Category Archives: Life Science

Attaching Biological Cells to Non-Biological Surfaces

images of cell adhesion system

Berkeley Researchers Lay Groundwork for Cell Version of DNA Chip

A new technique in which single strands of synthetic DNA are used to firmly fasten biological cells to non-biological surfaces has been developed by researchers with the Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California at Berkeley. This technique holds promise for a wide variety of applications, including biosensors, drug-screening technologies, the growing of artificial tissues and the design of neural networks.

Figure A: To test their cell adhesion system, researchers anchored single-stranded DNA to gold pads inside microfluidic chips. When the pads were washed with a mixture of DNA-coated cells, only those cells with complementary DNA adhered to the pads. Figure B: With a cell adhesion system based on matching DNA sequences, different cell types can be selectively attached to a chip surface in precise patterns.

Once it was established that cell surfaces could be coated with single-stranded DNA, Chandra worked with Douglas to demonstrate that this adhesion system could be used to attach cells to a non-biological surface. Douglas is a student under Mathies, director of UCB’s Center for Analytical Biotechnology. Chandra and Douglas used a commercial chemical handle, the sulfur-based thiolate ion, to anchor single-stranded DNA onto gold pads, which were incorporated into microfluidic chips through standard photolithography. After the DNA-coated Jurkat cells were rinsed over the chips, fluorescence microscopy revealed that only those cells coated with single-stranded DNA complementary to the anchored DNA adhered to the gold pads. Cells that were otherwise identical but bearing mismatched DNA sequences were washed away.

Evolution of Antibiotic Resistance

Inhibition of Mutation and Combating the Evolution of Antibiotic Resistance from the Public Library of Science Biology Journal:

The emergence of drug-resistant bacteria poses a serious threat to human health. In the case of several antibiotics, including those of the quinolone and rifamycin classes, bacteria rapidly acquire resistance through mutation of chromosomal genes during therapy. In this work, we show that preventing induction of the SOS response by interfering with the activity of the protease LexA renders pathogenic Escherichia coli unable to evolve resistance in vivo to ciprofloxacin or rifampicin, important quinolone and rifamycin antibiotics. We show in vitro that LexA cleavage is induced during RecBC-mediated repair of ciprofloxacin-mediated DNA damage and that this results in the derepression of the SOS-regulated polymerases Pol II, Pol IV and Pol V, which collaborate to induce resistance-conferring mutations. Our findings indicate that the inhibition of mutation could serve as a novel therapeutic strategy to combat the evolution of antibiotic resistance.

Magnetic Misfit Bacteria

Magnetic Misfits: South Seeking Bacteria in the Northern Hemisphere

Magnetotactic bacteria contain chains of magnetic iron minerals that allow them to orient in the earth’s magnetic field much like living compass needles. These bacteria have long been observed to respond to high oxygen levels in the lab by swimming towards geomagnetic north in the Northern Hemisphere and geomagnetic south in the Southern Hemisphere. In either hemisphere, this behavior would also lead them downward in the water column into areas with their preferred oxygen level. But an unusual bacterium in New England has been found doing just the opposite, a magnetic misfit of sorts.
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Simmons, a graduate student in the MIT/WHOI Joint Program in Oceanography and Applied Ocean Science and Engineering, received some additional support for her study from a National Defense Science and Engineering Graduate Fellowship. Edwards is her advisor.

Africa Scientific

Africa Scientific by Dr. Mohamed H.A. Hassan, Seed:

in Nigeria, the malaria group at the University of Ibadan is conducting research on a local disease problem, as is the Federal University of Technology-Minna, which has developed a typhoid vaccine for their own population. Makerere University’s Medical Biotechnology Laboratories in Kampala, Uganda, has an extensive molecular biology research and training program; among its most noteworthy efforts are studies of alternative treatments of river blindness, a fly-borne parasitic disease that just a decade ago afflicted one out of every three villagers in parts of Burkina Faso, Ghana, Nigeria and other nations.

I lived in Nigeria for a year, when I was a child, while my father taught chemical engineering as a Fulbright scholar. I still remember visiting factories, that I believe he was consulting for, as we traveled around West Africa. I returned to Africa in the 1990s to revisit Kenya and visit Egypt. See my travel photos from Kenya and a travel photo essay from Egypt.

John Hunter

Microbes

photo of T4 bacteriophage

Photo: T4 bacteriophage, middle, is a virus that invades bacterial cells. Courtesy of the MicrobeLibrary.org

The MicrobeWorld web site includes an introduction to microbes – Microbes: what they are and what they do:

Microbes are single-cell organisms so tiny that millions can fit into the eye of a needle.

They are the oldest form of life on earth. Microbe fossils date back more than 3.5 billion years to a time when the Earth was covered with oceans that regularly reached the boiling point, hundreds of millions of years before dinosaurs roamed the earth.

Microbes types:

Archaea
These bacteria look-alikes are living fossils that are providing clues to the earliest forms of life on Earth.

Bacteria
Often dismissed as “germs” that cause illness, bacteria help us do an amazing array of useful things, like make vitamins, break down some types of garbage, and maintain our atmosphere.

Fungi
From a single-celled yeast to a 3.5-mile-wide mushroom, fungi do everything from helping to bake bread to recycling to decomposing waste.

Protista
Plant-like algae produce much of the oxygen we breathe; animal-like protozoa (including the famous amoeba) help maintain the balance of microbial life.

Viruses
Unable to do much of anything on their own, viruses go into host cells to reproduce, often wreaking havoc and causing disease. Their ability to move genetic information from one cell to another makes them useful for cloning DNA and could provide a way to deliver gene therapy.

Symbiotic relationship between ants and bacteria

Study reveals classic symbiotic relationship between ants, bacteria

Ants that tend and harvest gardens of fungus have a secret weapon against the parasites that invade their crops: antibiotic-producing bacteria that the insects harbor on their bodies.

“Every ant species [that we have examined] has different, highly modified structures to support different types of bacteria,” says Currie. “This indicates the ants have rapidly adapted to maintain the bacteria. It also indicates that the co-evolution between the bacteria and the ants, as well as the fungus and parasites, has been occurring since very early on, apparently for tens of millions of years.”

Furthermore, Currie says, the fact that the species have coexisted for so long means there might be a mechanism in place to decrease the rate of antibiotic resistance – which could help address a significant problem facing modern medicine. “We can learn a lot about our own use of antibiotics from this system,” he says.

Read more about the overuse of antibiotics

DNA Offers New Insight Concerning Cat Evolution

DNA Offers New Insight Concerning Cat Evolution, Nicholas Wade, New York Times:

Before DNA, taxonomists had considerable difficulty in classifying the cat family. The fossil record was sparse and many of the skulls lacked distinctiveness. One scheme divided the family into Big Cats and Little Cats. Then, in 1997, Dr. Johnson and Dr. O’Brien said they thought most living cats fell into one of eight lineages, based on the genetic element known as mitochondrial DNA.

Having made further DNA analyses, the researchers have drawn a full family tree that assigns every cat species to one of the lineages. They have also integrated their tree, which is based solely on changes in DNA, with the fossil record. The fossils, which are securely dated, allow dates to be assigned to each fork in the genetic family tree.
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The leopard lineage appeared around 6.5 million years ago in Asia. The youngest of the eight lineages, which led eventually to the domestic cat, emerged some 6.2 million years ago in Asia and Africa, either from ancestors that had never left Asia or more probably from North American cats that had trekked back across the Bering land bridge.

Photos from Curious Cat Travel Photos – Kenya

Self-Assembling Cubes Could Deliver Medicine

Nanocubes photos

Tiny Self-Assembling Cubes Could Carry Medicine, Cell Therapy – News Release from Johns Hopkins (pdf format)

Details of photos: “Scanning electron microscopy images of image of (A) a hollow, open surfaced, biocontainer, and (B) a device loaded with glass microbeads. (C) Fluorescence microscopy images of a biocontainer loaded with cell-ECM-agarose with the cell viability stain, Calcein-AM. (D) Release of viable cells from the biocontainer.”

Johns Hopkins researchers have devised a self- assembling cube-shaped perforated container, no larger than a dust speck, that could serve as a delivery system for medications and cell therapy.

When the process is completed, they form a perforated cube. When the solution is cooled, the solder hardens again, and the containers remain in their box-like shape.

“To make sure it folds itself exactly into a cube, we have to engineer the hinges very precisely,” Gracias said. “The self-assembly technique allows us to make a large number of these microcontainers at the same time and at a relatively low cost.”

Gracias and his colleagues used micropipettes to insert into the cubes a suspension containing microbeads that are commonly used in cell therapy. The lab team showed that these beads could be released from the cubes through agitation. The researchers also inserted human cells, similar to the type used in medical therapy, into the cubes. A positive stain test showed that these cells remained alive in the microcontainers and could easily be released.

And they are “always on the lookout for exceptional and highly creative undergraduate, graduate students and post-doctoral candidates” – maybe you.

Overuse of Antibiotics

Stomach Bug Mutates Into Medical Mystery – Antibiotics, Heartburn Drugs Suspected

Shultz is one of a growing number of young, otherwise healthy Americans who are being stricken by the bacterial infection known as Clostridium difficile — or C. diff — which appears to be spreading rapidly around the country and causing unusually severe, sometimes fatal illness.
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“It’s a new phenomenon. It’s just emerging,” said L. Clifford McDonald of the federal Centers for Disease Control and Prevention in Atlanta. “We’re very concerned. We know it’s happening, but we’re really not sure why it’s happening or where this is going.”

It may, however, be the latest example of a common, relatively benign bug that has mutated because of the overuse of antibiotics.

Articles on the overuse of anti-biotics are available via the Curious Cat directory. From the US Center for Disease Control – Antibiotic / Antimicrobial Resistance section:

Antibiotic use promotes development of antibiotic-resistant bacteria. Antibiotic resistance occurs when bacteria change in some way that reduces or eliminates the effectiveness of drugs, chemicals, or other agents designed to cure or prevent infections. The bacteria survive and continue to multiply causing more harm. Widespread use of antibiotics promotes the spread of antibiotic resistance. While antibiotics should be used to treat bacterial infections, they are not effective against viral infections like the common cold, most sore throats, and the flu.

Unfortunately the continued overuse of antibiotics is increasing the danger of deadly antibiotic resistant bacteria. This problem is a significant challenge not only due to the scope of the consequences (which are huge) but due to the nature of the problem. Many thousands, hundreds of thousands maybe even millions of poor use of antibiotics incrementally put everyone at risks. But each of those individual steps of poor use of antibiotics is by itself not likely to be deadly.

Due to the way we tend to think about problems (searching for one simple cause or thing to blame and fixing that one thing), the cause of antibiotic resistance provides an opportunity for the millions of bad actions to go unchecked. Only after catastrophic consequences are recognized, and put in the proper context, are we likely to give this issue the attention it deserves. Thankfully CDC and others are trying to get us to take this issues seriously now. However, the risks are huge and each person (doctors, patients, consumers [use of antibiotics on animals used as food is a huge part of the problem], government regulators…) taking small actions that make the situation worse often don’t see any need to take more responsibility.

Wasps Used to Detect Explosives

Wasps Used to Detect Explosives, podcast from NPR:

The “Wasp Hound” is a device that utilizes trained wasps to detect explosives and other odors. Joe Lewis, research entomologist with the USDA Agriculture Research Service and the Wasp Hound’s lead inventor, discusses the device.

Wasps could replace bomb, drug dogs, USA Today:

Scientists say a species of non-stinging wasps can be trained in only five minutes and are just as sensitive to odors as man’s best friend, which can require up to six months of training at a cost of about $15,000 per dog.
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“There’s a tremendous need for a very flexible and mobile chemical detector,” said U.S. Department of Agriculture entomologist Joe Lewis, who has been studying wasps since the 1960s.

Parasitic Wasps Learn and Report Diverse Chemicals with Unique Conditionable Behaviors by Olson, D.M., Rains, G.C., Meiners, T., Takasu, K., Tertuliano, M., Tumlinson, J.H., Wackers, F.L., Lewis, W.J. 2003. Chemical Senses. 28:545-549.