Next frontier in bacterial engineering

New technique promises end-run around major barrier in genetic engineering of bacteria, setting stage for advances in medicine and beyond

HARVARD MEDICAL SCHOOL

From bacteria-made insulin that obviates the use of animal pancreases to a better understanding of infectious diseases and improved treatments, genetic engineering of bacteria has redefined modern medicine. Yet, serious limitations remain that hamper| progress in numerous other areas.

A decades-old bacterial engineering technique called recombineering (recombination-mediated genetic engineering) allows scientists to scarlessly swap pieces of DNA of their choosing for regions of the bacterial genome. But this valuable and versatile approach has remained woefully underused because it has been limited mainly to Escherichia coli--the lab rat of the bacterial world--and to a handful of other bacterial species.

Now a new genetic engineering method developed by investigators in the Blavatnik Institute at Harvard Medical School and the Biological Research Center in Szeged, Hungary, promises to super-charge recombineering and open the bacterial world at large to this underutilized approach.

A report detailing the team's technique is published May 28 in PNAS.

The investigators have developed a high-throughput screening method to look for the most efficient proteins that serve as the engines of recombineering. Such proteins, known as SSAPs, reside within phages--viruses that infect bacteria.

Applying the new method, which enables the screening of more than two hundred SSAPs, the researchers identified two proteins that appear to be particularly promising.

One of them doubled the efficiency of single-spot edits of the bacterial genome. It also improved tenfold the ability to perform multiplex editing--making multiple edits genome-wide at the same time. The other one enabled efficient recombineering in the human pathogen Pseudomonas aeruginosa, a frequent cause of life-threatening, hospital-acquired infections, for which there has long been a dearth of good genetic tools.

"Recombineering will be a very critical tool that will augment our DNA writing and editing capabilities in the future, and this is an important step in improving the efficiency and reach of the technology," said study first author Timothy Wannier, research associate in genetics in lab of George Church, the Robert Winthrop Professor of Genetics at HMS.

Previous genetic engineering methods, including CRISPR Cas9-based gene-editing, have been ill-suited to bacteria because these methods involve "cutting and pasting" DNA, the researchers said. This is because, unlike multicellular organisms, bacteria lack the machinery to repair double-stranded DNA breaks efficiently and precisely, thus DNA cutting can profoundly interfere with the stability of the bacterial genome, Wannier said. The advantage of recombineering is that it works without cutting DNA.

Instead, recombineering involves sneaking edits into the genome during bacterial reproduction. Bacteria reproduce by splitting in two. During that process, one strand of their double-stranded, circular DNA chromosomes goes to each daughter cell, along with a new second strand that grows during the early stages of fission. The raw materials for recombineering are short, approximately 90 base strands of DNA that are made to order. Each strand is identical to a sequence in the genome, except for edits in the strand's center. These short strands slip into place as the second strands of the daughter cells grow, efficiently incorporating the edits into their genomes.

Among many possible uses, edits might be designed to interfere with a gene in order to pinpoint its function or, alternatively, to improve production of a valuable bacterial product. SSAPs mediate attachment and proper placement of the short strand within the growing new half of the daughter chromosome.

Recombineering might enable the substitution of a naturally occurring bacterial amino acid--the building blocks of proteins--with an artificial one. Among other things, doing so could enable the use of bacteria for environmental cleanup of oil spills or other contaminants, that depend on these artificial amino acids to survive, meaning that the modified bacteria could be easily annihilated once the work is done to avoid the risks of releasing engineered microbes into the environment, Wannier said.

"The bacteria would require artificial amino acid supplements to survive, meaning that they are preprogrammed to perish without the artificial feed stock," Wannier added.

A version of recombineering, called multiplex automated genome engineering (MAGE), could greatly boost the benefits of the technique. The particular advantage of MAGE is its ability to make multiple edits throughout the genome in one fell swoop.

MAGE could lead to progress in projects requiring reengineering of entire metabolic pathways, said John Aach, lecturer in genetics at HMS. Case in point, Aach added, are large-scale attempts to engineer microbes to turn wood waste into liquid fuels.

"Many investigator-years' effort in that quest have made great progress, even if they have not yet produced market-competitive products," he said.

Such endeavors require testing many combinations of edits, Aach said.

"We have found that using MAGE with a library of DNA sequences is a very good way of finding the combinations that optimize pathways."

A more recent descendant of recombineering, named directed evolution with random genomic mutations (DIvERGE), promises benefits in the fight against infectious diseases and could open new avenues for tackling antibiotic resistance.

By introducing random mutations into the genome, DIvERGE can speed up natural bacterial evolution. This helps researchers quickly uncover changes that could arise naturally in harmful bacteria that would make them resistant to antibiotic treatment, explained Akos Nyerges, research fellow in genetics in Church's lab at HMSs, previously at the Biological Research Center of the Hungarian Academy of Sciences.

"Improvements in recombineering will allow researchers to more quickly test how bacterial populations can gain resistance to new antibacterial drugs, helping researchers to identify less resistance-prone antibiotics," Nyerges said.

Recombineering will likely usher in a whole new world of applications that would be hard to foresee at this juncture, the researchers said.

"The new method greatly improves our ability to modify bacteria," Wannier said. "If we could modify a letter here and there in the past, the new approach is akin to editing words all over a book and doing so opens up the scientific imagination in a way that was not previously possible."

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Church was a principal investigator on the study. Co-investigators on the research included Helene Kuchwara, Márton Czikkely, Dávid Balogh, Gabriel Filsinger, Nathaniel Borders, Christopher Gregg, Marc Lajoie, Xavier Rios, and Csaba Pál.

Paper DOI: https://doi.org/10.1073/pnas.2001588117

The work was funded by the U.S. Department of Energy (DE-FG02-02ER63445), the European Research Council (H2020-ERC-2014-CoG 648364), GINOP (MolMedEx TUMORDNS) GINOP-2.3.2-15-2016-00020, GINOP (EVOMER) GINOP-2.3.2-15-2016-00014; Momentum Program of the Hungarian Academy of Sciences, an EMBO Long-Term Fellowship, the Szeged Scientists Academy under the sponsorship of the Hungarian Ministry of Human Capacities (EMMI: 13725-2/2018/INTFIN), by the UNKP-18-2 New the National Excellence Program of the Hungarian Ministry of Human Capacities and UNKP 10-2, and the New National Excellence Program of the Hungarian Ministry for Innovation and Technology.

Relevant disclosures:

Church has related financial interests in enEvolv, GRO Biosciences and 64-x; with some coauthors; and has submitted a patent application relating to pieces of this work (WO2017184227A2). Wannier, Church and another coauthor have submitted a patent application related to the improved SSAP variants referenced here. Nyerges is listed as an inventor on a patent application related to DIvERGE.

The most common organism in the oceans harbors a virus in its DNA

UNIVERSITY OF WASHINGTON

 

IMAGE: THE VIRUSES, COLORED ORANGE, ATTACHED TO A MEMBRANE VESICLE FROM THE SAR11 MARINE BACTERIA, COLORED GRAY, THAT WAS THE SUBJECT OF THIS STUDY. view more 

CREDIT: MORRIS ET AL./NATURE MICROBIOLOGY

The most common organism in the oceans, and possibly on the entire planet, is a family of single-celled marine bacteria called SAR11. These drifting organisms look like tiny jelly beans and have evolved to outcompete other bacteria for scarce resources in the oceans.

We now know that this group of organisms thrives despite -- or perhaps because of -- the ability to host viruses in their DNA. A study published in May in Nature Microbiology could lead to new understanding of viral survival strategies.

University of Washington oceanographers discovered that the bacteria that dominate seawater, known as Pelagibacter or SAR11, hosts a unique virus. The virus is of a type that spends most of its time dormant in the host's DNA but occasionally erupts to infect other cells, potentially carrying some of its host's genetic material along with it.

"Many bacteria have viruses that exist in their genomes. But people had not found them in the ocean's most abundant organisms," said co-lead author Robert Morris, a UW associate professor of oceanography. "We suspect it's probably common, or more common than we thought -- we just had never seen it."

This virus' two-pronged survival strategy differs from similar ones found in other organisms. The virus lurks in the host's DNA and gets copied as cells divide, but for reasons still poorly understood, it also replicates and is released from other cells.

The new study shows that as many as 3% of the SAR11 cells can have the virus multiply and split, or lyse, the cell -- a much higher percentage than for most viruses that inhabit a host's genome. This produces a large number of free viruses and could be key to its survival.

"There are 10 times more viruses in the ocean than there are bacteria," Morris said. "Understanding how those large numbers are maintained is important. How does a virus survive? If you kill your host, how do you find another host before you degrade?"

Co-lead author Kelsy Cain fills a bottle with seawater off the coast of Oregon as an undergraduate aboard the RV Roger Revelle during a research cruise in July 2017. Cain diluted the water several times and then isolated a new strain of SAR11 bacteria that became the focus of the new paper.

The study could prompt basic research that could help clarify host-virus interactions in other settings.

"If you study a system in bacteria, that is easier to manipulate, then you can sort out the basic mechanisms," Morris said. "It's not too much of a stretch to say it could eventually help in biomedical applications."

The UW oceanography group had published a previous paper in 2019 looking at how marine phytoplankton, including SAR11, use sulfur. That allowed the researchers to cultivate two new strains of the ocean-dwelling organism and analyze one strain, NP1, with the latest genetic techniques.

Co-lead author Kelsy Cain collected samples off the coast of Oregon during a July 2017 research cruise. She diluted the seawater several times and then used a sulfur-containing substance to grow the samples in the lab -- a difficult process, for organisms that prefer to exist in seawater.

The team then sequenced this strain's DNA at the UW PacBio sequencing center in Seattle.

"In the past we got a full genome, first try," Morris said. "This one didn't do that, and it was confusing because it's a very small genome."

The researchers found that a virus was complicating the task of sequencing the genome. Then they discovered a virus wasn't just in that single strain.

"When we went to grow the NP2 control culture, lo and behold, there was another virus. It was surprising how you couldn't get away from a virus," said Cain, who graduated in 2019 with a UW bachelor's in oceanography and now works in a UW research lab.

Cain's experiments showed that the virus' switch to replicating and bursting cells is more active when the cells are deprived of nutrients, lysing up to 30% of the host cells. The authors believe that bacterial genes that hitch a ride with the viruses could help other SAR11 maintain their competitive advantage in nutrient-poor conditions.

"We want to understand how that has contributed to the evolution and ecology of life in the oceans," Morris said.

Pelagibacter, or SAR11, is a single-celled bacterium that survives off dissolved carbon throughout the oceans. It makes up one in four ce

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Other co-authors are postdoctoral researcher Kelli Hvorecny and associate professor Justin Kollman in the UW Department of Biochemistry. The study was funded by the National Science Foundation and the National Institutes of Health's National Institute of Allergy and Infectious Disease.

For more information, contact Morris at morrisrm@uw.edu or 206-221-7228 and Cain at kcain97@uw.edu.

Towards a climate neutral Europe: The land sector is key

CMCC FOUNDATION - EURO-MEDITERRANEAN CENTER ON CLIMATE CHANGE

 

In 2014, EU leaders agreed that all sectors should contribute to the European 2030 emission reduction target, including the land use sector, which did not count towards the achievement of the previous climate change mitigation goals. In 2018, this agreement was implemented by the Regulation on the inclusion of greenhouse gas emissions and removals from land use, land use change and forestry (LULUCF) in the 2030 EU climate and energy framework. The Regulation lays down new rules for the accounting of the sector's emissions and removals, and for assessing EU Member States' compliance with these. For the first time, this allows the land sector to contribute, at least in part, to the achievement of the EU's climate change mitigation targets.

The paper "Making sense of the LULUCF Regulation: Much ado about nothing?", realized with the collaboration of the CMCC Foundation, assesses the importance and highlights the weaknesses and strengths of the LULUCF Regulation in the context of current EU climate and sustainability policies.

The three authors - among which Maria Vincenza Chiriacò and Lucia Perugini, researchers at the CMCC within the division dedicated to the study of agriculture, forests and ecosystem services - explain that the land sector plays a crucial role in climate change mitigation due to a peculiarity: the sector can either release greenhouse gases into the atmosphere, acting as a source of emissions or, conversely, store carbon and therefore acting as a sink. Whereas some sectors can reduce or even eliminate their emissions by foregoing the use of fossil fuels (which can be achieved via a transition to renewable energy sources and increased energy efficiency interventions) , other sectors - such as food production and waste - cannot. With its capacity to absorb CO2, the land sector can therefore compensate for part of these unavoidable emissions, thus becoming an important player in the EU's mitigation targets of reducing emissions by 40% before 2030.

"Given the potential for climate change mitigation embedded in the good management of the LULUCF sector, and underlined in the latest IPCC Special Report on "Climate change and land", it is extremely important that emissions and removals of the land sector are accounted for, to incentivize virtuous forest and agricultural management in the EU. Thanks to this Regulation, the sector can finally contribute to the EU's mitigation targets. This was also necessary to align the EU with the Paris Agreement requirement for economy-wide mitigation targets. Although the new Regulation has much improved the accounting rules for the LULUCF, it is still constrained within certain limits. We can consider the LULUCF regulation as a first step towards its full recognition", affirms Perugini, who is currently involved in the negotiating process under the UNFCCC (United Nations Framework Convention on Climate Change) as part of the Italian delegation dedicated to defining the role of the land sector.

Indeed, the Regulation demands that EU Member States ensure, between 2021 and 2030, that the LULUCF sector remain emission "neutral", and therefore generate neither credits nor debits. As of today, only a small part of credits generated by the LULUCF can be used to compensate emissions generated in other sectors towards the EU climate goals. Furthermore, the Regulation allows for possible debts arising from the land sector, under given conditions, to go unaccounted for by single member states.

The authors look forward to a further review of the 2030 EU climate framework, as envisioned by the EU Green Deal, as an opportunity to better tap into the sector's sizeable mitigation potential. "With the increased ambitions foreseen by the 'European Green Deal', which includes the specific objective to make of the EU the first climate neutral continent, including the contributions of every economic sector into the EU targets is even more important, as it incentivizes all sectors to do their best in the fight against climate change", continues Chiriacò.

The roadmap designed by the EU Commission - with the final objective of having zero net emissions of greenhouse gases by 2050 - includes the target of reducing GHG emissions by at least 50%, and possibly towards 55%, by 2030 compared with 1990 levels, and therefore increasing current ambitions.

Achieving these climate goals will require a deep cut in emissions in all sectors.

"The subject matter of the LULUCF Regulation closely intersects with that of other EU law and policy instruments dealing with agriculture and forestry, most saliently the Common Agricultural Policy (CAP) and the Renewable Energy Directive (RED). The EU's ambitious targets ask for a strong coordination and integration among the various sustainability and climate policies linked to the land sector, where all debits and credits generated are accounted for, with no limitations. Only in this way will we have full accountability of emissions and removals from the agriculture and forestry sectors, which will be crucial to monitor progress and reward those that engage in virtuous behaviour, and penalize those who do not", concludes Perugini.

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For more information: Savaresi, A., Perugini, L., Chiriacò, M. V., Making sense of the LULUCF Regulation: Much ado about nothing?, Review of European, RECIEL - Comparative and International Environmental Law, DOI: https://doi.org/10.1111/reel.12332

Growing evidence that minority ethnic groups in England may be at higher risk of COVID-19

BMC (BIOMED CENTRAL)

 

Previous pandemics have often disproportionately impacted ethnic minorities and socioeconomically disadvantaged populations. While early evidence suggests that the same may be occurring in the current SARS-CoV-2 pandemic, research into the subject remains limited.

A team of researchers at the University of Glasgow and Public Health Scotland, UK analysed data on 392,116 participants in the UK Biobank study, a large long-term study investigating the contribution of genes and the environment to the development of disease. UK Biobank data, which include information on social and demographic factors, such as ethnicity and socioeconomic position, health and behavioural risk factors, were linked to results of COVID-19 tests conducted in England between 16th March 2020 and 3rd May 2020. Out of the total number of participants whose data were analysed, 348,735 were White British, 7,323 were South Asian and 6,395 were from black ethnic backgrounds. 2,658 participants had been tested for SARS-CoV-2 and 948 had at least one positive test. Out of those, 726 received a positive test in a hospital setting, suggesting more severe illness.

The authors found that, compared to people from white British backgrounds, the risks of testing positive were largest in in black and South Asian minority groups who were 3.4 and 2.4 times more likely to test positive, respectively, with people of Pakistani ethnicity at highest risk in the south Asian group (3.2 times more likely to test positive). Ethnic minorities also were more likely to receive their diagnosis in a hospital setting, which suggests more severe illness. The observed ethnic differences in infection risk did not appear to be fully explained by differences in pre-existing health, behavioural risk factors, country of birth, or socioeconomic differences. The authors also found that living in a disadvantaged area was associated with a higher risk of testing positive, particularly for the most disadvantaged (2.2 times more likely to test positive compared to the least disadvantaged), as was having the lowest level of education (2.0 times more likely to test positive compared to the highest level of education).

The findings suggest that some ethnic minority groups, especially black and South Asian people may be particularly vulnerable to the adverse consequences of COVID-19. An immediate policy response is needed to ensure that the health system is responsive to the needs of ethnic minority groups, according to the authors. This should include ensuring that health and care workers, who often are from minority ethnic populations, have access to the necessary protective personal equipment. Timely communication of guidelines to reduce the risk of being exposed to the virus in a range of languages should also be considered.

The authors caution that test result data was only available for England. Those who were more advantaged were more likely to participate in the UK Biobank study and ethnic minorities may be less well represented. Further research is needed to investigate whether these findings are reflective of the broader UK population, alongside analysis of other datasets examining how SARS-CoV-2 infection affects different ethnic and socioeconomic groups, including in representative samples across different countries.

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Fearful Great Danes provide new insights to genetic causes of fear

UNIVERSITY OF HELSINKI

 

IMAGE: PROFESSOR LOHI AND GREAT DANE RENO view more 

CREDIT: UNIVERSITY OF HELSINKI

The identified genomic region includes several candidate genes associated with brain development and function as well as anxiety, whose further analysis may reveal new neural mechanisms related to fear.

For the purposes of the study, carried out by Professor Hannes Lohi's research group and published in the Translational Psychiatry journal, data from a total of 120 Great Danes was collected. The Great Dane breed is among the largest dog breeds in the world.

The project was launched after a number of Great Dane owners approached the research group to tell them about their dogs' disturbing fearfulness towards unfamiliar human beings in particular.

"Fear in itself produces a natural and vital reaction, but excessive fear can be disturbing and results in behavioural disorders. Especially in the case of large dogs, strongly expressed fearfulness is often problematic, as it makes it more difficult to handle and control the dog," says Riika Sarviaho, PhD from the University of Helsinki.

In dogs, behavioural disorders associated with anxiety and fearfulness include generalised anxiety disorder and a range of phobias. Fear can be evidenced, for example, as the dog's attempt to flee from situations they experience as frightening. At its worst, fear can manifest as aggression, which may result in attacks against other dogs or humans.

"Previous studies have suggested that canine anxiety and fearfulness could correspond with anxiety disorder in humans. In fact, investigating fearfulness in dogs may also shed more light on human anxiety disorders and help understand their genetic background," Professor Lohi explains the broader goal of the study.

A new genomic region underlying fearfulness

The study utilised a citizen science approach as the dog owners contributed by completing a behavioural survey concerning their dogs, in which the dogs received scores according to the intensity of fear. Through genetic research, a genomic region associated with fearfulness was identified in chromosome 11. The analysis was repeated by taking into consideration the socialisation carried out in puppyhood, or the familiarisation of the dogs with new people, dogs and situations. The re-analysis reinforced the original finding.

"In the case of behavioural studies, it's important to keep in mind that, in addition to genes, the environment has a significant impact on the occurrence of specific traits. For dogs, the socialisation of puppies has been found to be an important environmental factor that strongly impacts fearfulness. In this study, the aim was to exclude the effect of puppyhood socialisation and, thus, observe solely the genetic predisposition to fearfulness," says Sarviaho.

The genomic region was studied in more detail also with the help of whole genome sequencing, but, so far, the researchers have not succeeded in identifying in it a specific gene variant that predisposes to fearfulness.

"Although no actual risk variant was identified, the genomic region itself is interesting, as it contains a number of genes previously associated in various study models with neural development and function, as well as anxiety. For example, the MAPK9 gene has been linked with brain development and synaptic plasticity as well as anxiety, while RACK1 has been associated with neural development and N4BP3 with neurological diseases," says Professor Lohi.

Link between accelerated puppyhood growth and timidity?

A genomic region in humans corresponding with the one now associated with canine fearfulness is linked to a rare syndrome, which causes both neurological symptoms and, among other things, accelerated growth in childhood.

"Research on the topic is only at the early stages and findings have to be carefully interpreted, but it's interesting to note, when focusing on a particularly large dog breed, that the genomic region associated with fearfulness appears to have a neurological role as well as one related to growth," Sarviaho adds.

So far, gene discoveries in canine behavioural research have remained fairly rare, and the genomic region now identified has not previously been linked with fearfulness. Lohi's research group has previously described two genomic regions associated with canine generalised fear and sensitivity to sound. The genetic research findings support the hypothesis that fearfulness and anxiety are inherited traits. To be able to identify more detailed risk factors and confirm the relevance of the findings, the study should be repeated with a more extensive dataset.

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Better prepared for future crises

Recommendations from risk resarchers

INSTITUTE FOR ADVANCED SUSTAINABILITY STUDIES E.V. (IASS)
NEWS RELEASE 29-MAY-2020

The article gives an overview of the spread of Covid-19 and outlines six causes of the crisis: the exponential infection rate, international integration, the insufficient capacity of health care systems in many countries, conflicts of competence and a lack of foresight on the part of many government agencies, the need to grapple with the economic impacts of the shutdown parallel to the health crisis, as well as weaknesses in capital markets resulting from the financial crisis of 2008. The solutions proposed by the team of authors were developed using a framework developed by the International Risk Governance Council to which Ortwin Renn contributed.

According to the study, five of the aspects of risk governance described in the framework are particularly relevant for efforts to overcome the Corona Crisis. Accordingly, the authors highlight the importance of increasing global capacities for the scientific and technical appraisal of risks in order to provide reliable early warning systems. This research must be supplemented by an analysis of the perceived risk - i.e. individual and public opinion, concerns, and wishes. The awareness of and acknowledgement of these perceptions facilitates effective crisis communication and enables authorities to issue effective public health guidelines. This leads to a key task for decision-makers - risk evaluation: Whether and to what extent are risk reduction measures necessary? What trade-offs are identified during the development of measures and restrictions and how can they be resolved on the basis of recognized ethical criteria in light of the considerable degree of uncertainty? This characterization and evaluation of the risk provides qualified options for risk management. The focus here is on the development of collectively binding decisions on measures to minimize the suffering of affected populations as a whole as well as strategies to minimize undesirable side effects. Coordinated crisis and risk communication underpinned by robust scientific and professional communications expertise is crucial to the success of efforts to tackle the crisis.

The team of authors has distilled ten recommendations from its findings:

1. Address risks at source: in the case of pandemics this means reducing the possibility of viruses being transmitted from animals to humans.
2. Respond to warnings: This includes the review of national and international risk assessments, and the development of better safeguards for risks with particularly serious impacts.
3. Acknowledge trade-offs: Measures to reduce a particular risk will impact other risks. Undesirable side effects must be identified in risk assessments.
4. Consider the role of technology: How can machine learning and other technologies be applied to support pandemic assessment, preparedness, and responses?
5. Invest in resilience: Gains in organizational efficiency have made critical systems such as health care more vulnerable. Their resilience must be strengthened, for example by reducing dependencies on important products and services.
6. Concentrate on the most important nodes in the system: The early imposition of restrictions on air travel have proved effective in combating a pandemic. A global emergency fund could be established to address the cost of such measures.
7. Strengthen links between science and policymaking: Those countries in which scientific information and science-based policy advice are readily available to policymakers have had greater success in combating the coronavirus.
8. Build state capacities: Tackling systemic risks should be viewed as an integral aspect of good governance that is performed on a continuing basis rather than as an emergency response.
9. Improve communication: Communications around Covid-19 was slow or deficient in a number of countries. One solution would be the establishment of national and international risk information and communication units.
10. Reflect on social disruption: The Corona Crisis is forcing people and organizations to experiment with new work and life patterns. Now is the time to consider which of these changes should be maintained over the longer term.

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Taking a deep look into animals

VIENNA UNIVERSITY OF TECHNOLOGY

IMAGE: LIGHT-SHEET IMGES OF DIFFERENT DEEP-CLEAR PROCESSED ANIMALS LABELLED WITH NEUROSYSTEM SPECIFIC MARKERS. view more 

CREDIT: TU WIEN / MAX PERUTZ LABS

Advances in neuroscience research and microscopy: a collaborative project driven by researchers of the Max Perutz Labs Vienna, a joint venture of the University of Vienna and the Medical University of Vienna, and the TU Wien (Vienna) allows researchers to look deep into organs and nervous systems of animals, ranging from squids and worms to fish and salamanders.

Analyses of individual cells in the context of whole organs or tissues is becoming increasingly important in biology. A standard approach so far was to cut larger tissues into thin layers, study each of these sections, and then piece the information again together into a 3D model. However, this is a laborious process, and often yields incomplete results. For instance, the cells that make up our nervous systems possess long extensions that can reach through the entire body. Reconstructing such projections from small slices is extremely challenging.

An elegant solution to avoid this is provided by tissue clearing techniques that can render opaque tissues transparent. When applied to complex tissues, including the brain, such techniques allow to visualize individual cells and their extensions, enabling scientists to capture 3D images of cells and tissues without the need of sectioning. However, existing clearing techniques so far were not optimized to remove a variety of pigments that are present in tissues, and that limit how deeply these specimens can be imaged. Therefore, despite the power of tissue clearing approaches, they have essentially remained restricted to specific unpigmented organs like the brain, and a handful of model species that have reduced pigmentation.

In a team effort, researchers from the Max Perutz Labs, the Medical University of Vienna and the TU Wien (Vienna) and their collaborators have now developed a new method that combines tissue clearing with the removal of various pigment types as they are characteristic for most animals. This new approach - dubbed "DEEP-Clear" - has now been published in the international journal Science Advances.


Depigmentation and tissue clearing enable 3D reconstruction with Light-sheet of squid nervous system.

A toolkit for imaging biomolecules in the nervous systems of a broad panel of species

An important observation that helped to develop the new method was that the combination of different chemical treatments had a synergistic effect, allowing for fast depigmentation and tissue clearing. "Shortening chemical processing preserves the integrity of tissues and organisms, so that the molecules and internal structures of interest are more likely to be retained", explains Marko Pende, the developer of the clearing method, from the lab of Hans-Ulrich Dodt at the TU Wien and the Center for Brain Research (CBR) of the Medical University of Vienna, and one of the first authors of the study. This way multiple organisms could be imaged from different clades ranging from mollusks to bony fish to amphibians. "These are just a few examples. We believe that the method is applicable to multiple organisms. It was just not tried yet", explains Prof. Hans Ulrich Dodt, senior author of the study.

The team then systematically explored which types of molecules could still be marked and detected in DEEP-Clear-processed samples, investigating species ranging from squids and worms to fish and salamanders. This work - largely performed by PhD student Karim Vadiwala in the lab of Florian Raible at the Max Perutz labs - showed that DEEP-Clear was compatible with the detection with a variety of important biomolecules, allowing to image specific proteins, DNA markers and RNA in intact specimens. "This versatility of DEEP-Clear makes it a highly attractive tool to explore a range of animals for which standard tissue clearing techniques currently would not be sufficient", explains Karim Vadiwala (Max Perutz Labs).

A 3D view of whole animal nervous systems to explore neural stem cell biology

Besides its compatibility with many species, another attractive feature of DEEP-Clear is that the transparency of the processed organisms allows to image samples across scales: On the one hand, the team looked into very small details such as contact points between neurons, or individual clusters of dividing cells. On the other hand, they took advantage of the latest generation of so-called light-sheet microscopes developed by the Dodt lab, in which two-dimensional laser light is used to rapidly scan a whole sample, resulting in a full three-dimensional model created on the computer. "Using a very thin light-sheet enables us to overcome a lot of optical limitations and allows us to generate such high-resolution images, even from samples that are several millimeters thick", says the designer of the microscopes, Dr. Saiedeh Saghafi (TU Wien).


Light-sheet images of DEEP-Clear processed zebrafish showing proliferative cells (pink) and the nervous system (green).

The expectation of the team is that "DEEP-Clear" will serve to popularize tissue clearing, allowing researchers around the world to intensify molecular and cellular research in a variety of species that exhibit highly interesting, but poorly explored neuroscientific features. For instance, worms, fish, and salamanders can regenerate parts of their central nervous system, suggesting that they possess molecular capacities that humans and other mammals have lost. "Visualizing the responsible stem cells, and investigating their molecular make-up, or their contribution to regenerated tissue, will be greatly facilitated by DEEP-Clear", believes Dr. Florian Raible (Max Perutz Labs), who coordinated the study that also involved additional researchers in the groups of Dr. Oleg Simakov (Uni Vienna) and Dr. Elly Tanaka (Institute for Molecular Pathology).

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Solution to century-old math problem could predict transmission of infectious diseases

UNIVERSITY OF BRISTOL

A Bristol academic has achieved a milestone in statistical/mathematical physics by solving a 100-year-old physics problem - the discrete diffusion equation in finite space.

The long-sought-after solution could be used to accurately predict encounter and transmission probability between individuals in a closed environment, without the need for time-consuming computer simulations.

In his paper, published in Physical Review X, Dr Luca Giuggioli from the Department of Engineering Mathematics at the University of Bristol describes how to analytically calculate the probability of occupation (in discrete time and discrete space) of a diffusing particle or entity in a confined space - something that until now was only possible computationally.

Dr Giuggioli said: "The diffusion equation models random movement and is one of the fundamental equations of physics. The analytic solution of the diffusion equation in finite domains, when time and space is continuous, has been known for a long time.

"However, to compare model predictions with empirical observations, one needs to study the diffusion equation in finite space. Despite the work of illustrious scientists such as Smoluchowski, Pólya, and other investigators of yore, this has remained an outstanding problem for over a century--until now.

"Excitingly, the discovery of this exact analytic solution allows us to tackle problems that were almost impossible in the past because of the prohibitive computational costs."

The finding has far-reaching implications across a range of disciplines and possible applications include predicting molecules diffusing inside cells, bacteria roaming in a petri dish, animals foraging within their home ranges, or robots searching in a disaster area.

It could even be used to predict how a pathogen is transmitted in a crowd between individuals.

Solving the conundrum involved the joint use of two techniques: special mathematical functions known as Chebyshev polynomials, and a technique invented to tackle electrostatic problems, the so-called method of images.

This approach allowed Dr Giuggioli to construct hierarchically the solution to the discrete diffusion equation in higher dimension from the one in lower dimensions.

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Study: Integrating satellite and socioeconomic data to improve climate change policy

UNIVERSITY OF ILLINOIS AT URBANA-CHAMPAIGN, NEWS BUREAU

 

IMAGE: ATUL JAIN LED A STUDY THAT USED A COMBINATION OF SATELLITE AND CENSUS DATA TO IDENTIFY DEFORESTATION AND EXPANDING SALTWATER FARMING AS THE KEY PHYSICAL AND SOCIOECONOMIC DRIVERS OF CLIMATE... view more 

CREDIT: PHOTO BY L. BRIAN STAUFFER

CHAMPAIGN, Ill. -- Bangladesh is on track to lose all of its forestland in the next 35-40 years, leading to a rise in CO2 emissions and subsequent climate change, researchers said. However, that is just one of the significant land-use changes that the country is experiencing. A new study uses satellite and census data to quantify and unravel how physical and economic factors drive land-use changes. Understanding this relationship can inform climate policy at the national scale in Bangladesh and beyond.

The study, led by University of Illinois at Urbana-Champaign atmospheric sciences professor Atul Jain and postdoctoral researcher Xiaoming Xu, is published in the journal Regional Environmental Change.

"Land usage changes when biophysical factors like temperature and soil quality change, but also when the economic needs of people change," Xu said. The study identifies two key areas where land use and cover have shifted because of biophysical and socioeconomic activities in Bangladesh - and suggests policies to mitigate their influence on climate change.

First, the team found that approximately 11% of the forests in Bangladesh have shifted to shrub land, cropland and urban land from 2000-10.

"Extreme climate events, such as drought and flood, changes in urban and rural population and economic conditions are driving the changes from forest to shrub land in the southeast region of Bangladesh," Jain said. "Here, the locals earn their livelihood by using land, lumber and fuel resources from forests. However, deforestation may be controlled by implementing simple policies such as road improvement, which can provide the people with a means to obtain alternative fuels and livelihoods that are not as dependent on forests."

The study also found that from 2000-10, the area of standing water bodies such as ponds, lakes and reservoirs increased by approximately 9%. This change occurred in the coastal southwest part of the country, where worsening floods during monsoon months have pushed aquaculture expansion at the cost of cropland in recent decades, the researchers said.

"The rapid conversion of traditional rice-farming land to saltwater shrimp ponds is now a well-established practice in the southwest coastal area of Bangladesh," Xu said. "Shrimp farming is 12 times more profitable than rice cultivation in this country."

The flooding and expansion of saltwater farming have led to increased soil salinity, spoiling the soil for farming purposes, the researchers said. "Policies need to be developed that encourage the development of saltwater aquaculture only in the regions with favorable conditions to prevent further soil degradation," Jain said.

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The U.S. Department of Energy supported this research.

Editor's notes:

To reach Atul Jain, call 217-333-2128; email jain1@illinois.edu.

To reach Xiaoming Xu, email xuxm@illinois.edu.

The paper "Dynamics and drivers of land use and land cover changes in Bangladesh" is available online and from the U. of I. News Bureau. DOI: 10.1007/s10113-020-01650-5

Scientists develop sorbent for purifying water from radioactive elements

FAR EASTERN FEDERAL UNIVERSITY

 

IMAGE: SEM IMAGES OF TUNGSTEN OXIDE SAMPLES, A WO3-100, B WO3-300, C WO3-600, D WO3-900. view more 

CREDIT: FEFU PRESS OFFICE, THE INSTITUTE OF CHEMISTRY FEB RAS

Scientists from Far Eastern Federal University (FEFU) in collaboration with colleagues from the Institute of Chemistry FEB RAS come up with a smart technology for the synthesis of sorbent based on a "tungsten bronze" compound powder (Na2WO4) aimed to purify industrial and drinking water from hazardous radionuclides cesium (137Cs), and strontium (90Sr), as well as for effective processing of liquid radioactive waste. A related article appears in the Journal of Materials Science.

The new sorbent is appropriate when the concentration of hazardous radioactive elements is extremely higher than the acceptable level, i.e. for processing of liquid radioactive waste from nuclear plants and to eliminate the consequences of technological accidents.

The development resolves one of the pressing problems of modern radioecology, which is to completely or down to the level of regulative standards extract the hazardous radioactive elements cesium (137Cs) and strontium (90Sr) capable of accumulating in the body, replacing potassium and calcium.

The waste sorbent is supposed to convert into high-density ceramics with subsequent safe disposal.

"We propose to apply a sorbent in several ways. First, in the static version, granules based on tungsten bronze powder can simply be introduced into the volume of contaminated water bodies. Second, in a dynamic mode, porous sorbent tablets can be a component of flow filters. The high filtration efficiency registered by calculation methods determining the residual amount of radionuclides in sorbent-purified solutions, as well as the number of radionuclides retained in the sorbent body. We appreciate the Institute of Chemistry FEB RAS for the partial development of these methods in the frame of state assignment. We have studied physicochemical properties of the sorbent material via high-class Shimadzu equipment (Japan) and do believe that the operational properties of the material are up to analogs produced by more expensive technologies. Thus, we hope that our synthesis method will be recognized by the industry as most practical and technologically effective," says Arthur Drankov, a member of the creative team, postgraduate student of FEFU School of Natural Science.

The scientist points out that, if regenerated, the sorbent can serve five or more cycles. However, re-using of "tungsten bronze" sorbents is not the main idea, given that its absorbing abilities with respect to 137Cs and 90Sr radionuclides are well known.

The advantage proposed by researchers of FEFU School of Natural Science and FEB RAS is to convert waste granules or sorption tablets to high-density ceramics for further safe disposal during the half-life of hazardous radioactive elements. For cesium, this period is about 30 years, for strontium is about 29 years.

Scientists will develop a transforming-to-ceramics technology at the next stage of the work supported by a grant of the Russian Foundation for Basic Research (Grant chief is I. G. Tananaev, Director of FEFU School of Natural Science, corresponding member of the Russian Academy of Sciences).

Researchers suggest that the total outcome will be a cost-effective technology that guarantees environmental safety when dealing with radioactive waste.

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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.

Paid sick leave mandates hold promise in containing COVID-19

Mandates like those found in the federal government's Families First Coronavirus Response Act may be helping to slow the pandemic

GEORGIA STATE UNIVERSITY

 

ATLANTA--Paid sick leave (PSL) mandates like those found in the federal government's Families First Coronavirus Response Act may be helping to slow the spread of COVID-19, according to a new study by health economists at Georgia State and Tulane universities.

Since 2007, several state and local governments have enacted laws requiring employers to provide their workers with paid sick leave. Michael Pesko, an associate professor in Georgia State's Andrew Young School of Policy Studies, and co-author Kevin Callison studied the effects of these staggered mandate adoptions using multiple government-collected survey data sources from 2005 to 2018.

The mandates were effective in increasing the number of workers holding Paid Sick Leave coverage, particularly those in low-wage industries who were unlikely to have previously received PSL benefits from their employers, they found. Women and racial/ethnic minorities benefitted disproportionately from the PSL mandates.

"These mandates reduced the number of people attending work while sick, which is similar to an earlier study showing influenza-like disease rates decreased after employees gained access to paid sick leave," said Pesko. "If paid sick leave helps stop people from attending work while sick and prevents the spread of disease as a result, this has important policy implications in today's fight to contain COVID-19."

Paid Sick Leave reduces the rate of those working while sick by 4.5 percentage points on average for workers in industries with historically low rates of PSL, such as the accommodation and food service industries. PSL mandates are particularly likely to increase work absences among women and households with children, where workers may be using their benefits to care for a sick child or other family obligations.

"What are the policy implications? The Families First Coronavirus Response Act, which went into effect April 1, is the first congressionally passed bill that provides Paid Sick Leave for employees in medium- and small-sized businesses with coronavirus issues," Pesko said. "We believe that the bill will reduce people attending work with COVID-19 because it pays for them to stay home and recover. This bill is, therefore, an important component in COVID-19 containment efforts."

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Study: Public health campaigns can do better on cannabis harm reduction

UB, University of Michigan researchers surveyed cannabis enthusiasts about their knowledge of effective harm reduction strategies

UNIVERSITY AT BUFFALO

 

IMAGE: JESSICA KRUGER, PHD, IS A CLINICAL ASSISTANT PROFESSOR IN THE DEPARTMENT OF COMMUNITY HEALTH AND HEALTH BEHAVIOR IN THE UNIVERSITY AT BUFFALO'S SCHOOL OF PUBLIC HEALTH AND HEALTH PROFESSIONS. view more 

CREDIT: UNIVERSITY AT BUFFALO

BUFFLO, N.Y. -- Harm reduction strategies have proven effective for use of opioids, alcohol, and tobacco products. University at Buffalo and University of Michigan researchers say harm reduction techniques also have potential for cannabis users - but first, public health practitioners and organizations need to do a better job of making cannabis users aware of those strategies.

Researchers assessed harm reduction awareness by surveying nearly 500 participants at the 2019 Hash Bash, a popular marijuana advocacy event on the campus of the University of Michigan.

The research team has published a series of papers in recent years based on data collected by surveying Hash Bash attendees. Their latest study, published in Health Promotion Practice, shows that frequent cannabis users aren't as knowledgeable as they should be about harm reduction strategies, such as not driving within six hours of using cannabis. And that, the researchers argue, falls more squarely on public health's failure to properly provide that knowledge.

"Our findings should serve as a wake-up call to public health professionals to integrate harm reduction strategies into practice," said Jessica Kruger, PhD, the study's lead author and a clinical assistant professor of community health and health behavior in UB's School of Public Health and Health Professions.

"As more states legalize medicinal and recreational use of cannabis, it's important that public health equip people with proper knowledge about using cannabis. We know that abstinence just isn't realistic or desirable for some users. We can minimize the costs and risks of cannabis use by creating awareness around harm reduction strategies," Kruger added.

Fewer than half of the study participants believed that any of the listed strategies reduced the harm of using cannabis. Only 42% identified avoiding use when pregnant as an effective harm reduction strategy. Even less, 36%, identified avoiding driving within six hours of using cannabis as an effective strategy.

"This is really remarkable, given that both of these are common warnings for a variety of psychoactive and pharmaceutical substances," said co-author Daniel Kruger, PhD, a research associate professor of community health and health behavior in UB's School of Public Health and Health Professions. He is also a research investigator with the Population Studies Center at the University of Michigan.

About one-quarter of participants believed that using strains with high cannabidiol (CBD) CBD to tetrahydrocannabinol (THC) ratios, using a concentrate or dab without plant material, and putting ice in a bong to reduce cannabis potency were effective harm reduction techniques. Only using strains with a high CBD to THC ratio has been empirically supported, the researchers note.

Less than half of participants reported using any harm reduction strategy, and 39% reported using no effective strategy.

Although knowledge doesn't guarantee behavior or behavior change, the researchers note that providing cannabis users with accurate information on the risks and benefits of the drug will at least help users make informed decisions.

They point to two public health campaigns in Colorado, a state where cannabis is legal for adult use. That state's "Good to Know" campaign educated Colorado residents on new cannabis laws. The state's "Responsibility Grows Here" campaign shares information about the potential risks for teens and pregnant and breastfeeding women, and calls on users to consume cannabis responsibly.

"As more and more people have legal access to medical and recreational cannabis, the importance of effective cannabis-specific health education increases," said study co-author R. Lorraine Collins, PhD, associate dean for research in UB's School of Public Health and Health Professions and a professor of community health and health behavior.