Nanotechnology Helps Measure Interaction Forces Between Cells in Biofilms

At the University of Cologne, biophysicists in the lab of Professor Berenike Maier were now able to show how differential mechanical forces can lead to cell sorting in biofilms, thereby determining their architecture.
In their publication in the journal eLife, the team headed by the biophysicist Enno Oldewurtel showed how specific mechanical forces can be the key to the structure of a biofilm. Bacteria with different surface structures organized themselves in a “tug of war”: the cells actively moved in the direction in which they could pull the strongest onto neighboring bacteria.

The bacterium Neisseria gonorrhoeae controls mechanical interactions among cells with extensions called pili. These rod-shaped structures function like grappling hooks between cells: the pili of different cells get caught and then shortened. This creates mechanical forces between cells. By means of targeted genetic modifications, the research team succeeded in steering the degree of entanglement between pili and hence the interaction forces between cells. These forces were measured using nanotechnology. In a mix of bacteria that interact with each other to different degrees, the cells sorted themselves according to the mechanical forces they exerted among one another.

All in all, the research showed that different mechanical interactions among bacteria can determine the architecture of biofilms. Similar mechanisms have already been identified in the positioning of cells in embryonic development. Hence the research has uncovered a fundamental similarity in the development processes of biofilms and embryos: differential physical interactions between the cells are important for their sorting. In the future, the question will be in how far this cell sorting strengthens the biofilm’s resilience towards external stress.


High-Resolution Microscope Brings Tiny Worlds Closer to Researchers

Modern microelectronic devices contain billions of components crammed into thumbnail-size flakes. The chemical industry uses nanoparticles to make better cleaning products, while pharmaceutical companies use them for delivery of medicines straight into human cells.

Scientists at the Luxembourg Institute of Science and Technology have combined a specially designed spectrometer with a commercially available helium ion microscope to build a very high-resolution optical device capable of looking into these tiny worlds. It allows them to see objects 100,000 times smaller than the diameter of a human hair.

“We can follow where those nanoparticles have been uptaken into, for example, human cells,” said LIST senior researcher David Dowsett. “And also we can see whether or not a labeled drug is present within the cell, in the same place as the nanoparticle. So we can really start to test whether or not a delivery system is effective.”

One of the first practical uses was checking the effectiveness of new cosmetic products. For instance, the new microscope helped scientists test the effectiveness of shampoos containing silver nanoparticles, which are highly toxic to bacteria living in human hair.

“We can also analyze the hair as well to see whether the shampoo, for example, penetrates just onto the outside or to see how deeply it’s penetrated,” Dowsett said.

Researchers say the new microscope could also find applications in the development of more efficient batteries for electric cars and portable electronic devices.

David Suzuki given Vancouver city honour reserved for few

David Suzuki accepted an honour from the City of Vancouver.

Mayor Gregor Robertson and city council granted Suzuki Freedom of the City for his years of environmental work.

The award dates back to 1936 and is granted only in exceptional cases to individuals of the highest merit.

Robertson says Suzuki has touched the lives of countless communities and people across Canada, and his voice continues to ring loud and true.

Long-term aerobic exercise prevents age-related brain deterioration

October 30, 2015

Schematic illustration of age-related changes in the neurovascular unit that are prevented by exercise. In the aged cortex of sedentary mice, neurovascular dysfunction is evident by decreased numbers of pericytes (surrounding capillaries, pink), decline in basement membrane (BM) coverage (blue), increased transcytosis (a process that transports macromolecules across cells, allowing pathogens to invade) on endothelial cells (green), reduced expression of AQP4 in astrocytes, down-regulation of Apoe (an essential protein, light purple), decrease in synaptic proteins such as synaptophysin (SYN, green), and increased proinflammatory IBA1+ microglia/monocytes (indicating age-related neuroinflammation, yellow). These age-related changes were successfully prevented (horizontal T line, “Exercise”) by 6 months of voluntary running during aging. (credit: Ileana Soto et al./PLOS Biology

A study of the brains of mice shows that structural deterioration associated with old age can be prevented by long-term aerobic exercise starting in mid-life, according to the authors of an open-access paper in the journal PLOS Biology yesterday (October 29).

Old age is the major risk factor for Alzheimer’s disease, like many other diseases, as the authors at The Jackson Laboratory in Bar Harbor, Maine, note. Age-related cognitive deficits are due partly to changes in neuronal function, but also correlate with deficiencies in the blood supply to the brain and with low-level inflammation.

“Collectively, our data suggests that normal aging causes significant dysfunction to the cortical neurovascular unit, including basement membrane reduction and pericyte (cells that wrap around blood capillaries) loss. These changes correlate strongly with an increase in microglia/monocytes in the aged cortex,” said Ileana Soto, lead author on the study.*

Benefits of aerobic exercise

However, the researchers found that if they let the mice run freely, the structural changes that make the blood-brain barrier leaky and result in inflammation of brain tissues in old mice can be mitigated. That suggests that there are also beneficial effects of exercise on dementia in humans.**

Further work will be required to establish the mechanism(s): what is the role of the complement-producing microglia/macrophages, how does Apoe decline contribute to age-related neurovascular decline, does the leaky blood-brain barrier allow the passage of damaging factors from the circulation into the brain?

This work was funded in part by The Jackson Laboratory Nathan Shock Center, the Fraternal Order of the Eagle, the Jane B Cook Foundation and NIH.

* The authors investigated the changes in the brains of normal young and aged laboratory mice by comparing by their gene expression profiles using a technique called RNA sequencing, and by comparing their structures at high-resolution by using fluorescence microscopy and electron microscopy. The gene expression analysis indicated age-related changes in the expression of genes relevant to vascular function (including focal adhesion, vascular smooth muscle and ECM-receptor interactions), and inflammation (especially related to the complement system, which clears foreign particles) in the brain cortex.

These changes were accompanied by a decline in the function of astrocytes (key support cells in the brain) and loss of pericytes (the contractile cells that surround small capillaries and venules and maintain the blood-brain barrier). There were also effects on the basement membrane, which forms an integral part of the blood-brain barrier, as well as an increase in the density and functional activation of the immune cells known as microglia/monocytes, which scavenge the brain for infectious agents and damaged cells.

** To investigate the impact of long-term physical exercise on the brain changes seen in the aging mice, the researchers provided the animals with a running wheel from 12 months old (equivalent to middle aged in humans) and assessed their brains at 18 months (equivalent to ~60yrs old in humans, when the risk of Alzheimer’s disease is greatly increased). Young and old mice alike ran about two miles per night, and this physical activity improved the ability and motivation of the old mice to engage in the typical spontaneous behaviors that seem to be affected by aging.

This exercise significantly reduced age-related pericyte loss in the brain cortex and improved other indicators of dysfunction of the vascular system and blood-brain barrier. Exercise also decreased the numbers of microglia/monocytes expressing a crucial initiating component of the complement pathway that others have shown previously to play are role in age-related cognitive decline. Interestingly, these beneficial effects of exercise were not seen in mice deficient in a gene called Apoe, variants of which are a major genetic risk factor for Alzheimer’s disease. The authors also report that Apoe expression in the brain cortex declines in aged mice and this decline can also be prevented by exercise.

Abstract of APOE Stabilization by Exercise Prevents Aging Neurovascular Dysfunction and Complement Induction

Aging is the major risk factor for neurodegenerative diseases such as Alzheimer’s disease, but little is known about the processes that lead to age-related decline of brain structures and function. Here we use RNA-seq in combination with high resolution histological analyses to show that aging leads to a significant deterioration of neurovascular structures including basement membrane reduction, pericyte loss, and astrocyte dysfunction. Neurovascular decline was sufficient to cause vascular leakage and correlated strongly with an increase in neuroinflammation including up-regulation of complement component C1QA in microglia/monocytes. Importantly, long-term aerobic exercise from midlife to old age prevented this age-related neurovascular decline, reduced C1QA+ microglia/monocytes, and increased synaptic plasticity and overall behavioral capabilities of aged mice. Concomitant with age-related neurovascular decline and complement activation, astrocytic Apoe dramatically decreased in aged mice, a decrease that was prevented by exercise. Given the role of APOE in maintaining the neurovascular unit and as an anti-inflammatory molecule, this suggests a possible link between astrocytic Apoe, age-related neurovascular dysfunction and microglia/monocyte activation. To test this, Apoe-deficient mice were exercised from midlife to old age and in contrast to wild-type (Apoe-sufficient) mice, exercise had little to no effect on age-related neurovascular decline or microglia/monocyte activation in the absence of APOE. Collectively, our data shows that neurovascular structures decline with age, a process that we propose to be intimately linked to complement activation in microglia/monocytes. Exercise prevents these changes, but not in the absence of APOE, opening up new avenues for understanding the complex interactions between neurovascular and neuroinflammatory responses in aging and neurodegenerative diseases such as Alzheimer’s disease.

Ileana Soto, Leah C. Graham, Hannah J. Richter, Stephen N. Simeone, Jake E. Radell, Weronika Grabowska, W. Keith Funkhouser, Megan C. Howell, Gareth R. Howell. APOE Stabilization by Exercise Prevents Aging Neurovascular Dysfunction and Complement Induction. PLOS Biology, October 29, 2015; DOI: 10.1371/journal.pbio.1002279 (open access)
Long-term aerobic exercise prevents age-related brain changes

Flexible phototransistor is world’s fastest, most sensitive

May dramatically improve performance of cameras and other light-capturing devices
October 30, 2015

New phototransistor is flexible yet fastest and most responsive in the world, according to UW engineers (credit: Jung-Hun Seo)

University of Wisconsin-Madison (UW) electrical engineers have created the fastest, most responsive flexible silicon phototransistor ever made, inspired by mammals’ eyes.

Phototransistors (an advanced type of photodetector) convert light to electricity. They are widely used in products ranging from digital cameras, night-vision goggles, and smoke detectors to surveillance systems and satellites.

Developed by UW-Madison collaborators Zhenqiang “Jack” Ma, professor of electrical and computer engineering, and research scientist Jung-Hun Seo, the new phototransistor design uses thin-film single-crystalline silicon nanomembranes and has the highest-ever sensitivity and response time, the engineers say.

They suggest it could improve performance of products that rely on electronic light sensors. Integrated into a digital camera lens, for example, it could reduce bulkiness and boost the acquisition speed and quality of video or still photos.

Silicon nanomembrane phototransistor design. An anti-reflection coating (ARC) with a low refractive index increases light absorption by the silicon nanomembrane (Si NM) below, which is backed by transistor electrodes (source, gate, and drain), a reflective metal layer, and protective polyethylene terephthalate (PET). (credit: Jung-Hun Seo et al./Advanced Optical Materials)

While many phototransistors are fabricated on rigid surfaces, and therefore are flat, the new devices are flexible, meaning they more easily mimic the behavior of mammalian eyes. “We actually can make the curve any shape we like to fit the optical system,” Ma says. The new “flip-transfer” fabrication method deposits electrodes under the phototransistor’s ultrathin silicon nanomembrane layer and a reflective metal layer on the bottom. The metal layer and electrodes act as reflectors and improve light absorption sensitivity without the need for an external amplifier.

“Light absorption can be much more efficient because light is not blocked by any metal layers or other materials,” Ma says.

The researchers published details this week in the journal Advanced Optical Materials. The work was supported by the U.S. Air Force. The researchers are patenting the technology through the Wisconsin Alumni Research Foundation.

Abstract of Flexible Phototransistors Based on Single-Crystalline Silicon Nanomembranes

In this work, flexible phototransistors with a back gate configuration based on transferrable single-crystalline Si nanomembrane (Si NM) have been demonstrated. Having the Si NM as the top layer enables full exposure of the active region to an incident light and thus allows for effective light sensing. Flexible phototransistors are performed in two operation modes: 1) the high light detection mode that exhibits a photo-to-dark current ratio of 105 at voltage bias of VGS < 0.5 V, and VDS = 50 mV and 2) the high responsivity mode that shows a maximum responsivity of 52 A W−1 under blue illumination at voltage bias of VGS = 1 V, and VDS = 3 V. Due to the good mechanical flexibility of Si NMs with the assistance of a polymer layer to enhance light absorption, the device exhibits stable responsivity with less than 5% of variation under bending at small radii of curvatures (up to 15 mm). Overall, such flexible phototransistors with the capabilities of high sensitivity light detection and stable performance under the bending conditions offer great promises for high-performance flexible optical sensor applications, with easy integration for multifunctional applications.

Jung-Hun Seo, Kan Zhang, Munho Kim, Deyin Zhao, Hongjun Yang, Weidong Zhou and Zhenqiang Ma. Flexible Phototransistors Based on Single-Crystalline Silicon Nanomembranes. Advanced Optical Materials 2015; DOI: 10.1002/adom.201500402
UW-Madison engineers reveal record-setting flexible phototransistor

Is this the ‘ultimate’ battery?

October 30, 2015

False-color microscopic view of a reduced graphene oxide electrode (black), which hosts the large (about 20 micrometers) lithium hydroxide particles (pink) that form when a lithium-oxygen battery discharges (credit: T. Liu et al./Science)

University of Cambridge scientists have developed a working laboratory demonstrator of a lithium-oxygen battery that has very high energy density (storage capacity per unit volume), is more than 90% efficient, and can be recharged more than 2000 times (so far), showing how several of the problems holding back the development of more powerful batteries could be solved.

Lithium-oxygen (lithium-air) batteries have been touted as the “ultimate” battery due to their theoretical energy density, which is ten times higher than a lithium-ion battery. Such a high energy density would be comparable to that of gasoline — allowing for an electric car with a battery that is a fifth the cost and a fifth the weight of those currently on the market and that could drive about 666 km (414 miles) on a single charge. (This compares to 500 kilometers (311 miles) with the new University of Waterloo design, using a silicon anode — see “Longer-lasting, lighter lithium-ion batteries from silicon anodes.”)

The challenges associated with making a better battery are holding back the widespread adoption of two major clean technologies: electric cars and grid-scale storage for solar power.

A lab demonstrator based on graphene

The researchers have now demonstrated how some of the obstacles to the ultimate battery could be overcome in a lab-based demonstrator of a lithium-oxygen battery with higher capacity, increased energy efficiency, and improved stability over previous attempts.

SEM images of pristine, fully discharged, and charged reduced graphene oxide electrodes in lab demonstrator. Scale bars: 20 micrometers. (credit: Tao Liu et al./Science)

Their demonstrator relies on a highly porous, “fluffy” carbon electrode made from reduced graphene oxide (comprising one-atom-thick sheets of carbon atoms), and additives that alter the chemical reactions at work in the battery, making it more stable and more efficient. While the results, reported in the journal Science, are promising, the researchers caution that a practical lithium-air battery still remains at least a decade away.

“What we’ve achieved is a significant advance for this technology and suggests whole new areas for research — we haven’t solved all the problems inherent to this chemistry, but our results do show routes forward towards a practical device,” said Professor Clare Grey of Cambridge’s Department of Chemistry, the paper’s senior author.

Batteries are made of three components: a positive electrode, a negative electrode and an electrolyte. In the lithium-ion (Li-ion) batteries currently used in laptops and smartphones, the negative electrode is made of graphite (a form of carbon), the positive electrode is made of a metal oxide, such as lithium cobalt oxide, and the electrolyte is a lithium salt dissolved in an organic solvent. The action of the battery depends on the movement of lithium ions between the electrodes. Li-ion batteries are light, but their capacity deteriorates with age, and their relatively low energy densities mean that they need to be recharged frequently.

Over the past decade, researchers have been developing various alternatives to Li-ion batteries, and lithium-air batteries are considered the ultimate in next-generation energy storage, because of their extremely high theoretical energy density. However, attempts at working demonstrators so far have had low efficiency, poor rate performance, and unwanted chemical reactions. Also, they can only be cycled in pure oxygen.

What Liu, Grey and their colleagues have developed uses a very different chemistry: lithium hydroxide (LiOH) instead of lithium peroxide (Li2O2). With the addition of water and the use of lithium iodide as a “mediator,” their battery showed far less of the chemical reactions which can cause cells to die, making it far more stable after multiple charge and discharge cycles.

By precisely engineering the structure of the electrode, changing it to a highly porous form of graphene, adding lithium iodide, and changing the chemical makeup of the electrolyte, the researchers were able to reduce the “voltage gap” between charge and discharge to 0.2 volts. A small voltage gap equals a more efficient battery. Previous versions of a lithium-air battery have only managed to get the gap down to 0.5 – 1.0 volts, whereas 0.2 volts is closer to that of a Li-ion battery, and equates to an energy efficiency of 93%.

Problems to be solved

The highly porous graphene electrode also greatly increases the capacity of the demonstrator, although only at certain rates of charge and discharge. Other issues that still have to be addressed include finding a way to protect the metal electrode so that it doesn’t form spindly lithium metal fibers known as dendrites, which can cause batteries to explode if they grow too much and short-circuit the battery.

Additionally, the demonstrator can only be cycled in pure oxygen, while the air around us also contains carbon dioxide, nitrogen and moisture, all of which are generally harmful to the metal electrode.

The authors acknowledge support from the U.S. Department of Energy, the Engineering and Physical Sciences Research Council (EPSRC), Johnson Matthey, the European Union via Marie Curie Actions, and the Graphene Flagship. The technology has been patented and is being commercialized through Cambridge Enterprise, the University’s commercialization arm.

Abstract of Cycling Li-O2 batteries via LiOH formation and decomposition

The rechargeable aprotic lithium-air (Li-O2) battery is a promising potential technology for next-generation energy storage, but its practical realization still faces many challenges. In contrast to the standard Li-O2 cells, which cycle via the formation of Li2O2, we used a reduced graphene oxide electrode, the additive LiI, and the solvent dimethoxyethane to reversibly form and remove crystalline LiOH with particle sizes larger than 15 micrometers during discharge and charge. This leads to high specific capacities, excellent energy efficiency (93.2%) with a voltage gap of only 0.2 volt, and impressive rechargeability. The cells tolerate high concentrations of water, water being the dominant proton source for the LiOH; together with LiI, it has a decisive impact on the chemical nature of the discharge product and on battery performance.

Tao Liu, Michal Leskes, Wanjing Yu, Amy J. Moore, Lina Zhou, Paul M. Bayley, Gunwoo Kim, Clare P. Grey. Cycling Li-O2 batteries via LiOH formation and decomposition. Science 30 October 2015; DOI: 10.1126/science.aac7730
New design points a path to the ‘ultimate’ battery

New and Unusual DNA Repair Activity Identified

Hot on the heels of the recent announcement of the Nobel Prize in Chemistry being awarded for seminal discoveries in the area of DNA repair, researchers at Vanderbilt University have published data describing new enzymatic activity for a DNA glycosylase discovered previously in the bacteria Bacillus cereus.

When Watson and Crick first published their now famous double-helix structure of DNA, many scientists imagined the molecule to be extremely chemically stable—acting as the template for passing along inheritable genetic traits. However, over the years investigators have since discovered DNA’s susceptibility to damage and its dynamic nature to repair itself, to maintain genomic stability.

“It’s a double-edged sword,” remarked senior author and project leader Brandt Eichman, Ph.D., associate professor of biological sciences and biochemistry at Vanderbilt. “If DNA were too reactive then it wouldn’t be capable of storing genetic information. But, if it were too stable, then it wouldn’t allow organisms to evolve.”

There are many ways that DNA can become damaged, but they can be classified into two basic groups: environmental sources including ultraviolet light, toxic chemicals, and ionizing radiation and internal sources, which include, reactive oxygen species, a number of chemicals the cell produces during normal metabolism, and even water.

“More than 10,000 DNA damage events occur each day within every cell of the human body, which must be repaired for DNA to function properly,” explained lead author Elwood Mullins, Ph.D., a postdoctoral research associate in Dr. Eichman’s laboratory.

The Vanderbilt team discovered the new repair activity while studying the DNA glycosylase AlkD. Glycosylases are part of a family of enzymes discovered by Tomas Lindahl, Ph.D., who received this year’s Nobel prize for recognizing that these enzymes removed damaged DNA bases through a process called base-excision repair (BER).

Briefly, during BER, a specific glycosylase molecule binds to DNA at the location of a lesion and bends the double-helix in a way that causes the damaged base to flip from the inside of the helix to the outside. The enzyme fits around the flipped out base and holds it in a position that exposes its link to the DNA’s sugar backbone, allowing the enzyme to detach it. After the damaged base has been removed, additional DNA-repair proteins move in to replace it with a new, undamaged base.

Dr. Eichman and his team found that AlkD from B. cereus works in a totally different fashion—as it does not require base flipping to recognize damaged DNA or repair it. Using crystallography techniques, the researchers were able to determine that AlkD forms a series of interactions with the DNA backbone at and around the lesion while the lesion is still stacked in the double helix. Several of these interactions are contributed by three amino acids in the enzyme that catalyze excision of the damaged base.

The findings from this study were published recently in Nature through an article entitled “The DNA glycosylase AlkD uses a non-base-flipping mechanism to excise bulky lesions.”

Additionally, the investigators found that AlkD identifies lesions by interacting with the DNA backbone without contacting the damaged base itself and can repair many different types of lesions as long as they are positively charged. Since the enzyme doesn’t have the same type of binding pocket, it isn’t restricted in the same way as other glycosylases. Lastly, AlkD can excise much bulkier lesions than other glycosylases. Base excision repair is limited to relatively small lesions. A different pathway called nucleotide excision repair typically handles larger lesions like those caused by UV radiation damage. However, Dr. Eichman’s team discovered that AlkD could excise lesions that would normally default to other DNA repair pathways.

“Our discovery shows that we still have a lot to learn about DNA repair and that there may be alternative repair pathways yet to be discovered. It certainly shows us that a much broader range of DNA damage can be removed in ways that we didn’t think were possible,” Dr. Eichman stated. “Bacteria are using this to their advantage to protect themselves against the antibacterial agents they produce. Humans may even have DNA-repair enzymes that operate in similar fashion to remove complex types of DNA damage. This could have clinical relevance because these enzymes if they exist, could be reducing the effectiveness of drugs designed to kill cancer cells by shutting down their ability to replicate.”