long enough to perform subtle quantum operations on the atomic state during storage” – explains Dr. Wojciech Wasilewski, group leader of the Quantum Memories Laboratory team.

The entanglement in the real and momentum space, described in the Optica article, can be used jointly with other well-known degrees of freedom such as polarization, allowing generation of so-called hyper-entanglement. Such elaborate ideas constitute new and original test of the fundamentals of quantum mechanics – a theory that is unceasingly mysterious yet brings immense technological progress.

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

Einstein–Podolsky–Rosen paradox in a hybrid bipartite system by Michał Dąbrowski, Michał Parniak, and Wojciech Wasilewski. Optica Vol. 4, Issue 2, pp. 272-275 (2017) •https://doi.org/10.1364/OPTICA.4.000272

This paper appears to be open access.

International Women’s Day March 8, 2017 and UNESCO/L’Oréal’s For Women in Science (Rising Talents)

Before getting to the science, here’s a little music in honour of March 8, 2017 International Women’s Day,

There is is a Wikipedia entry devoted to Rise Up (Parachute Club song), Note: Links have been removed<

“Rise Up” is a pop song recorded by the Canadian group Parachute Club on their self-titled 1983 album. It was produced and engineered by Daniel Lanois, and written by Parachute Club members Billy Bryans, Lauri Conger, Lorraine Segato and Steve Webster with lyrics contributed by filmmaker Lynne Fernie.

An upbeat call for peace, celebration, and “freedom / to love who we please,” the song was a national hit in Canada, and was hailed as a unique achievement in Canadian pop music:

“ Rarely does one experience a piece of music in white North America where the barrier between participant and observer breaks down. Rise Up rises right up and breaks down the wall.[1] ”

According to Segato, the song was not written with any one individual group in mind, but as a universal anthem of freedom and equality;[2] Fernie described the song’s lyrics as having been inspired in part by West Coast First Nations rituals in which young girls would “rise up” at dawn to adopt their adult names as a rite of passage.[3]

It remains the band’s most famous song, and has been adopted as an activist anthem for causes as diverse as gay rights, feminism, anti-racism and the New Democratic Party.[4] As well, the song’s reggae and soca-influenced rhythms made it the first significant commercial breakthrough for Caribbean music in Canada.

L’Oréal UNESCO For Women in Science

From a March 8, 2017 UNESCO press release (received via email),

Fifteen outstanding young women researchers, selected
among more than 250 candidates in the framework of the 19th edition of
the L’Oréal-UNESCO For Women in Science awards, will receive the
International Rising Talent fellowship during a gala on 21 March at the
hotel Pullman Tour Eiffel de Paris. By recognizing their achievements at
a key moment in their careers, the _For Women in Science programme aims
to help them pursue their research.

Since 1998, the L’Oréal-UNESCO _For Women in Science programme [1]
has highlighted the achievements of outstanding women scientists and
supported promising younger women who are in the early stages of their
scientific careers. Selected among the best national and regional
L’Oréal-UNESCO fellows, the International Rising Talents come from
all regions of the world (Africa and Arab States, Asia-Pacific, Europe,
Latin America and North America).

Together with the five laureates of the 2017 L’Oreal-UNESCO For Women
in Science awards [2], they will participate in a week of events,
training and exchanges that will culminate with the award ceremony on 23
March 2017 at the Mutualité in Paris.

The 2017 International Rising Talent are recognized for their work in
the following five categories:

WATCHING THE BRAIN AT WORK

* DOCTOR LORINA NACI, Canada
Fundamental medicine
In a coma: is the patient conscious or unconscious?     * ASSOCIATE
PROFESSOR MUIREANN IRISH, Australia

Clinical medicine
Recognizing Alzheimer’s before the first signs appear.

ON THE ROAD TO CONCEIVING NEW MEDICAL TREATMENTS

* DOCTOR HYUN LEE, Germany
Biological Sciences
Neurodegenerative diseases: untangling aggregated proteins.
* DOCTOR NAM-KYUNG YU, Republic of Korea
Biological Sciences
Rett syndrome: neuronal cells come under fire
* DOCTOR STEPHANIE FANUCCHI, South Africa
Biological Sciences
Better understanding the immune system.
* DOCTOR JULIA ETULAIN, Argentina
Biological Sciences
Better tissue healing.

Finding potential new sources of drugs

* DOCTOR RYM BEN SALLEM, Tunisia
Biological Sciences
New antibiotics are right under our feet.
* DOCTOR HAB JOANNA SULKOWSKA, Poland
Biological Sciences
Unraveling the secrets of entangled proteins.

GETTING TO THE HEART OF MATTER

* MS NAZEK EL-ATAB, United Arab Emirates
Electrical, Electronic and Computer Engineering
Miniaturizing electronics without losing memory.
* DOCTOR BILGE DEMIRKOZ, Turkey
Physics
Piercing the secrets of cosmic radiation.
* DOCTOR TAMARA ELZEIN, Lebanon
Material Sciences
Trapping radioactivity.
* DOCTOR RAN LONG, China
Chemistry
Unlocking the potential of energy resources with nanochemistry.

EXAMINING THE PAST TO SHED LIGHT ON THE FUTURE – OR VICE VERSA

* DOCTOR FERNANDA WERNECK, Brazil
Biological Sciences
Predicting how animal biodiversity will evolve.
* DOCTOR SAM GILES, United Kingdom
Biological Sciences
Taking another look at the evolution of vertebrates thanks to their
braincases.
* DOCTOR ÁGNES KÓSPÁL, Hungary
Astronomy and Space Sciences
Looking at the birth of distant suns and planets to better understand
the solar system.

Congratulations to all of the winners!

You can find out more about these awards and others on the 2017 L’Oréal-UNESCO For Women in Science Awards webpage or on the For Women In Science website. (Again in honour of the 2017 International Women’s Day, I was the 92758th signer of the For Women in Science Manifesto.)

International Women’s Day origins

Thank you to Wikipedia (Note: Links have been removed),

International Women’s Day (IWD), originally called International Working Women’s Day, is celebrated on March 8 every year.[2] It commemorates the movement for women’s rights.

The earliest Women’s Day observance was held on February 28, 1909, in New York and organized by the Socialist Party of America.[3] On March 8, 1917, in the capital of the Russian Empire, Petrograd, a demonstration of women textile workers began, covering the whole city. This was the beginning of the Russian Revolution.[4] Seven days later, the Emperor of Russia Nicholas II abdicated and the provisional Government granted women the right to vote.[3] March 8 was declared a national holiday in Soviet Russia in 1917. The day was predominantly celebrated by the socialist movement and communist countries until it was adopted in 1975 by the United Nations.

It seems only fitting to bookend this post with another song (Happy International Women’s Day March 8, 2017),

While the lyrics are unabashedly romantic, the video is surprisingly moody with a bit of a ‘stalker vive’ although it does end up with her holding centre stage while singing and bouncing around in time to Walking on Sunshine.

Synthetic genetics and imprinting a sequence of a single DNA (deoxyribonucleic acid) strand

Caption: A polymer negative of a sequence of the genetic code, chemically active and able to bind complementary nucleobases, has been created by researchers from the Institute of Physical Chemistry of the Polish Academy of Sciences in Warsaw. Credit: IPC PAS, Grzegorz Krzyzewski

Those are very large hands! In any event, I think they left out the word ‘model’ when describing what the researcher is holding.

A Jan. 19, 2017 news item on phys.org announces the research from the Institute of Physical Chemistry of the Polish Academy of Sciences (IPC PAS),

In a carefully designed polymer, researchers at the Polish Academy of Sciences have imprinted a sequence of a single strand of DNA. The resulting negative remained chemically active and was capable of binding the appropriate nucleobases of a genetic code. The polymer matrix—the first of its type—thus functioned exactly like a sequence of real DNA.

A Jan. 18, 2017 IPC PAS press release, which originated the news item, provides more detail about the breakthrough and explains how it could lead to synthetic genetics,

Imprinting of chemical molecules in a polymer, or molecular imprinting, is a well-known method that has been under development for many years. However, no-one has ever before used it to construct a polymer chain complementing a sequence of a single strand of DNA. This feat has just been accomplished by researchers from the Institute of Physical Chemistry of the Polish Academy of Sciences (IPC PAS) in Warsaw in collaboration with the University of North Texas (UNT) in Denton, USA, and the University of Milan in Italy. In an appropriately selected polymer, they reproduced a genetically important DNA sequence, constructed of six nucleobases.

Typically, molecular imprinting is accomplished in several steps. The molecules intended for imprinting are first placed to a solution of monomers (i.e. the basic “building blocks” from which the future polymer is to be formed). The monomers are selected so as to automatically arrange themselves around the molecules being imprinted. Next, the resulting complex is electrochemically polymerized and then the imprinted molecules are extracted from the fixed structure. This process results in a polymer structure with molecular cavities matching the original molecules with their size and shape, and even their local chemical properties.

“Using molecular imprinting, we can produce, e.g. recognition films for chemical sensors, capturing molecules of only a specific chemical compound from the surroundings – since only these molecules fit into the existing molecular cavities. However, there’s no rose without a thorn. Molecular imprinting is perfect for smaller chemical molecules, but the larger the molecule, the more difficult it is to imprint it accurately into the polymer,” explains Prof. Wlodzimierz Kutner (IPC PAS).

Molecules of deoxyribonucleic acid, or DNA, are really large: their lengths are of the order of centimetres. These molecules generally consist of of two long strands, paired up with each other. A single strand is made up of nucleotides with multiple repetitions, each of which contains one of the nucleobases: adenine (A), guanine (G), cytosine (C), or thymine (T). The bases on both strands are not arranged freely: adenine on one strand always corresponds to thymine on the other, and guanine to cytosine. So, when we have one thread, we can always recreate its complement, which is the second strand.

The complementarity of nucleobases in DNA strands is very important for cells. Not only does it increase the permanence of the record of the genetic code (damage in one strand can be repaired based on the construction of the other), but it also makes it possible to transfer it from DNA to RNA in the process known as transcription. Transcription is the first step in the synthesis of proteins.

“Our idea was to try to imprint in the polymer a sequence of a single-stranded DNA. At the same time, we wanted to reproduce not only the shape of the strand, but also the sequential order of the constituent nucleobases,” says Dr. Agnieszka Pietrzyk-Le (IPC PAS).

In the study, financed on the Polish side by grants from the Foundation for Polish Science and the National Centre for Science, researchers from the IPC PAS used sequences of the genetic code known as TATAAA. This sequence plays an important biological role: it participates in deciding on the activation of the gene behind it. TATAAA is found in most eukaryotic cells (those containing a nucleus); in humans it is present in about every fourth gene.

A key step of the research was to design synthetic monomers undergoing electrochemical polymerization. These had to be capable of accurately surrounding the imprinted molecule in such a way that each of the adenines and thymines on the DNA strand were accompanied by their complementary bases. The mechanical requirements were also important, because after polymerization the matrix had to be stable. Suitable monomers were synthesized by the group of Prof. Francis D’Souza (UNT).

“When all the reagents and apparatus have been prepared, the imprinting itself of the TATAAA oligonucleotide is not especially complicated. The most important processes take place automatically in solutions in no more than a few dozen minutes. Finally, on the electrode used for electropolymerization, we obtain a layer of conductive polymer with molecular cavities where the nucleobases are arranged in the TTTATA sequence, that is, complementary to the extracted original”, describes doctoral student Katarzyna Bartold (IPC PAS).

Do polymer matrices prepared in this manner really reconstruct the original sequence of the DNA chain? To answer this question, at the IPC PAS careful measurements were carried out on the properties of the new polymers and a series of experiments was performed that confirmed the interaction of the polymers with various nucleobases in solutions. The results leave no doubt: the polymer DNA negative really is chemically active and selectively binds the TATAAA oligonucleotide, correctly reproducing the sequence of nucleobases.

The possibility of the relatively simple and low-cost production of stable polymer equivalents of DNA sequences is an important step in the development of synthetic genetics, especially in terms of its widespread applications in biotechnology and molecular medicine. If an improvement in the method developed at the IPC PAS is accomplished in the future, it will be possible to reproduce longer sequences of the genetic code in polymer matrices. This opens up inspiring perspectives associated not only with learning about the details of the process of transcription in cells or the construction of chemosensors for applications in nanotechnologies operating on chains of DNA, but also with the permanent archiving and replicating of the genetic code of different organisms.

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

Programmed transfer of sequence information into molecularly imprinted polymer (MIP) for hexa(2,2’-bithien-5-yl) DNA analog formation towards single nucleotide polymorphism (SNP) detection by Katarzyna Bartold, Agnieszka Pietrzyk-Le, Tan-Phat Huynh, Zofia Iskierko, Marta I. Sosnowska, Krzysztof Noworyta, Wojciech Lisowski, Francesco Maria Enrico Sannicolo, Silvia Cauteruccio, Emanuela Licandro, Francis D’Souza, and Wlodzimierz Kutner. ACS Appl. Mater. Interfaces, Just Accepted Manuscript
DOI: 10.1021/acsami.6b14340 Publication Date (Web): January 10, 2017

Copyright © 2017 American Chemical Society

This paper is behind a paywall.

Monitoring the life of bacteria in microdroplets

Trying to establish better ways to test the effect of drugs on bacteria has led the Institute of Physical Chemistry of the Polish Academy of Sciences to develop a new monitoring technique. From a Jan.  11, 2017 news item on Nanowerk,

So far, however, there has been no quick or accurate method of assessing the oxygen conditions in individual microdroplets. This key obstacle has been overcome at the Institute of Physical Chemistry of the Polish Academy of Sciences.

Not in rows of large industrial tanks, nor on shelves laden with test tubes and beakers. The future of chemistry and biology is barely visible to the eye: it’s hundreds and thousands of microdroplets, whizzing through thin tubules of microfluidic devices. The race is on to find technologies that will make it possible to carry out controlled chemical and biological experiments in microdroplets. At the Institute of Physical Chemistry of the Polish Academy of Sciences (IPC PAS) in Warsaw a method of remote, yet rapid and accurate assessment of oxygen consumption by micro-organisms living in individual microdroplets has been demonstrated for the first time.

“Devices for the cultivation of bacteria in microdroplets have the chance to revolutionize work on the development of new antibiotics and the study of mechanisms responsible for the acquisition of drug resistance by bacteria. In one small microfluidic system it is possible to accommodate several hundred or even several thousand microdroplets – and to carry out a different experiment in each of them, for example with different types of microorganisms and at different concentrations of antibiotic in each drop,” describes Prof. Piotr Garstecki (IPC PAS), then explains: “For such studies to be possible, one has to provide the bacteria with conditions for development for even a few weeks. Thus, knowledge about the flow of oxygen to the droplets and the rate of its consumption by the microorganisms becomes extremely important. In our latest system we demonstrate how to read this key information.”

A Jan. 11, 2017 IPC PAS press release on EurekAlert, which originated the  news item, describes the work in more detail,

The bioreactors of the future are water droplets with culture medium suspended in a carrier liquid with which they are immiscible (usually this is oil). In the channel of the microfluidic device each droplet is longer than it is wide and it almost completely fills its lumen; sizes matched in this manner ensure that the drops do not swop places in the channel and throughout the duration of the experiment they can be identified without any problems. At the same time, there has to be a thin layer of oil maintained continuously between each microdroplet and the wall of the channel. Without this, the bacteria would be in direct contact with the walls of the channel so they would be able to settle on them and move from drop to drop. Unfortunately, when the microdroplet is stationary, with time it pushes out the oil separating it from the walls, laying it open to contamination. For this reason the drops must be kept in constant motion – even for weeks.

Growing bacteria need culture medium, and waste products need to be removed from their environment at an appropriate rate. Information about the bacterial oxygen consumption in individual droplets is therefore crucial to the operation of microbioreactors.

“It is immediately obvious where the problem lies. In each of the hundreds of moving droplets measurements need to be carried out at a frequency corresponding to the frequency of division of the bacteria or more, in practice at least once every 15 minutes. In addition, the measurement cannot cause any interference in the microdroplets,” says PhD student Michal Horka (IPC PAS), a co-author of the publication in the journal Analytical Chemistry.

Help was at hand for the Warsaw researchers from chemists from the Austrian Institute of Analytical Chemistry and Food Chemistry at the Graz University of Technology. They provided polymer nanoparticles with a phosphorescent dye, which after excitation emit light for longer the higher the concentration of oxygen in the surrounding solution (the nanoparticles underwent tests at the IPC PAS on bacteria in order to determine their possible toxicity – none was found).

Research on monitoring oxygen consumption in the droplets commenced with the preparation of an aqueous solution with the bacteria, the culture medium and a suitable quantity of nanoparticles. The mixture was injected into the microfluidic system constructed of tubing with Teflon connectors with correspondingly shaped channels. The first module formed droplets with a volume of approx. 4 microlitres, which were directed to the incubation tube wound on a spool. In the middle of its length there was another module, with detectors for measuring oxygen and absorbance.

“In the incubation part in one phase of the cycle the droplets flowed in one direction, in the second – in another, electronically controlled by means of suitable solenoid valves. All this looks seemingly simple enough, but in practice one of the biggest challenges was to ensure a smooth transition between the detection module and the tubing, so that bacterial contamination did not occur at the connections,” explains PhD student Horka.

During their passage through the detection module the droplets flowed under an optical sensor which measured the so-called optical density, which is the standard parameter used to evaluate the number of cells (the more bacteria in the droplets, the less light passes through them). In turn, the measurement of the duration of the phosphorescence of the nanoparticles, evaluating the concentration of oxygen in the microdroplets, was carried out using the Piccolo2 optical detector, provided by the Austrian group. This detector, which looks like a big pen drive, was connected directly to the USB port on the control computer. Comparing information from both sensors, IPC PAS researchers showed that the microfluidic device they had constructed made it possible to regularly and quickly monitor the metabolic activity of bacteria in the individual microdroplets.

“We carried out our tests both with bacteria floating in water singly – this is how the common Escherichia coli bacteria behave – as well as with those having a tendency to stick together in clumps – as is the case for tuberculosis bacilli or others belonging to the same family including Mycobacterium smegmatis which we studied. Evaluation of the rate of oxygen consumption by both species of microorganisms proved to be not only possible, but also reliable,” stresses PhD student Artur Ruszczak (IPC PAS).

The results of the research, funded by the European ERC Starting Grant (Polish side) and the Maria Sklodowska-Curie grant (Austrian side) are an important step in the process of building fully functional microfluidic devices for conducting biological experiments lasting many weeks. A system for culturing bacteria in microdroplets was developed at the IPC PAS a few years ago, however it was constructed on a polycarbonate plate. The maximum dimensions of the plate did not exceed 10 cm, which greatly limited the number of droplets; in addition, as a result of interaction with the polycarbonate, after four days the channels were contaminated with bacteria. Devices of Teflon modules and tubing would not have these disadvantages, and would be suitable for practical applications.

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

Lifetime of Phosphorescence from Nanoparticles Yields Accurate Measurement of Concentration of Oxygen in Microdroplets, Allowing One To Monitor the Metabolism of Bacteria by Michał Horka, Shiwen Sun, Artur Ruszczak, Piotr Garstecki, and Torsten Mayr. Anal. Chem., 2016, 88 (24), pp 12006–12012 DOI: 10.1021/acs.analchem.6b03758 Publication Date (Web): November 23, 2016

Copyright © 2016 American Chemical Society

This paper is behind a paywall.

Nanotech business news from Turkey and from Northern Ireland

I have two nanotech business news bits, one from Turkey and one from Northern Ireland.

Turkey

A Turkish company has sold one of its microscopes to the US National Aeronautics and Space Administration (NASA), according to a Jan. 20, 2017 news item on dailysabah.com,

Turkish nanotechnology company Nanomanyetik has begun selling a powerful microscope to the U.S. space agency NASA, the company’s general director told Anadolu Agency on Thursday [Jan. 19, 2017].

Dr. Ahmet Oral, who also teaches physics at Middle East Technical University, said Nanomanyetik developed a microscope that is able to map surfaces on the nanometric and atomic levels, or extremely small particles.

Nanomanyetik’s foreign customers are drawn to the microscope because of its higher quality yet cheaper price compared to its competitors.

“There are almost 30 firms doing this work,” according to Oral. “Ten of them are active and we are among these active firms. Our aim is to be in the top three,” he said, adding that Nanomanyetik jumps to the head of the line because of its after-sell service.

In addition to sales to NASA, the Ankara-based firm exports the microscope to Brazil, Chile, France, Iran, Israel, Italy, Japan, Poland, South Korea and Spain.

Electronics giant Samsung is also a customer.

“Where does Samsung use this product? There are pixels in the smartphones’ displays. These pixels are getting smaller each year. Now the smallest pixel is 15X10 microns,” he said. Human hair is between 10 and 100 microns in diameter.

“They are figuring inner sides of pixels so that these pixels can operate much better. These patterns are on the nanometer level. They are using these microscopes to see the results of their works,” Oral said.

Nanomanyetik’s microscopes produces good quality, high resolution images and can even display an object’s atoms and individual DNA fibers, according to Oral.

You can find the English language version of the Nanomanyetik (NanoMagnetics Instruments) website here . For those with the language skills there is the Turkish language version, here.

Northern Ireland

A Jan. 22, 2017 news article by Dominic Coyle for The Irish Times (Note: Links have been removed) shares this business news and mention of a world first,

MOF Technologies has raised £1.5 million (€1.73 million) from London-based venture capital group Excelsa Ventures and Queen’s University Belfast’s Qubis research commercialisation group.

MOF Technologies chief executive Paschal McCloskey welcomed the Excelsa investment.

Established in part by Qubis in 2012 in partnership with inventor Prof Stuart James, MOF Technologies began life in a lab at the School of Chemistry and Chemical Engineering at Queen’s.

Its metal organic framework (MOF) technology is seen as having significant potential in areas including gas storage, carbon capture, transport, drug delivery and heat transformation. Though still in its infancy, the market is forecast to grow to £2.2 billion by 2022, the company says.

MOF Technologies last year became the first company worldwide to successfully commercialise MOFs when it agreed a deal with US fruit and vegetable storage provider Decco Worldwide to commercialise MOFs for use in a food application.

TruPick, designed by Decco and using MOF Technologies’ environmentally friendly technology, enables nanomaterials control the effects of ethylene on fruit produce so it maintains freshness in storage or transport.

MOFs are crystalline, sponge-like materials composed of two components – metal ions and organic molecules known as linkers.

“We very quickly recognised the market potential of MOFs in terms of their unmatched ability for gas storage,” said Moritz Bolle from Excelsa Ventures. “This technology will revolutionise traditional applications and open countless new opportunities for industry. We are confident MOF Technologies is the company that will lead this seismic shift in materials science.

You can find MOF Technologies here.

Unbreakable encrypted message with key that’s shorter than the message

A Sept. 5, 2016 University of Rochester (NY state, US) news release (also on EurekAlert), makes an intriguing announcement,

Researchers at the University of Rochester have moved beyond the theoretical in demonstrating that an unbreakable encrypted message can be sent with a key that’s far shorter than the message—the first time that has ever been done.

Until now, unbreakable encrypted messages were transmitted via a system envisioned by American mathematician Claude Shannon, considered the “father of information theory.” Shannon combined his knowledge of algebra and electrical circuitry to come up with a binary system of transmitting messages that are secure, under three conditions: the key is random, used only once, and is at least as long as the message itself.

The findings by Daniel Lum, a graduate student in physics, and John Howell, a professor of physics, have been published in the journal Physical Review A.

“Daniel’s research amounts to an important step forward, not just for encryption, but for the field of quantum data locking,” said Howell.

Quantum data locking is a method of encryption advanced by Seth Lloyd, a professor of quantum information at Massachusetts Institute of Technology, that uses photons—the smallest particles associated with light—to carry a message. Quantum data locking was thought to have limitations for securely encrypting messages, but Lloyd figured out how to make additional assumptions—namely those involving the boundary between light and matter—to make it a more secure method of sending data.  While a binary system allows for only an on or off position with each bit of information, photon waves can be altered in many more ways: the angle of tilt can be changed, the wavelength can be made longer or shorter, and the size of the amplitude can be modified. Since a photon has more variables—and there are fundamental uncertainties when it comes to quantum measurements—the quantum key for encrypting and deciphering a message can be shorter that the message itself.

Lloyd’s system remained theoretical until this year, when Lum and his team developed a device—a quantum enigma machine—that would put the theory into practice. The device takes its name from the encryption machine used by Germany during World War II, which employed a coding method that the British and Polish intelligence agencies were secretly able to crack.

Let’s assume that Alice wants to send an encrypted message to Bob. She uses the machine to generate photons that travel through free space and into a spatial light modulator (SLM) that alters the properties of the individual photons (e.g. amplitude, tilt) to properly encode the message into flat but tilted wavefronts that can be focused to unique points dictated by the tilt. But the SLM does one more thing: it distorts the shapes of the photons into random patterns, such that the wavefront is no longer flat which means it no longer has a well-defined focus. Alice and Bob both know the keys which identify the implemented scrambling operations, so Bob is able to use his own SLM to flatten the wavefront, re-focus the photons, and translate the altered properties into the distinct elements of the message.

Along with modifying the shape of the photons, Lum and the team made use of the uncertainty principle, which states that the more we know about one property of a particle, the less we know about another of its properties. Because of that, the researchers were able to securely lock in six bits of classical information using only one bit of an encryption key—an operation called data locking.

“While our device is not 100 percent secure, due to photon loss,” said Lum, “it does show that data locking in message encryption is far more than a theory.”

The ultimate goal of the quantum enigma machine is to prevent a third party—for example, someone named Eve—from intercepting and deciphering the message. A crucial principle of quantum theory is that the mere act of measuring a quantum system changes the system. As a result, Eve has only one shot at obtaining and translating the encrypted message—something that is virtually impossible, given the nearly limitless number of patterns that exist for each photon.

The paper by Lum and Howell was one of two papers published simultaneously on the same topic. The other paper, “Quantum data locking,” was from a team led by Chinese physicist Jian-Wei Pan.

“It’s highly unlikely that our free-space implementation will be useful through atmospheric conditions,” said Lum. “Instead, we have identified the use of optic fiber as a more practical route for data locking, a path Pan’s group actually started with. Regardless, the field is still in its infancy with a great deal more research needed.”

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

Quantum enigma machine: Experimentally demonstrating quantum data locking by Daniel J. Lum, John C. Howell, M. S. Allman, Thomas Gerrits, Varun B. Verma, Sae Woo Nam, Cosmo Lupo, and Seth Lloyd. Phys. Rev. A, Vol. 94, Iss. 2 — August 2016 DOI: http://dx.doi.org/10.1103/PhysRevA.94.022315

©2016 American Physical Society

This paper is behind a paywall.

There is an earlier open access version of the paper by the Chinese researchers on arXiv.org,

Experimental quantum data locking by Yang Liu, Zhu Cao, Cheng Wu, Daiji Fukuda, Lixing You, Jiaqiang Zhong, Takayuki Numata, Sijing Chen, Weijun Zhang, Sheng-Cai Shi, Chao-Yang Lu, Zhen Wang, Xiongfeng Ma, Jingyun Fan, Qiang Zhang, Jian-Wei Pan. arXiv.org > quant-ph > arXiv:1605.04030

The Chinese team’s later version of the paper is available here,

Experimental quantum data locking by Yang Liu, Zhu Cao, Cheng Wu, Daiji Fukuda, Lixing You, Jiaqiang Zhong, Takayuki Numata, Sijing Chen, Weijun Zhang, Sheng-Cai Shi, Chao-Yang Lu, Zhen Wang, Xiongfeng Ma, Jingyun Fan, Qiang Zhang, and Jian-Wei Pan. Phys. Rev. A, Vol. 94, Iss. 2 — August 2016 DOI: http://dx.doi.org/10.1103/PhysRevA.94.020301

©2016 American Physical Society

This version is behind a paywall.

Getting back to the folks at the University of Rochester, they have provided this image to illustrate their work,

The quantum enigma machine developed by researchers at the University of Rochester, MIT, and the National Institute of Standards and Technology. (Image by Daniel Lum/University of Rochester)

The quantum enigma machine developed by researchers at the University of Rochester, MIT, and the National Institute of Standards and Technology. (Image by Daniel Lum/University of Rochester)