A team of geneticists made a biological breakthrough last week.
Researchers led by the renowned Craig Venter, Ph.D. created a synthetic
organism named syn3.0. It is a microbe capable of surviving and
replicating with only 473 genes,reported The Guardian, establishing that this genetic number is the minimum needed for life whereas humans have a rough estimate of 20,000 genes.
Qantaexplained Venter and his team made this discovery after analyzing the genome of a cattle-based bacterium called Mycoplasma mycoides through a process that took years.
The images show a liver cell before and after processing the data with the software developed at Bielefeld University. (Credit: Bielefeld University)With their special microscopes, experimental physicists can already observe single molecules. However, unlike conventional light microscopes, the raw image data from some ultra-high resolution instruments first have to be processed for an image to appear. For the ultra-high resolution fluorescence microscopy that is also employed in biophysical research at Bielefeld University, members of the Biomolecular Photonics Group have developed a new open source software solution that can process such raw data quickly and efficiently. The Bielefeld physicist Dr. Marcel Müller reports on this new open source software in the latest issue of Nature Communications published on 21 March.
Conventional light microscopy can attain only a defined lower resolution limit that is restricted by light diffraction to roughly 1/4 of a micrometre. High resolution fluorescence microscopy makes it possible to obtain images with a resolution markedly below these physical limits. The physicists Stefan Hell, Eric Betzig, and William Moerner were awarded the Nobel Prize in 2014 for developing this important key technology for biomedical research. Currently, one of the ways in which researchers in this domain are trying to attain a better resolution is by using structured illumination. At present, this is one of the most widespread procedures for representing and presenting dynamic processes in living cells. This method achieves a resolution of 100 nanometres with a high frame rate while simultaneously not damaging the specimens during measurement. Such high resolution fluorescence microscopy is also being applied and further developed in the Biomolecular Photonics Group at Bielefeld‘s Faculty of Physics. For example, it is being used to study the function of the liver or the ways in which the HI virus spreads.
However, scientists cannot use the raw images gained with this method straight away. ‘The data obtained with the microscopy method require a very laborious mathematical image reconstruction. Only then do the raw data recorded with the microscope result in a high-resolution image,’ explains Professor Thomas Huser,Ph.D., head of the Biomolecular Photonics Group. Because this stage requires a complicated mathematical procedure that has been accessible for only a few researchers up to now, there was previously no open source software solution that was easily available for all researchers. Huser sees this as a major obstacle to the use and further development of the technology. The software developed in Bielefeld is now filling this gap.
Müller from the Biomolecular Photonics Group has managed to produce such universally implementable software. ‘Researchers throughout the world are working on building new, faster, and more sensitive microscopes for structured illumination, particularly for the two-dimensional representation of living cells. For the necessary post-processing, they no longer need to develop their own complicated solutions but can use our software directly, and, thanks to its open source availability, they can adjust it to fit their problems,’ Müller explains. The software is freely available to the global scientific community as an open source solution, and as soon as its availability was announced, numerous researchers, particularly in Europe and Asia, requested and installed it. ‘We have already received a lot of positive feedback,’ says Marcel Müller. ‘That also reflects how necessary this new development has been.’ source: http://www.rdmag.com
Tissue-cultured American chestnut shoots are shown in a post-rooting medium containing activated charcoal. Experiments showed that activated charcoal enhanced root growth but slightly decreased shoot tip survival. Source: Allison Oakes.The American chestnut was once a mainstay in hardwood forests as far north as Maine and as far south as Georgia and Mississippi. A massive chestnut blight in the early part of the 20th century ended the mighty chestnut's domination, wiping out billions of mature trees. Scientists are now working to restore the American chestnut's place in U.S. forests. A study published in the February issue ofHortScience provides new recommendations that can help increase the stock of blight-resistant trees.
According to the authors, genetic engineering is now poised to offer a solution: blight-resistant American chestnut trees. "The addition of one gene, oxalate oxidase, can protect the American chestnut by breaking down the oxalic acid secreted by the fungus," explained Dr. Allison Oakes, corresponding author of the study. The fungus still infects wounds in the bark, but after the initial infection the resistant tree halts the spread of the fungus behind a layer of plant tissue.
Oakes and colleagues Tyler Desmarais, William Powell, and Charles Maynard from the State University of New York College of Environmental Science and Forestry say that hundreds of American chestnut trees are needed for field trials and eventual restoration plantings, but noted that "production is bottlenecked" because of the difficulty of making hardwood trees produce roots through micropropagation. "The presence of roots and living shoot tips precede successful acclimatization of tissue culture-produced American chestnut plantlets," they explained. To improve the post-rooting stage of American chestnut propagation protocol, the scientists designed four experiments in which they examined vessel type, concentrations of humic acid and activated charcoal, and use of a vermiculite substrate.
Results showed that the presence of activated charcoal in the postrooting medium significantly increased the percentage of rooted plantlets, but increasing the concentration did not significant affect root presence. However, increasing concentrations of activated charcoal did have a significant effect on number of roots, and length of the longest root.
In regard to vessel type, results showed that using disposable clamshell containers during postrooting significantly decreased the survival of shoot tips, but significantly increased root formation. The presence of activated charcoal across vermiculite treatments increased root presence and number of roots while decreasing shoot tip survival. "High concentrations of humic acid combined with activated charcoal had excellent and significantly higher root presence than all the treatments without activated charcoal," the authors noted. They added that this trend was similar for root number.
According to the report, an "overarching trend" evidenced across the experiments was that activated charcoal enhanced root growth but slightly decreased shoot tip survival.
"Our findings have broad implications for tissue culture and genetic engineering of target hardwood species," Oakes said. "The combination of humic acid and activated charcoal in rooting medium more than doubled the number of roots produced by micropropagated shoots than either compound alone. Vermiculite substrate may be an alternative with additional research and methods development."
The authors said that the recommendations could be applicable to other difficult-to-root hardwood trees in transgenic programs, such as American butternut, white oak, and black walnut.
Researchers decided to investigate why so few people choose to invest in annuities.Roughly 52 percent of American households will not have enough retirement income to maintain their standard of living if they retire at 65.
The reason? People are afraid of thinking about their own death, according to findings in a new study published online in the Journal of Consumer Psychology. Fear of death tempts people to avoid making decisions about how to manage their savings during retirement.
Researchers from Boston College in Massachusetts decided to investigate why so few people choose to invest in annuities, a guaranteed steady stream of income during retirement. The public's lack of interest in annuities, known as the "annuity puzzle," has stumped researchers for decades.
The investigators explored a new solution to the annuity puzzle: What if people avoid this option because it evokes thoughts about mortality?
(Credit: Wiley)In order for a machine to perform work, it needs parts that move relative to each other. This also holds true for nanoscale machines. German scientists have now used DNA molecules to make a nanoscale component that makes it possible for two individual parts to move relative to each other. As reported in the journal Angewandte Chemie, this component could be used as a molecular guide bearing and may form the basis for more complex systems.
DNA is an excellent material for the nanoscale: It forms a very stable framework and additional components can be attached at any desired location by the removal of one strand for use as an attachment site. Addition of functional groups is also no problem. It is thus possible to build complex systems from DNA molecules.
The team headed by Michael Famulok at the University of Bonn has chosen to build their moveable components as rotaxanes. These are a class of molecule in which one or more molecular rings are "threaded" onto an axis. They can move freely along and around the axis and are prevented from slipping off by "stoppers". If the DNA rings themselves are bound to the end of an axle, the rings can be threaded onto a second axle and vice versa. In this case, the stoppers consist of two mutually entwined DNA rings with a spherical shape. After attaching stoppers to the free ends of the axles, the researchers obtained two interwoven, dumbbell-shaped structures that can move freely along the axles. This allows the two dumbbells to be pushed toward each other linearly along the axles. Daisy chains are formed in a similar way, so these special rotaxanes are also known as daisy chain rotaxanes.
How do the researchers thread the two DNA molecules together? To achieve this, Famulok and his co-workers turned to specific base pairing. Both in the middle of the axles and at one location on the edge of the ring, they left a "gap" of single-stranded DNA. The sequences of these single strands are complementary to each other. When the single-stranded regions of the ring and axle come into contact with each other, they bind to each other, "gluing" the rings and axles of two molecules together. If short, single strands of DNA complementary to these regions are then added, this "sticking point" between the axle and ring is released, allowing the ring to slide along the axle.
This results in a moving structure that can act as a molecular slide bearing or transmission for nanomachines. More nanoscopic machine components should follow. The researchers can imagine a whole series of novel components based on mechanically bound double-stranded DNA.
A beam of X-rays scattering off a thin film of silicon form this speckle pattern that corresponds to the details of the surface. University of Vermont scientists used these kinds of images as part of a discovery that is providing a new view at the nanoscale. Source: Courtesy Randall Headrick, UVMX-rays have long been used to make pictures of tiny objects, even single atoms. Now a team of scientists has discovered a new use for X-rays at the atomic scale: using them like a radar gun to measure the motion and velocity of complex and messy groups of atoms.
"It's a bit like a police speed trap -- for atomic and nanoscale defects," said Randall Headrick, a professor of physics at the University of Vermont who led the research team. The new technique was reported on March 28 in the journal Nature Physics.
TINY PORES
X-rays have great power to look within. It's not just Superman; scientists have been pushing closer to what might seem like science fiction, training X-rays onto tiny objects, including chains of DNA, viruses, and individual atoms. But as they probe the structure of ever-smaller things, the random arrangement of those objects makes it increasingly difficult to distinguish between them. A long-standing problem has been that good X-ray pictures require nearly perfect crystals--identical objects in precise order. At the scale of atoms, complex and disordered objects -- like the thin films that are used to make the screen on a cell phone or the metal layers used in electronic circuits -- give a blurry X-ray picture. "It's like blending many different faces in a composite image," Headrick said, "or trying to see what an average car looks like by watching traffic zip along a highway."
(Credit: Leiden Institute of Physics)Leiden physicists have detected a single molecule called dibenzoterrylene in a new crystal and found that it is a candidate component for a quantum network. Future quantum computers will need such a network to work together while maintaining their advantages.The physicists have published their results in the journal ChemPhysChem.
Quantum computers hold big promise for the future. With exponentially faster calculations, they should be able to solve scientific problems and crack codes that are currently untouchable for modern computers. And realizing the full potential of quantum computers requires connection through a quantum network. In regular networks, the so-called qubits must transform into ordinary bits in order for a classical wire to carry them. Thus, the speed advantage of the quantum computer would be completely lost.
Individual molecule
Leiden physicist Michel Orrit studies single molecules as candidate building blocks for the necessary quantum network using a technique that he developed in the early '90s with which he observed an individual molecule with the use of fluorescence for the first time. Orrit's invention laid the groundwork for a follow-up technique that earned the 2015 Nobel Prize in Chemistry. And to this date, his original technique still proves to be valuable in modern research. Apart from bringing him the 2016 Physica Prize, it enabled Orrit to detect an individual dibenzoterrylene molecule, together with Ph.D. student Nico Verhart, and check its properties for use in quantum networks.
