Saturday, January 23, 2021

Online courses reinforce inequalities

Gifted students improve their grades when they take online courses, whereas students in difficulty do not.

UNIVERSITÉ DE GENÈVE

Research News

With the global student community taking online courses as a result of the anti-Covid-19 measures, a study led by the University of Geneva (UNIGE) reveals that online courses deepen inequalities between gifted and less gifted students by 5%. The results of the study, which was based on data collected in 2016-2017 prior to the anti-Covid lockdown initiatives, are published in the Journal of the European Economic Association. They indicate that this learning gap between different student profiles is mainly due to their behaviour and motivation. The study gives higher education establishments worldwide practical ways to deal with lockdown or the chronic lack of space in lecture theatres, including via co-educational curricula.

To gain insight into the impact of online courses on the success of university students (and to measure the interest they generate), 1,459 first-year students at UNIGE took part in a study run by UNIGE's Geneva School of Economics and Management (GSEM). Students were randomly offered online courses (while others, as a check, were not) to study their eight compulsory programmes covering subjects such as mathematics and economics. The content of the courses was then linked to specific exams in order to assess their level of knowledge. Every student had the opportunity to attend face-to-face classes if they wanted to. The data for the study was collected before the Covid-19 health crisis.

The inequality gap is widening

The results of the study show that online courses improve exam results for high-potential students by 2.5%. At the same time, however, the results for students with learning difficulties decrease by 2%. "Access to online education seems to widen the gap between gifted and less gifted students," begins Michele Pellizzari, GSEM co-director and co-author of the study. "That's a fact that universities around the world need to take note of, as the coronavirus is accelerating the shift to online learning."

The study found that students adopt different patterns of behaviour when it comes to online course options depending on their learning abilities. When the weather is bad, for example, students who have the best results often choose to study by themselves at home, while students who are not so well equipped go the extra mile to attend face-to-face classes. Furthermore, students with high potential choose streaming when it is offered, while students in difficulty once more prefer in-person classes. The authors argue that these different behaviours create educational inequalities when streaming is introduced.

Limited appetite

In overall terms, if university students have the choice, they prefer to attend face-to-face classes. They only opt for the online solution when confronted with unexpected situations caused by illness or even bad weather. Accordingly, offering streaming courses only reduces face-to-face participation by 8%. "That means these figures," continues the researcher, "don't solve the current problems of overcrowded lecture theatres in higher education."

The study helps to show the impact of e-learning on results as well as emphasising its limits. This data is useful for higher education institutions around the world given the current health crisis and shortage of classroom space. The article also offers effective blended learning solutions, where streaming complements face-to-face teaching. "At the same time, more data is needed so we can draw definitive conclusions about 100% online courses," concludes Professor Pellizzari.

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This study was carried out in collaboration with the EPFL and the University of St. Gallen.

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

Could "Power Walking" fuel the energy revolution? India is ready to step up

A survey finds that energy generated from footsteps could help tackle the country's reliance on coal

DE GRUYTER

Research News

India has an energy problem. It currently relies heavily on coal and consumer demand is expected to double by 2040, making its green energy targets look out of reach. Part of the solution could come from harvesting energy from footsteps, say Hari Anand and Binod Kumar Singh from the University of Petroleum and Energy Studies in Dehradun, India. Their new study, published in the De Gruyter journal Energy Harvesting and Systems, shows that Indian attitudes towards power generated through piezoelectric tiles are overwhelmingly positive.

Cities like Delhi and Mumbai are famously crowded, especially at railway stations, temples and big commercial buildings. This led researchers to wonder whether piezoelectric tiles, which produce energy through mechanical pressure, could turn this footfall into something useful.

Piezoelectric tiles are made using special materials, such as crystals and ceramics, in which electric charge builds up when mechanical stress is applied - such as a foot pressing down.

Anand and Singh ran a survey in which they explored how people in India view the reliability of their household power and what their attitudes were towards generating their own electricity. They also asked participants how much they walked on average and whether they would consider implementing piezoelectric tiles into their homes.

They found that more than one in five people suffered frequent power-cuts in their area, highlighting the potential benefits of household energy generators such a piezoelectric tiles. Around 40% of respondents said they walked for more than three hours a day, and roughly 70% were willing to produce their own electricity using their feet.

The researchers also suggest that while household tiles can be used to solve problems of energy reliability and generation for individual families, piezoelectric tiles will also be a good investment for public or commercial areas with heavy footfall. They estimate that for the cost of a single 1 kW solar panel, three times more power could be generated a year using piezoelectric tiles.

"As a gadget, the piezoelectric tiles can be attractive home décor that will also help in producing household electricity," says Singh. "In this paper the output generated through the piezoelectric tiles has been studied in comparison with solar power generation."

As the efficiency and durability of piezoelectric tiles improve and as the need for green solutions becomes more urgent, the researchers predict that this type of energy production will experience a boom on the green energy market.

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The paper was published online ahead of print here: https://doi.org/10.1515/ehs-2020-0002

Disclaimer: AAAS and EurekAlert! are not responsible for the acc

Benvitimod cream: a new topical treatment for plaque psoriasis

New non-steroidal topical drug benvitimod proven to be safe and effective for plaque psoriasis in a phase III clinical trial in China

CACTUS COMMUNICATIONS

Research News

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IMAGE: THE NOVEL NON-STEROIDAL CREAM, BENVITIMOD, CAN SAFELY AND EFFECTIVELY TREAT PSORIASIS OVER THE LONG TERM WITHOUT SIDE-EFFECTS view more 

CREDIT: PEXELS

Psoriasis is a chronic inflammatory skin disease characterized by erythematous (red) patches and plaques. In some patients, psoriasis may be associated with comorbidities such as arthritis, obesity, diabetes, cardiovascular diseases, hyperlipidemia, or depression. Psoriasis lesions can occur on the scalp and face, in addition to all other areas of the body, causing considerable physical discomfort and psychosocial trauma from the stigma surrounding appearance defects.

More than 90% of patients with psoriasis have what is called psoriasis vulgaris, which is characterized by plaques, and less than 5% have the other varieties: arthritic psoriasis, pustular psoriasis, and erythrodermic psoriasis. The most common treatments for mild to moderate plaque psoriasis are topical corticosteroids and vitamin D3 analogs.

However, the long-term use of these topical steroids often causes various side-effects such as skin atrophy, hypo- or hyper-pigmentation, telangiectasia, and skin infections. And the long-term use of vitamin D3 analogs may add the requirement of interventions to regulate calcium and phosphate metabolism. These effects on the body are significant and there is a need for novel topical and systemic treatments for psoriasis.

In a study recently published in Chinese Medical Journal, scientists from renowned research institutes and hospitals across China, led by Prof. Jian-Zhong Zhang from Peking University People's Hospital, have met this need in part. They have reported that benvitimod, a novel non-steroid topical drug, is effective and safe for treating plaque psoriasis.

Speaking of their research journey, Prof. Zhang says, "Benvitimod (also known as tapinarof) is a small molecule that was first isolated from the bacterium Photorhabdus luminescens and was synthesized by late Genhui Chen and his team from Beijing Wenfeng Tianji Pharma. It took more than 20 years to study the mechanism of action, come up with the formulation, and evaluate the efficacy and safety of this compound in patients with psoriasis. It was hard work indeed."

In their study, Prof. Zhang and his colleagues carried out a double blinded, placebo controlled, phase III clinical trial in twenty-three dermatological centers in China to evaluate the safety and efficacy of topical benvitimod cream in patients with mild-to-moderate plaque psoriasis.

Six hundred and eighty-six adult patients with mild to moderate plaque psoriasis were included in this study. Patients were randomized to receive 1% benvitimod cream, 0.005% calcipotriol ointment--a standard treatment for plaque psoriasis--or a similar-looking "placebo." They were treated for 12 weeks. The efficacy of benvitimod was assessed at the end of the treatment period.

Of the patients receiving treatment with benvitimod cream, 50.4% achieved a psoriasis area and severity index (PASI) score of 75 at 12 weeks, which indicates a 75% or greater decrease in psoriasis size and severity compared to pre-treatment levels. In contrast, PASI 75 was achieved in only 38.5% and 13.9% of patients receiving calcipotriol ointment and placebo, respectively. Similarly, a significantly higher proportion of patients who received benvitimod cream (66.3%) achieved a static physicians' global assessment (sPGA) score of 0 or 1 (which indicate very low disease severity) compared to those who were put on placebo (33.5%).

This phase III trial also showed that the benvitimod cream was well tolerated. The most common side-effects were only mild irritation and itching at the site of application and these symptoms resolved spontaneously in most patients. No serious systemic side-effects were found.

Prof. Zhang remarks, "The results of this phase III trial are encouraging. The benvitimod cream can soon be a new treatment option for Chinese patients with plaque psoriasis. Given that most patients with psoriasis have plaque psoriasis, this will have a significant impact in terms of reducing the psoriasis disease burden in the country."

Perhaps, in time, it can become a standard method of psoriasis management all over the world.

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Reference

Titles of original papers: A double-blind, randomized, placebo- and positive-controlled phase III trial of 1% envitimod cream in mild-to-moderate plaque psoriasis
Journal: Chinese Medical Journal
DOI: 10.1097/CM9.0000000000001221

Fishing out the bad apples: Novel quantitative method to assess the safety of food

Scientists from Korea develop an effective yet simple strategy to quantify histamine levels in fish samples

CHUNG ANG UNIVERSITY

Research News

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IMAGE: SPOILED FOOD, ESPECIALLY FISH, CAN HAVE HIGH LEVELS OF HISTAMINE, WHICH CAN BE DANGEROUS TO HUMANS; THUS, IT IS IMPORTANT TO DEVISE METHODS FOR THE DETECTION OF SUCH HARMFUL CHEMICALS... view more 

CREDIT: UNSPLASH

Consumers of purchased foods have no way of ascertaining the quality and safety of the food that existing distribution systems deliver to their plates. Unfortunately, inappropriate refrigeration can sometimes lead to food spoilage, which is often difficult to detect. Such is the case for mackerel fish, which readily develop harmful levels of a substance called histamine when left at room temperature for too long. Histamine is neurotoxic and can trigger severe allergic reactions, including rashes, vomiting, and diarrhea. Because spoiled fish can sometimes look and smell completely normal, it is important to accurately quantify histamine levels in fish samples to ensure food quality has been properly maintained during transportation and storage.

Although several techniques to detect histamine exist, they generally require expensive and bulky equipment, as well as the presence of a qualified analyst. To address these limitations, a team of scientists at Chung-Ang University, Korea, recently developed a new quantification method that is simultaneously simple, effective, and inexpensive. In their study, which was led by Professor Tae Jung Park and Jong Pil Park and published in Biosensors and Bioelectronics, the team describes their novel approach based on the use of fluorescent carbon nanoparticles and a protein that binds strongly to histamine.

First, the scientists looked for peptides--short chains of amino acids--with the highest affinity and selectivity against histamine. To do this, they employed phage-display technology, in which the external proteins of genetically modified viruses are used to check for chemical interactions. After screening with a large peptide library, they identified the best one for their purposes, called "Hisp3."

Then, the scientists produced fluorescent carbon nanoparticles called "carbon quantum dots (CQDs)" and coated them with N-Acetyl-L-Cysteine (NAC), a naturally occurring compound that also binds to Hisp3. The CQDs are fluorescent, meaning that upon irradiation with ultraviolet light, they re-emit the captured energy at a lower, visible frequency. However, their fluorescence is "quenched" when Hisp3 is added to the mix, which binds to the NAC and covers the CQDs' surface.

This last part is essential to the method because, when a histamine-containing sample is mixed with the CQDs, the Hisp3 unbinds from the NAC and binds to the histamine, restoring the original fluorescence levels of the CQDs in direct proportion to the concentration of histamine (as shown in the accompanying figure). By comparing the initial and final fluorescence levels of the CQDs using a fluorescence detection instrument or a handheld UV-irradiation flashlight, it is possible to indirectly quantify the concentration or intensity of histamine in the sample.

The proposed strategy was validated using fish samples with known histamine concentrations and other established techniques as well. Surprisingly, the new method proved to be more powerful than existing ones despite being simpler, as Prof. Park remarks, "We managed to accurately measure histamine concentrations ranging from 0.1 to 100 parts per million, with a limit of detection as low as 13 parts per billion. This means our approach is not only more convenient but also more effective and sensitive than those currently available methods."

Thus, this new method can not only detect dangerous histamine levels, but can also assess the state and quality of food products, as Prof. Park explains, "While the detection of histamine as a harmful factor is important, our approach can further serve to objectively measure the quality and freshness of food, thereby contributing to increasing food safety and benefitting consumers."

Additionally, the proposed methodology could be applied using other peptides to accurately determine the concentration of different chemicals in food samples and biomedical specimens. If adopted by the food and medical diagnostic industries, this method could provide us with the much-needed assurance that the food we consume and the environmental conditions we live in are safe.

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Reference

Authors: Rongjia Shi (a), Shuaihui Feng (a), Chan Yeong Park (a), Kyung Yeol Park (a), Jeonghun Song (b), Jong Pil Park (b), Hyang Sook Chun (b), Tae Jung Park (a)

Title of original paper: Fluorescence detection of histamine based on specific binding bioreceptors and carbon quantum dots

Journal: Biosensors and Bioelectronics

DOI: 10.1016/j.bios.2020.112519

Affiliations:

(a) Department of Chemistry, Research Institute of Chem-Bio Diagnostic Technology, Chung-Ang University
(b) Department of Food Science and Biotechnology, School of Food Science and Technology, Chung-Ang University

About Chung-Ang University

Chung-Ang University is a private comprehensive research university located in Seoul, South Korea. It was started as a kindergarten in 1918 and attained university status in 1953. It is fully accredited by the Ministry of Education of Korea. Chung-Ang University conducts research activities under the slogan of "Justice and Truth." Its new vision for completing 100 years is "The Global Creative Leader." Chung-Ang University offers undergraduate, postgraduate, and doctoral programs, which encompass a law school, management program, and medical school; it has 16 undergraduate and graduate schools each. Chung-Ang University's culture and arts programs are considered the best in Korea.

Website: https://neweng.cau.ac.kr/index.do

About Professor Tae Jung Park from Chung-Ang University

Dr. Tae Jung Park is a Distinguished Professor in the Chemistry Department of Chung-Ang University, and his research interests include exploring novel technologies for bio-nano convergence studies, such as biosensors and nanocomplex fabrication. He received bachelor's and master's degrees from the Chungnam National University, Korea, in 1998 and 2000, respectively. He received his doctoral degree from the Department of Chemical & Biomolecular Engineering of KAIST in 2004. He previously served as a research professor and chief researcher at the BioProcess Engineering Research Center in KAIST. He has more than 215 publications to his credit.

Website: http://nbc.cau.ac.kr/

Crystal structures in super slow motion

Physicists from Göttingen first to succeed in filming a phase transition with extremely high spatial and temporal resolution

UNIVERSITY OF GÖTTINGEN

Research News

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IMAGE: AT THE HEART OF THE IMAGING TECHNIQUE IS A COMPLEX ARRAY OF 72 CIRCULAR APERTURES view more 

CREDIT: DR MURAT SIVIS

Laser beams can be used to change the properties of materials in an extremely precise way. This principle is already widely used in technologies such as rewritable DVDs. However, the underlying processes generally take place at such unimaginably fast speeds and at such a small scale that they have so far eluded direct observation. Researchers at the University of Göttingen and the Max Planck Institute (MPI) for Biophysical Chemistry in Göttingen have now managed to film, for the first time, the laser transformation of a crystal structure with nanometre resolution and in slow motion in an electron microscope. The results have been published in the journal Science.

The team, which includes Thomas Danz and Professor Claus Ropers, took advantage of an unusual property of a material made up of atomically thin layers of sulphur and tantalum atoms. At room temperature, its crystal structure is distorted into tiny wavelike structures - a "charge-density wave" is formed. At higher temperatures, a phase transition occurs in which the original microscopic waves suddenly disappear. The electrical conductivity also changes drastically, an interesting effect for nano-electronics.

In their experiments, the researchers induced this phase transition with short laser pulses and recorded a film of the charge-density wave reaction. "What we observe is the rapid formation and growth of tiny regions where the material was switched to the next phase," explains first author Thomas Danz from Göttingen University. "The Ultrafast Transmission Electron Microscope developed in Göttingen offers the highest time resolution for such imaging in the world today." The special feature of the experiment lies in a newly developed imaging technique, which is particularly sensitive to the specific changes observed in this phase transition. The Göttingen physicists use it to take images that are composed exclusively of electrons that have been scattered by the crystal's waviness.

CAPTION

Artist's impression of the charge density wave in the ultrafast transmission electron microscope.

Florian Sterl (Sterltech Optics)

Their cutting-edge approach allows the researchers to gain fundamental insights into light-induced structural changes. "We are already in a position to transfer our imaging technique to other crystal structures," says Professor Claus Ropers, leader of Nano-Optics and Ultrafast Dynamics at Göttingen University and Director at the MPI for Biophysical Chemistry. "In this way, we not only answer fundamental questions in solid-state physics, but also open up new perspectives for optically switchable materials in future, intelligent nano-electronics."

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Original publication: Thomas Danz et al., Ultrafast nanoimaging of the order parameter in a structural phase transition, Science 2021, doi:10.1126/science.abd2774

Russian chemists developed polymer cathodes 
for ultrafast batteries

SKOLKOVO INSTITUTE OF SCIENCE AND TECHNOLOGY (SKOLTECH)

NEWS RELEASE 19-JAN-2021

Scientists are searching for lithium technology alternatives in the face of the surging demand for lithium-ion batteries and limited lithium reserves. Russian researchers from Skoltech, D. Mendeleev University, and the Institute of Problems of Chemical Physics of RAS have synthesized and tested new polymer-based cathode materials for lithium dual-ion batteries. The tests showed that the new cathodes withstand up to 25,000 operating cycles and charge in a matter of seconds, thus outperforming lithium-ion batteries. The cathodes can also be used to produce less expensive potassium dual-ion batteries. The research was published in the journal Energy Technology.

The amount of electricity consumed worldwide grows by the year, and so does the demand for energy storage solutions since many devices often operate in autonomous mode. Lithium-ion batteries can generate enormous power while showing fairly high discharge and charge rates and storage capacity per unit mass, making them a popular storage device in electronics, electric transport, and global power grids. For instance, Australia is launching a series of large-scale lithium-ion battery storage projects to manage excess solar and wind energy.

If lithium-ion batteries continue to be produced in growing quantities, the world may sooner or later run out of lithium reserves. With Congo producing 60% of cobalt for lithium-ion batteries' cathodes, cobalt prices may skyrocket. The same goes for lithium, as lithium mining's water consumption poses a great challenge for the environment. Therefore, researchers are looking for new energy storage devices relying on more accessible materials while using the same operating principle as lithium-ion batteries.

The team used a promising post-lithium dual-ion technology based on the electrochemical processes involving the electrolyte's anions and cations to attain a manifold increase in lithium-ion batteries' charging rate. Another plus is that the cathode prototypes were made of polymeric aromatic amines synthesized from various organic compounds.

"Our previous research addressed polymer cathodes for ultra-fast high-capacity batteries that can be charged and discharged in a few seconds, but we wanted more," says Filipp A. Obrezkov, a Skoltech Ph.D. student and the first author of the paper. "We used various alternatives, including linear polymers, in which each monomeric unit bonds with two neighbors only. In this study, we went on to study new branched polymers where each unit bonds with at least three other units. Together they form large mesh structures that ensure faster kinetics of the electrode processes. Electrodes made of these materials display even higher charge and discharge rates."

A standard lithium-ion cell is filled with lithium-containing electrolyte and divided into the anode and the cathode by a separator. In a charged battery, the majority of lithium atoms are incorporated in the anode's crystal structure. As the battery discharges, lithium atoms move from the anode to the cathode through the separator. The Russian team studied the dual-ion batteries in which the electrochemical processes involved the electrolyte's cations (i.e., lithium cations) and anions that get in and out of the anode and cathode material's structures, respectively.

Another novel feature is that, in some experiments, the scientists used potassium electrolytes instead of expensive lithium ones to obtain potassium dual-ion batteries.

The team synthesized two novel copolymers of dihydrophenazine with diphenylamine (PDPAPZ) and phenothiazine (PPTZPZ), which they used to produce cathodes. As anodes, they used metallic lithium and potassium. Since the cathode drives the key features of these battery prototypes called half-cells, the scientists assemble them to assess the capabilities of new cathode materials quickly.

While PPTZPZ half-cells showed average performance, PDPAPZ turned out to be more efficient: lithium half-cells with PDPAPZ were fairly quick to charge and discharge while displaying good stability and retaining up to a third of their capacity even after 25,000 operating cycles. If a regular phone battery were as stable, it could be charged and discharged daily for 70 years. PDPAPZ potassium half-cells exhibited a high energy density of 398 Wh/kg. For comparison, the value for common lithium cells is 200-250 Wh/kg, the anode and electrolyte weights included. Thus the Russian team demonstrated that polymer cathode materials could create efficient lithium and potassium dual-ion batteries.

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Skoltech is a private international university located in Russia. Established in 2011 in collaboration with the Massachusetts Institute of Technology (MIT), Skoltech is cultivating a new generation of leaders in the fields of science, technology, and business is researching in breakthrough fields, and is promoting technological innovation intending to solve critical problems that face Russia and the world. Skoltech is focusing on six priority areas: data science and artificial intelligence, life sciences, advanced materials and modern design methods, energy efficiency, photonics, and quantum technologies, and advanced research.
Web: https://www.skoltech.ru/.

The D. Mendeleev University of Chemical Technology of Russia, a mainstay university for the Russian chemical industry, aims to generate and integrate new knowledge in the industry. This study was performed by the researchers of the Skolkovo Institute of Science and Technology (Skoltech) and the Institute of Problems of Chemical Physics of RAS, as well as the students of D. Mendeleev University's Institute of Chemistry and Problems of Sustainable Development, with financial support from the Ministry of Science and Higher Education of Russia and the Russian Foundation for Basic Research (RFBR).

POSTMODERN ALCHEMY

Experimental evidence of an intermediate state of matter between a crystal and a liquid

MOSCOW INSTITUTE OF PHYSICS AND TECHNOLOGY

Research News

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IMAGE: INTERMEDIATE PHASE. ILLUSTRATION. view more 

CREDIT: SCIENTIFIC REPORTS

Scientists from the Joint Institute for High Temperatures Russian Academy of Sciences (JIHT RAS) and Moscow Institute of Physics and Technology (MIPT) have experimentally confirmed the presence of an intermediate phase between the crystalline and liquid states in a monolayer dusty plasma system. The theoretical prediction of the intermediate - hexatic - phase was honoured with the Nobel Prize in Physics in 2016: the prize was awarded to Michael Kosterlitz, David Thouless and Duncan Haldane with the formulation "for theoretical discoveries of topological phase transitions and topological phases of matter."

In a scientific article in the journal Scientific Reports, the JIHT RAS scientists published their observations and detailed descriptions of experiments, during which they first observed the hexatic phase in two-dimensional structures in plasma. The paper describes methods for accurately identifying phase transition points and presents a detailed analysis of the structural properties of such a system. The data obtained during the experiment are fully consistent with the Berezinsky-Kosterlitz-Thouless theory.

"Our design of experiment makes it possible to clearly observe a two-stage process of crystal melting and to identify the points of the phase transition "solid-hexatic phase " and "hexatic phase-liquid," said Ph.D. Elena Vasilieva, the senior researcher in Laboratory of Dusty Plasma Diagnostics, JIHT RAS. "The long time of the experiment, sufficient to establish a stationary state of the system, in combination with precise methods of controlling the temperature of particles, made it possible to smoothly change the parameters of the system and "catch" the hexatic phase."

According to Elena Vasilieva, despite the existence of the Berezinsky-Kosterlitz-Thouless theory for more than 40 years, which predicts two-stage melting from a crystal to a liquid phase with the formation of an intermediate hexatic phase, it has not yet been possible to study these processes in laboratory plasma systems. Two-dimensional transitions have already been observed in polymer colloids, magnetic bubbles in thin films, liquid crystals, and superconductors, but there has been no experimental evidence of two-stage melting in dusty plasmas for a long time.

"Our experiment was successful due to a number of factors. For example, we used an unconventional approach to form a monolayer dusty system, namely we used particles with a metal surface that are capable of absorbing laser radiation and converting it into the energy of their own motion. The particle system had a long time for relaxation before recording the experimental series. In addition, a homogeneous laser beam was used to uniformly influence the structure and its precise heating," commented Oleg Petrov, the director of the Joint Institute for High Temperatures Russian Academy of Sciences.

The study of the physical properties of two-dimensional systems is of great practical importance. Such research is now rapidly developing, promising in the future new materials with desired properties and devices based on them in microelectronics, medicine for DNA sequencing, etc.

The results presented in the article were obtained with the support of the Russian Science Foundation in the framework of the project "Active Brownian motion of Coulomb particles in plasma and superfluid helium."

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Genetic rewiring behind spectacular evolutionary explosion in East Africa

EARLHAM INSTITUTE

Research News

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IMAGE: SAMPLING CICHLID FISH TISSUES FOR GENOME AND TRANSCRIPTOME SEQUENCING IN TANZANIA AND ZANZIBAR ARCHIPELAGO. TILAPIA AND HAPLOCHROMINE CICHLID FISH SPECIES WERE SAMPLED FOR ASSOCIATED STUDIES ON CHARACTERISING GENOMIC SIGNATURES OF... view more 

CREDIT: DR GRAHAM ETHERINGTON AND DR TARANG MEHTA, EARLHAM INSTITUE (EI)

Genetic rewiring could have driven an evolutionary explosion in the shapes, sizes and adaptations of cichlid fish, in East Africa's answer to Darwin's Galapagos finches.

Published in BMC Genome Biology, an Earlham Institute (EI) study, with collaborators at the University of East Anglia (UEA) and Wisconsin Institute for Discovery, shows that 'genetic rewiring' at non-coding regions - rather than mutations to protein-coding regions of genes - may play an important role in how cichlid fish are able to rapidly adapt to fill a staggeringly wide range of environmental niches in the East African Rift lakes.

The results could help future studies to improve breeding of economically important cichlid species such as tilapia - a staple in aquaculture.

Darwin's famous finches are one of the most well-known examples of evolution by natural selection, and specifically adaptive radiation. The birds he observed on the Galapagos archipelago had differences in their beaks that could be matched to fit their specific feeding habits - whether they ate big or small seeds, insects, or even used tools to find food.

Amazingly, in the 2-3 million years it took 14 species of finch to evolve on the Galapagos Islands, around 1,000 species of cichlid evolved in Lake Malawi alone.

"In the Great Lakes of East Africa, and within the last few million years, a few ancestral lineages of cichlid fish have independently radiated and given rise to well over 2,000 species - and we're still finding new ones," says first author Dr Tarang Mehta, a postdoctoral scientist in EI's Haerty Group.

"They occupy a really large diversity of freshwater ecological niches in lakes, rivers and even swamps: this includes sandy substrates, mud, rocks, and vegetated bottoms. As a result, they are all adapted to different dietary habits and niches in these areas."

By looking at gene expression across different cichlid tissues in five representative species from East African rivers and the Great Rift Lakes, the team discovered an evolutionary rewiring of several important genes linked to the adaptability seen in cichlids. The effect which was particularly prominent in the vision of fish species.

"We found out that the most rewired genes are associated with the visual system," explains Dr Mehta. "Essentially, if you look at the different species of fish we used in the study, you could see major differences in the regulation network around opsin genes they use for vision depending on where they live and what they eat.

"For example, the Lake Malawi rock-dwelling species, M. zebra, feeds on UV-absorbing phytoplankton algae. That generally requires increased expression of a particular opsin, SWS1, which helps with sensitivity to UV light. That may well explain why it has a more complex regulatory network around SWS1 compared with the Lake Tanganyika benthivore, N. brichardi, which does not share the same diet or habitat."

Armed with some genes of interest, the team confirmed the mechanisms behind these gene regulatory differences in the lab. Looking at the fine scale, they identified small changes in the DNA sequence of regulatory regions at the start of genes important for trait differences between species, including the visual system.

Rather than the gene itself being modified, it was the regions of DNA known as binding sites that are targeted by transcription factors - the proteins which determine whether a gene is turned on or turned off. In this way, the different species of fish can be said to have had their visual system 'rewired' for different functions.

Taking this further, the team was able to show that these changes could be commonly associated throughout cichlid fish in Lake Malawi, with diet and ecology-dependent rewiring showing that changes in transcription factor binding could be key to fine-tuning visual sensitivity.

Depending on the trait, cichlids appear to utilise an array of genetic mechanisms to generate phenotypic novelty however, the 'tinkering' of regulatory systems appears more widespread in cichlid fish than previously discovered. This evolutionary plasticity could well explain the explosion of species in such a small area over a relatively short time.

"It's a proof of concept," says Dr Mehta. "As more data comes out, we'll be able to look at this in depth in representative clades from each of the different radiations, not just in Lake Malawi but also Lake Tanganyika, Lake Victoria and even in some of the cichlids in South America."

Professor Federica Di Palma, Professorial Fellow of Biodiversity at UEA, said: "We have released an impressive amount of expression data which will further aid studies into the adaptive radiation of cichlids for the future. We are now deciphering the complexity of these cis-regulatory regions by using genome-wide CRISPR screens.

"The wider impact of our regulatory gene network approach will also help inform evolution of agriculturally important traits for tilapia such as growth rate and tolerance to different local water conditions, as well as for general aquaculture and fisheries."

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You can access the paper, here: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-020-02208-8

Scientists present novel approach for monitoring freshwater health

Study describes how the world's smallest portable DNA sequencing device helps simplify the monitoring of bacteria in freshwater ecosystems

ELIFE

Research News

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IMAGE: THE MINION IS A PORTABLE DEVICE THAT CAN SEQUENCE GENETIC MATERIAL SAMPLED FROM THE ENVIRONMENT - HERE, FROM THE RIVER CAM IN CAMBRIDGE, UK. view more 

CREDIT: TEAM PUNTSEQ (CC BY 4.0)

Researchers have used the world's smallest, smartphone-sized DNA sequencing device to monitor hundreds of different bacteria in a river ecosystem.

Writing in the journal eLife, the interdisciplinary team from the University of Cambridge, UK, provide practical and analytical guidelines for using the device, called the MinION (from Oxford Nanopore Technologies), to monitor freshwater health. Their guidelines promise a significantly more cost-effective and simple approach to this work outside the lab, compared to existing methods.

Rowers and swimmers in Cambridge are regularly affected by waterborne infections such as Weil's disease, sometimes leading to public closures of the city's iconic waterways. Monitoring the microbial species in freshwater can help indicate the presence of disease-causing microorganisms and even water pollution. But traditional tests for freshwater bacteria often require well-equipped laboratories and complex methods for growing colonies of individual bacterial species.

"The direct measurement of all bacterial DNA traces in freshwater, an approach known as metagenomics, is a valuable alternative, but still requires large, expensive equipment that can be hard to operate," says Andre Holzer, co-first author and PhD student at the Department of Plant Sciences, University of Cambridge. "We aimed to describe the bacterial species present in the River Cam using the new portable DNA sequencing technology."

The team used the MinION device to sequence the DNA of entire groups of microorganisms found in water samples from the River Cam. But before they could use the sequence data, they needed to optimise their experimental methods and analysis software. "It was essential to account for the quality of this new type of bacterial DNA sequence information," Holzer explains. "We tested many different algorithms for processing the data to find the most accurate methods."

The researchers then used their optimised guidelines to analyse the data and successfully measure the proportions of hundreds of different bacterial species present in the water. They took samples from nine different sites along the river, often sampling the sites at three different time points so they could compare the proportions of species in different locations and seasons.

The team was also able to distinguish closely related, harmful microbial species from non-harmful ones. By comparing the samples from different locations, they found that there were more potentially harmful bacteria and those associated with wastewater downstream of the most built-up, urban areas of the river. Chemical follow-up analyses of the water samples collected from the same urban areas revealed a matching trend of increasing wastewater pollution in those areas.

"Our work shows how MinION and the associated DNA sequencing technology can be used in the effective monitoring of freshwater health," says Lara Urban, co-lead investigator of the work and now an Alexander von Humboldt Research Fellow at the University of Otago, New Zealand. "This expands on the technology's existing applications which include the accurate tracing of viral transmissions between patients during the recent Ebola, Zika and SARS-CoV-19 virus outbreaks."

"We hope our results will encourage other independent scientists and collectives to engage in simplified freshwater management and biodiversity tests around the globe,"concludes senior author Maximilian Stammnitz, a PhD student at the Department of Veterinary Medicine, University of Cambridge.

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References

The paper 'Freshwater monitoring by nanopore sequencing' can be freely accessed online at https://doi.org/10.7554/eLife.61504. Contents, including text, figures and data, are free to reuse under a CC BY 4.0 license.

This study was supported by grants from the OpenPlant Fund (BBSRC), University of Cambridge RCUK Catalyst Seed Fund (Public Engagement Starter Grant), Natural Environment Research Council and Gates Cambridge Trust.

To find out more about the Punting & Sequencing (PuntSeq) project and the team behind it, visit http://www.puntseq.co.uk.

Media contact

Emily Packer, Media Relations Manager
eLife
e.packer@elifesciences.org
01223 855373

About eLife

eLife is a non-profit organisation created by funders and led by researchers. Our mission is to accelerate discovery by operating a platform for research communication that encourages and recognises the most responsible behaviours. We work across three major areas: publishing, technology and research culture. We aim to publish work of the highest standards and importance in all areas of biology and medicine, including Ecology and Microbiology and Infectious Disease, while exploring creative new ways to improve how research is assessed and published. We also invest in open-source technology innovation to modernise the infrastructure for science publishing and improve online tools for sharing, using and interacting with new results. eLife receives financial support and strategic guidance from the Howard Hughes Medical Institute, the Knut and Alice Wallenberg Foundation, the Max Planck Society and Wellcome. Learn more at https://elifesciences.org/about.

To read the latest Ecology research published in eLife, visit https://elifesciences.org/subjects/ecology.

And for the latest in Microbiology and Infectious Disease, see https://elifesciences.org/subjects/microbiology-infectious-disease.

A sea of rubbish: ocean floor landfills

The long journey of litter to seafloor










The Messina Strait, a submarine bridge separating the island of Sicily from the Italian Peninsula, is the area with the largest marine litter density worldwide -more than a million objects per square kilometre in some parts-, as reported in a new review paper published in the journal Environmental Research Letters.

Also, over the next thirty years, the volume of rubbish in the sea could surpass three billion metric tons (Mt), as cited in the study, whose corresponding authors are the experts Miquel Canals, from the Faculty of Earth Sciences of the University of Barcelona, and Georg Hanke from the European Commission's Joint Research Centre (JRC), where scientists carry out research in order to provide independent scientific advice and support to EU policies.

Led by the University of Barcelona, this paper gathers the results of the scientific meeting on macrolitter that took place in May 2018, promoted by the European Commission's Joint Research Centre (JRC) and the German Alfred Wegener Institute (AWI). A team of twenty-five scientists from across the world treated issues such as data needs, methodologies, harmonisation and needs for further development.

The study provides a synthesis of current knowledge on human-sourced materials lying on the seafloor and goes through the methodologies to improve future studies, "highlighting the need to understand litter occurrence, distribution and quantities in order to provide insight for appropriate (policy) measures", notes Georg Hanke, who adds that "the paper also shows the need to employ new methodologies -i.e. imaging approaches- to cover areas that had not been considered previously, and provides tools to enable quantitative assessments such as those under the EU Marine Strategy Framework Directive (MSFD)".

Among other signatories of the article are experts from the University of Açores (Portugal), Alfred Wegener Institute (Germany), Utrecht University (Netherlands), the Norwegian Institute of Marine Research (Norway), the Secretariat of the Barcelona Convention on the protection of the Mediterranean Sea, Monterey Bay Aquarium Research Institute (MBARI, California, United States), the Institute for Global Change of the Japan Agency for Marine Earth Science and Technology Research (JAMSTEC, Japan), IFREMER (France) and Oxford University (United Kingdom), among other institutions.

When litter arrives before humans do

The ocean floor is increasingly accumulating marine litter. Whereas the largest seafloor litter hotspots -likely in the deep sea- are still to be found, plastics have already been found in the deepest point on Earth, the Mariana Trench -at a depth of 10,900 meters- in the Pacific Ocean. In some cases, litter concentrations reach densities comparable to large landfills, experts warn.

Despite the scientific community efforts, "the extent of marine litter on our seas and oceans is not yet fully known. The marine regions most affected by this problem are in landlocked and semi-enclosed seas, coastal bottoms, marine areas under the influence of large river mouths, and places with high fishing activity, even far from land", says Professor Miquel Canals, head of the Consolidated Research Group on Marine Geosciences at UB.

Canals highlights that "the level of waste treatment in coastal countries is decisive: the less treatment -or the more deficient-, the more waste reaching the ocean, and therefore, the ocean floor, which is a problem that affects specially third world countries".

The long journey of litter to seafloor

Plastics, fishing gears, metal, glass, ceramics, textiles and paper are the most abundant materials in seafloor litter hotspots. Geomorphological features, the submarine relief and the nature of the seafloor determine the distribution of litter items on the seabed. Ocean dynamics, --that is, processes such as dense water cascades, ocean currents and storms-- ease the transport and dispersal of litter across the ocean, from coasts to abyssal plains, thousands of meters deep. However, these factors do not occur in all ocean ecosystems and also vary over time and in intensity where they take place.

Due to a gravitational effect, light waste is usually transported along and into marine regions where dense currents flow --i.e. submarine canyons and other submarine valleys-- and where flow lines concentrate, such as nearby large submarine reliefs. Finally, materials transported by ocean dynamics accumulate in depressions and quiet marine areas.

The properties of materials dumped in the marine environment also affect their dispersion and accumulation on the ocean floor. It is estimated that 62% of the dirt accumulated on seabeds is made of plastics, "which is relatively light and easy to transport over long distances. On the other hand, heavy objects such as barrels, cables or nets are usually left at the point where they are initially fell or got entangled", says Canals.

Litter drowns marine life

Litter is a new threat to marine biodiversity. It is already known that nearly 700 marine species, 17% of which are on the IUCN red list, have been affected by this problem in several ways. Seabed entangled fishing gears can cause serious ecological impacts for decades because of ghost fishing. The slow decomposition of fishing nets -usually made of high-strength polymers- aggravates the detrimental effects of this type of waste on the marine ecosystem.

Other human activities -dredging, trawling, etc.- trigger secondary dispersal by remobilization and fragmentation of seafloor litter. In addition, seabed waste concentrations can easily trap other objects, thus generating larger and larger litter accumulations. It is paradoxical that waste may increase the heterogeneity of the substrate, which can benefit some organisms. Some xenobiotic compounds -pesticides, herbicides, pharmaceuticals, heavy metals, radioactive substances, etc.- associated to litter are highly resistant to degradation and endanger marine life. However, the extent of the effects of litter on the habitats of the vast expanses of the deep ocean still is a chapter to be written by the scientific community.

"In the Mediterranean Sea -says Miquel Canals- seafloor marine litter already is a serious ecological problem. In some places of the Catalan coast, there are large accumulations of waste. When there are strong storms, such as Gloria, in January 2020, waves throw this waste on the beach. Some beaches in the country were literally paved with rubbish, thus showing to which extent the coastal seabed is littered. There are also noticeable concentrations of waste in some submarine canyons outside Catalonia".

Robotic technology for large depths

Beach litter and floating garbage can be identified and monitored by simple, low-cost methods. In contrast, the study of seafloor litter is a technological challenge, the complexity of which increases with water depth and remoteness of the marine area to be investigated. The study reviews both methodologies allowing physical sampling of seafloor waste and in situ observations.

New technologies have enabled major advances in the study of the environmental status of the seabed worldwide. The use of unmanned remotely operated vehicles (ROVs) is critical for in situ observation, despite the limitations for physical sampling. Classic technologies such as bottom trawling also have limitations, as they do not allow determining the precise location of the bottom-sampled objects. "Future methodologies should aim at easing the comparison of scientific data from different places. It should also be easier for observation and sampling efforts to generate consistent data sets, something that we are still far from achieving", says Canals.

Avoiding excess waste generation to take care of the planet

Knowledge and data about seafloor litter are necessary for the implementation of the Marine Strategy Framework Directive (MSFD) and other international policy frameworks, including global agreements. The publication shows how research on seafloor macrolitter can inform these international protection and conservation frameworks to prioritize efforts and measures against marine litter and its deleterious impacts.

The authors warn about the need to promote specific policies to minimize such a serious environmental problem. The study also addresses the debate on the removal of litter from the seabed, a management option that should be safe and efficient. In relation to this, the Joint Research Centre (JRC) is co-chairing the MSFD Technical Group on Marine Litter, which provides an information exchange and discussion platform to provide agreed guidance for MSFD implementation.

"Marine litter has reached the most remote places in the ocean, even the least (or never) frequented by our species and not yet mapped by science," says Miquel Canals. "In order to correct something bad, we must attack its cause. And the cause of the accumulation of waste on the coasts, seas and oceans, and all over the planet, is the excess waste generation and spillage in the environment, and poor or insufficient management practices. As humans, we have little or no care at all to prevent litter from accumulating everywhere".

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JAMSTEC's Deep-sea Debris Database [video] |

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