Saturday, December 25, 2010

Seasons Greetings from

Seasons Greetings from the staff at and Microbiology Consultants, LLC.

We hope you and all your coworkers, family, and friends have a lovely holiday season filled with joy and meaning. Best wishes for a healthy, peaceful and prosperous New Year.

Wednesday, December 22, 2010

Immunochromatographic strip test for detection of genus Cronobacter

This just in from the December 2010 issue of Biosensors and Bioelectronics. Researchers at the Department of Biochemistry and Microbiology, Institute of Chemical Technology, Prague, Czech Republic, have published a paper that describes a novel method for the rapid detection of Enterobacter sakazakii, now known as Cronobacter sakazakii. Here is the abstract:

Members of the genus Cronobacter are opportunistic pathogens formerly known as Enterobacter sakazakii, which induce severe meningitis and sepsis in neonates and infants, with a high fatality rate. In this work, a simple and rapid immunochromatographic strip test for the detection of this pathogen was developed. Following the shortened bacteria cultivation and isolation of DNA, a specific gene sequence targeting 16S rRNA from Cronobacter spp. was amplified by PCR using 5'-end labelled specific primers. The PCR product, amplicon labelled with digoxigenin on one side and biotin on the other side, was directly added to the immunochromatographic strip test, composed of nitrocellulose membrane with bound antibody against digoxigenin in the test line. The visualization was mediated by colloidal carbon conjugated to neutravidin, and the appearance of grey/black line was indicative of the presence of specific amplicon. Colour intensity of the test line in pathogen-positive assay was visually distinguishable from that of negative sample within 10min. The visual detection limit of PCR product was 8ng. The specificity of the developed method was confirmed by standard microbiological techniques. Whole detection procedure with the incorporated immunostrip was applied to analysis of infant formulae samples, contaminated with less than 10 cells of Cronobacter spp. per 10g. The results from immunochromatographic test indicated the absolute agreement with those from standard microbiological methods. Moreover, the developed procedure considerably reduced the total analysis time to 16h whereas the reference microbiological method needs 6-7 days.

Tuesday, December 21, 2010

MIT Researchers Reconstruct Evolution of 3 Billion-Year-Old Microbes

Computational biologists at the Massachusetts Institute of Technology (MIT) have developed a mathematical model that is capable of using modern genomes to mimic the evolution of ancient microbes. Lawrence David and Eric Alm have traced the evolution of microbes back billions of years using modern genomes in an effort to identify points of change through history.

The Cambrian Explosion, which occurred approximately 580 million years ago, was a period of rapid change on Earth where new life forms came about and contributed to the modern diversity of animals. Paleontologists are able to understand and archive the evolution of life from the Cambrian Explosion until now because of fossils, but recording the evolution of life before the Cambrian Explosion has been difficult due to the fact that soft Precambrian cells hardly left "fossil imprints" behind.

But now, Alm and David have created a mathematical model that paints the picture of life more clearly over the 3 billion year period before the Cambrian Explosion. To do this, they used 100 modern genomes because all living organisms "inherit their genomes from ancestral genomes." All of the possible ways that genes evolve was combined with the mathematical model, such as the fact that new gene families can be born and inherited, duplicated in the same genome, lost, or swapped or horizontally transferred between organisms.

With the 100 modern genomes, researchers were able to trace thousands of genes back to their very first moment on Earth and were able to tell which ancient microbes carried these genes. According to the results, the genome of all life experienced an expansion between 3.3 and 2.8 billion years ago where 27 percent of all existing gene families were born. Alm and David are calling this period of time the Archean Expansion.

"What is really remarkable about these findings is that they prove that the histories of very ancient events are recorded in the shared DNA of living organisms," said Alm. "And now that we are beginning to understand how to decode that history, I have hope that we can reconstruct some of the earliest events in the evolution of life in great detail."

At first, Alm and David believed that the emergence of oxygen was the cause of the Archean Expansion since the new genes they've found are related to oxygen, and oxygen was not available on Earth until around 2.5 billion years ago when it started accumulating and killing off anaerobic life forms during the Great Oxidation Event. But when investigating further, they found that oxygen-utilizing genes didn't exist until the end of the Archean Expansion, which is when geochemists dated the Great Oxidation Event.

After eliminating that possibility, Alm and David now believe they've identified the beginnings of modern electron transport, which is the biochemical process that moves electrons around within cell membranes. The process is necessary for breathing, and is used by plants and some microbes during photosynthesis. It is believed that during the Great Oxide Event, a type of photosynthesis called oxygenic photosynthesis generated the oxygen we breathe today. Ultimately, electron transport's evolution through the Archean Expansion would be responsible for photosynthesis and respiration.

"Our results can't say if the development of electron transport directly caused the Archean Expansion," said David. "Nonetheless, we can speculate that having access to a much larger energy budget enabled the biosphere to host larger and more complex microbial ecosystems."

Micro- and nanocantilever devices and systems for biomolecule detection

I recently came across a review article on the use of micro and nanocantilevers as a rapid way of detecting the presence of a variety of microorganisms. A microcantilever is a device that can act as a physical, chemical or biological sensor by detecting changes in cantilever bending or vibrational frequency. It is the miniaturized counterpart of a diving board that moves up and down at a regular interval based on mass. The mass changes when contaminants land on the devices, causing them to vibrate at a different "resonant frequency, " which can be quickly detected. The authors are from the Korea Institute of Science and Technology. Their abstract is provided below:

Micro- and nanocantilever devices and systems for biomolecule detection. Hwang KS, Lee SM, Kim SK, Lee JH, Kim TS. Annu Rev Anal Chem (Palo Alto Calif). 2009; 2:77-98.

Recent research trends in biosensing have been geared toward developing bioanalytical devices that are label free, small in size, and portable and that can operate in a rapid manner. The performance of these devices has been dramatically improved through the advent of new materials and micro-/nanofabrication technologies. This is especially true for micro-/nanosized cantilever sensors, which undergo a change in mechanical properties upon the specific binding of biomolecules. In this review, we introduce the basic principles of cantilever biosensors in static and dynamic modes. We also summarize a range of approaches to cantilever design, fabrication, and instrumentation according to their applications. More specifically, we describe cantilever-based detections of proteins, DNA molecules, bacteria, and viruses and discuss current challenges related to the targets' biophysical characteristics.

Monday, December 13, 2010

DNA Sequencing Matches Cholera Strain in Haiti with Bacteria from South Asia

A team of researchers from Harvard Medical School, Brigham and Women's Hospital, and Massachusetts General Hospital, with others from the United States and Haiti, has determined that the strain of cholera erupting in Haiti matches bacterial samples from South Asia and not those from Latin America. These findings, which appeared in the New England Journal of Medicine, conclude that the cholera bacterial strain introduced into Haiti probably came from an infected human, contaminated food or other item from outside of Latin America.

To identify the probable origin of the cholera strain in Haiti, scientists used a third-generation, single-molecule DNA sequencing method developed by Pacific Biosciences. They determined the genome sequences of two Haitian cholera samples and three cholera samples from elsewhere around the world. Based on advanced imaging technology, the method enables researchers to observe a natural enzyme synthesizing a strand of DNA in real time. As such, the technology actually tracks and documents nature at work, a rapid approach compared to other sequencing technologies. The method allowed a comprehensive analysis and comparison of critical DNA features among the various cholera samples, which included single nucleotide variations, insertions and deletions of particular portions of the genome, and structural variations. The analysis showed a close relationship between the Haitian samples and the seventh pandemic variant strains isolated in Bangladesh in 2002 and 2008.

Genetic changes occur quickly, within hours in the lab and probably weeks within the environment, through natural modes of DNA swapping and mutation among bacteria. Their evolution is based, in part, on the acquisition, loss, and alteration of mobile genetic elements, including DNA from the CTX bacterial virus, which bears the genes encoding the cholera toxin, and other genetic sequences that may make a particular strain more adapted to a given ecosystem. The resulting heterogeneity has been used to categorize strains of the seventh pandemic and to understand their transmission around the globe.

Wednesday, December 8, 2010

UTHealth professor to receive service award from American Society for Microbiology

Known nationally for her research into single-cell organisms that affect oral health, Millicent "Mimi" Goldschmidt, Ph.D., a professor of microbiology and molecular genetics at The University of Texas Health Science Center at Houston (UTHealth), has been selected to receive the 2011 American Society for Microbiology (ASM) Founders Distinguished Service Award. The award will be presented at the ASM General Meeting Awards Banquet and Dinner in New Orleans on May 22.

"Dr. Goldschmidt has furthered the understanding of the basic microbiology of the mouth," said Larry R. Kaiser, M.D., president of UTHealth. "She has done an exemplary job of serving her professional community, her scientific community and her teaching community." Microbiology is the study of cells that are invisible to the naked eye. These tiny cells include bacteria, viruses and fungi. Goldschmidt studies microbes involved with dental decay, gum disease and oral cancer, as well as rapid methods of detection (biosensors, microarrays and nanoparticles).

Before joining the UTHealth faculty in the early 1970s, Goldschmidt was the coordinator of the protocol to plan the biological tests that would be employed in the lunar receiving laboratory on the first returned moon rocks. She was also instrumental in developing isolation protocols for Apollo astronauts returning from the moon, which ensured that infectious organisms would be detected and contained.

When she started her professional career in Texas five decades ago, Goldschmidt said there were really no rapid methods to detect microorganisms. Her research contributed to the development of rapid immunological and biosensor types of detection methods to pinpoint salmonellae, E. coli and oral microbes. She consults and lectures nationally and internationally on biosensors, microarrays and nanoparticles.