Vical Confirms Advantages of DNA Technology Platform With Vaccine for H1N1 Influenza

Vical Incorporated announced the publication of data documenting the successful pilot lot production and initiation of animal immunogenicity testing of a Vaxfectin(R)-adjuvanted DNA vaccine for H1N1 influenza before conventional vaccine manufacturers even received the seed virus needed to start production.

The U.S. Navy has awarded a contract for $1.25 million to support large-scale cGMP vaccine manufacturing and related clinical and regulatory preparations for a Phase 1 clinical trial of the company's vaccine against H1N1 pandemic influenza. The trial will be conducted in collaboration with the U.S. Naval Medical Research Center (NMRC), a biomedical research organization within the Navy, and is expected to begin within the next few weeks.

"DNA vaccines offer unprecedented speed in development and production," said Larry Smith, Ph.D., Vical's Vice President of Vaccine Research and an author on the paper, "and the 2009 outbreak of H1N1 pandemic influenza provided an opportunity to demonstrate the advantages of our approach. We do not have to handle the pathogen, and derive our vaccine instead from a gene sequence posted on the Internet. We can develop a vaccine quickly and match it exactly to the circulating pathogen, providing the greatest possible vaccine effectiveness. Our manufacturing process does not rely on chicken eggs or other time- and labor-intensive cell culture processes that require vaccine-specific facilities. We produce our vaccines through rapid and reliable bacterial fermentation. The inherent stability of DNA does not require the precise temperature control needed for conventional vaccines, and allows great flexibility in shipping and storage. In short, the DNA vaccine platform is well-suited to addressing emerging infectious disease threats even before they become pandemics." The vical press room offers complete study details

Sex-specific and lineage-specific alternative splicing in primates

Comparative studies of gene regulation suggest an important role for natural selection in shaping gene expression patterns within and between species. Most of these studies, however, estimated gene expression levels using microarray probes designed to hybridize to only a small proportion of each gene. Here, we used recently developed RNA sequencing protocols, which sidestep this limitation, to assess intra- and interspecies variation in gene regulatory processes in considerably more detail than was previously possible. Specifically, we used RNA-seq to study transcript levels in humans, chimpanzees, and rhesus macaques, using liver RNA samples, RNA samples from three males and three females from each species. Our approach allowed us to identify a large number of genes whose expression levels likely evolve under natural selection in primates.

These include a subset of genes with conserved sexually dimorphic expression patterns across the three species, which we found to be enriched for genes involved in lipid metabolism. Our data also suggest that while alternative splicing is tightly regulated within and between species, sex-specific and lineage-specific changes in the expression of different splice forms are also frequent. Intriguingly, among genes in which a change in exon usage occurred exclusively in the human lineage, we found an enrichment of genes involved in anatomical structure and morphogenesis, raising the possibility that differences in the regulation of alternative splicing have been an important force in human evolution. Review the complete abstract or order this article via the Genome Research portal

Boston University reseachers develop innovative DNA sequencing method (Nature Nanotechnology)

Boston University biomedical engineers have devised a method for making future genome sequencing faster and cheaper by dramatically reducing the amount of DNA required, thus eliminating the expensive, time-consuming and error-prone step of DNA amplification.

In a study published in the Dec. 20 online edition of Nature Nanotechnology, a team led by Boston University Biomedical Engineering Associate Professor Amit Meller details pioneering work in detecting DNA molecules as they pass through silicon nanopores. The technique uses electrical fields to feed long strands of DNA through four-nanometer-wide pores, much like threading a needle. The method uses sensitive electrical current measurements to detect single DNA molecules as they pass through the nanopores.

"The current study shows that we can detect a much smaller amount of DNA sample than previously reported," said Meller. "When people start to implement genome sequencing or genome profiling using nanopores, they could use our nanopore capture approach to greatly reduce the number of copies used in those measurements."

Currently, genome sequencing utilizes DNA amplification to make billions of molecular copies in order to produce a sample large enough to be analyzed. In addition to the time and cost DNA amplification entails, some of the molecules – like photocopies of photocopies – come out less than perfect. Meller and his colleagues at BU, New York University and Bar-Ilan University in Israel have harnessed electrical fields surrounding the mouths of the nanopores to attract long, negatively charged strands of DNA and slide them through the nanopore where the DNA sequence can be detected. Since the DNA is drawn to the nanopores from a distance, far fewer copies of the molecule are needed. Visit the Nature Nanotechnology portal for complete details

Transcriptome and Proteome Exploration Model in Lactococcus lactis (PLoS)

This genome-scale study analysed the various parameters influencing protein levels in cells. To achieve this goal, the model bacterium Lactococcus lactis was grown at steady state in continuous cultures at different growth rates, and proteomic and transcriptomic data were thoroughly compared. Ratios of mRNA to protein were highly variable among proteins but also, for a given gene, between the different growth conditions. The modeling of cellular processes combined with a data fitting modeling approach allowed both translation efficiencies and degradation rates to be estimated for each protein in each growth condition. Estimated translational efficiencies and degradation rates strongly differed between proteins and were tested for their biological significance through statistical correlations with relevant parameters such as codon or amino acid bias. These efficiencies and degradation rates were not constant in all growth conditions and were inversely proportional to the growth rate, indicating a more efficient translation at low growth rate but an antagonistic higher rate of protein degradation.

Estimated protein median half-lives ranged from 23 to 224 min, underlying the importance of protein degradation notably at low growth rates. The regulation of intracellular protein level was analysed through regulatory coefficient calculations, revealing a complex control depending on protein and growth conditions. The modeling approach enabled translational efficiencies and protein degradation rates to be estimated, two biological parameters extremely difficult to determine experimentally and generally lacking in bacteria. This method is generic and can now be extended to other environments and/or other micro-organisms. Review the abstract or order this article via the PLoS portal

Trade-off for Design of Protein Stability: From Lattice Models to Real Proteins (PLoS)

Two different strategies for stabilizing proteins are (i) positive design in which the native state is stabilized and (ii) negative design in which competing non-native conformations are destabilized. Here, the circumstances under which one strategy might be favored over the other are explored in the case of lattice models of proteins and then generalized and discussed with regard to real proteins.

The balance between positive and negative design of proteins is found to be determined by their average “contact-frequency”, a property that corresponds to the fraction of states in the conformational ensemble of the sequence in which a pair of residues is in contact. Lattice model proteins with a high average contact-frequency are found to use negative design more than model proteins with a low average contact-frequency. A mathematical derivation of this result indicates that it is general and likely to hold also for real proteins. Comparison of the results of correlated mutation analysis for real proteins with typical contact-frequencies to those of proteins likely to have high contact-frequencies (such as disordered proteins and proteins that are dependent on chaperonins for their folding) indicates that the latter tend to have stronger interactions between residues that are not in contact in their native conformation. Hence, our work indicates that negative design is employed when insufficient stabilization is achieved via positive design owing to high contact-frequencies. Visit the PLoS portal to review the abstract or complete article

CombiMatrix Launches New ElectraSense MicroArray Reader

CombiMatrix announced today the launch of its next-generation ElectraSense(R) microarray reader. The new ElectraSense(R) provides a robust, affordable, and user-friendly microarray reader that electrochemically measures up to 12,000 probes on an array in less than 25 seconds. The palm-sized reader achieves compact size and affordability by eliminating optics, light sources, and complicated alignment components. Common enzymes and substrates replace expensive fluorescent dyes required in existing technologies. In combination with CombiMatrix arrays, this system for array-based analysis is the most economic package available commercially.

The ElectraSense reader was developed with funding from the U.S. Department of Defense, whose interest is a portable, rugged, and compact instrument. The reader is about the size of a can of soda pop and can be carried in a pocket, held by hand, or placed in a laboratory.

"The combination of the new ElectraSense reader with CombiMatrix reusable CustomArrays(R) will appeal to those laboratories wishing to drive down overall costs in their microarray analysis," said Craig Bury, Director of Global Sales and Marketing at CombiMatrix. "The ElectraSense offers a high-value array reader in a compact, inexpensive, easy-to-use device. The capabilities of our reader enable several methodologies for purchase, lease, and overall utilization that would not be possible with more expensive readers. We encourage potential customers to call us about these commercial programs."

"While the primary commercial focus of our company has been our diagnostic services business and the development of our Comprehensive Cancer Array, we continue to receive funding from the U.S. government to develop specific products. These products are designed for dual use addressing military and government needs, but also general research and development needs, as well as potential diagnostic applications," stated Dr. Amit Kumar, President and CEO of CombiMatrix. The CombiMatrix product portal includes complete technical and performance details

TGen analysis identifies biomarkers for diabetic kidney failure

Researchers using a DNA analysis tool developed by the Translational Genomics Research Institute (TGen) and UCLA have identified genetic markers that could help treat chronic kidney disease among diabetics. Study results, published in the December edition of Diabetic Medicine, show it is possible to identify biomarkers associated with end-stage renal disease (ESRD) from the pooled DNA of more than 1,000 diabetics. Specifically, TGen researchers identified genes that could potentially contribute to ESRD among those with Type 1 Diabetes. ESRD almost always follows chronic kidney failure and although treatable with dialysis or transplantation, mortality rates remain high. While diabetic kidney disease is one of the most common complications of diabetes, it is currently not possible to determine who is at risk for ESRD.

"Identification of specific DNA variants may enhance our understanding of genetic risk factors for renal disease and may provide diagnostic value in determining which patients are at greatest risk of developing ESRD," said Dr. Johanna DiStefano, Director of TGen's Diabetes, Cardiovascular & Metabolic Diseases Division and the paper's senior author.

The need to rapidly identify individuals with a predisposition to ESRD and to discover new drugs to prevent and treat this devastating condition is becoming critical, as the average onset of this disease affects ever-younger populations. Although Type 1 diabetes is distinctly different from Type 2 diabetes, the development of kidney disease is similar in individuals with either form. Researchers expect the current findings to impact individuals with both forms of the disease. Visit the TGen press room for complete findings

The GAAS Metagenomic Tool and Its Estimations of Viral and Microbial Average Genome Size

Metagenomic studies characterize both the composition and diversity of uncultured viral and microbial communities. BLAST-based comparisons have typically been used for such analyses; however, sampling biases, high percentages of unknown sequences, and the use of arbitrary thresholds to find significant similarities can decrease the accuracy and validity of estimates. Here, we present Genome relative Abundance and Average Size (GAAS), a complete software package that provides improved estimates of community composition and average genome length for metagenomes in both textual and graphical formats. GAAS implements a novel methodology to control for sampling bias via length normalization, to adjust for multiple BLAST similarities by similarity weighting, and to select significant similarities using relative alignment lengths. In benchmark tests, the GAAS method was robust to both high percentages of unknown sequences and to variations in metagenomic sequence read lengths.

Re-analysis of the Sargasso Sea virome using GAAS indicated that standard methodologies for metagenomic analysis may dramatically underestimate the abundance and importance of organisms with small genomes in environmental systems. Using GAAS, we conducted a meta-analysis of microbial and viral average genome lengths in over 150 metagenomes from four biomes to determine whether genome lengths vary consistently between and within biomes, and between microbial and viral communities from the same environment. Significant differences between biomes and within aquatic sub-biomes (oceans, hypersaline systems, freshwater, and microbialites) suggested that average genome length is a fundamental property of environments driven by factors at the sub-biome level. The behavior of paired viral and microbial metagenomes from the same environment indicated that microbial and viral average genome sizes are independent of each other, but indicative of community responses to stressors and environmental conditions. Review the complete article via the PLoS portal

Proteomic analysis of blastema formation in regenerating axolotl limbs (BMC Biology)

The most comprehensive study to date of the proteins in a species of salamander that can regrow appendages may provide important clues to how similar regeneration could be induced in humans. Researchers at the School of Science at Indiana University-Purdue University Indianapolis and colleagues investigated over three hundred proteins in the amputated limbs of axolotls, a type of salamander that has the unique natural ability to regenerate appendages from any level of amputation, with the hope that this knowledge will contribute to a better understanding of the mechanisms that allow limbs to regenerate. Their findings were published online in the journal Biomedical Central Biology on November 30 (BMC Biology 7:83, 2009).

"In some ways this study of the axoltol's proteins was a fishing expedition. Fishing expedition can be a derogatory term in biology but for us it was positive, since we caught some important "fish" that enable us to formulate hypotheses as to how limb regeneration occurs," said David L. Stocum, Ph.D., professor of biology and director of the Indiana University Center for Regenerative Biology and Medicine, both in the School of Science at IUPUI, who led the study.

"Comparison of these proteins to those expressed in the amputated frog limb, which regenerates poorly, will hopefully allow us to determine how we might enhance limb regeneration in the frog and ultimately in humans, Dr. Stocum said.

With few exceptions – notably the antlers of moose, deer and their close relatives, the tips of the fingers and toes of humans and rodents, and the ear tissue of certain strains of mice and rabbits – the appendages of mammals do not regenerate after amputation. Limb regeneration in the axolotl occurs when undifferentiated cells accumulate under the wound epidermis at the amputation site, a process known as the establishment of a blastema. These cells are derived by the reprogramming of differentiated cells to a less specialized state, and from resident stem cells. Review the complete study findings via the BMC Biology portal

Princeton scientists find way to catalog all that goes wrong in a cancer cell

A team of Princeton University scientists has produced a systematic listing of the ways a particular cancerous cell has "gone wrong," giving researchers a powerful tool that eventually could make possible new, more targeted therapies for patients.

"For a very long time, cancer therapies have been developed by trial and error to essentially kill a broad variety of rapidly dividing cells, good and bad -- that's why they have massive side effects," said Saeed Tavazoie, a professor in the Department of Molecular Biology and the Lewis-Sigler Institute for Integrative Genomics, who led the research. "The goal of cancer biology is to come up with therapies that are much more rational in terms of attacking the pathways that have been co-opted by cancer cells. The big challenge is to discover these pathways so that we can restore them to their normal state."

Writing in the Dec. 11 issue of Molecular Cell, Tavazoie, along with his colleagues Hani Goodarzi, a graduate student in molecular biology, and Olivier Elemento, a former postdoctoral researcher in the department, found they were able to systematically categorize and pinpoint the alterations in cancer pathways and to reveal the underlying regulatory code in DNA. Elemento is now on the faculty of Weill Cornell Medical College in New York. Review the complete article via the Princeton University portal

XOMA Presents Its Multiple Antibody Formulation Technologies at Antibody Engineering Conference

XOMA Ltd. reported results demonstrating the advantages of its monoclonal antibody technologies in the rapid development of a first-in-class multiple antibody product candidate, XOMA 3AB. XOMA 3AB is designed to neutralize botulinum neurotoxin Type A, which causes paralysis and is a bioterror threat. The results were presented at the 20th Annual International Conference on Antibody Engineering being held December 6 to 10 in San Diego, CA.

A major problem with treating botulism and many infectious diseases is that a single antibody may not be effective in neutralizing a toxin or infectious agent, particularly when multiple strains or subtypes exist. XOMA's technologies enable it to co-formulate and deliver multiple antibodies in a single injectable solution, which facilitates delivery and has the potential to increase efficacy for infectious and other diseases. XOMA 3AB is comprised of three human antibodies that bind to unique epitopes on the botulinum A toxin, which in composite provide unprecedented potency against the toxin. XOMA is developing XOMA 3AB under existing research contracts with the National Institute of Allergy and Infectious Diseases (NIAID) of the National Institutes of Health (NIH).

This project has been funded in whole or in part with federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, and Department of Health and Human Services under contract numbers HHSN266200600008C and HHSN272200800028C. Contract HHSN272200800028C was awarded in 2008 for a total of $65 million.

"These results highlight the breadth of XOMA's advanced expertise in antibody development, optimization and formulation. We are utilizing multiple technologies to provide stable products with longer shelf lives and lower costs than third generation biologics," said Patrick J. Scannon, M.D., Ph.D., XOMA's Executive Vice President and Chief Medical Officer. "For the first time, we have also solved a key quality problem in ensuring the mix and potency of multiple antibodies. Specialized assays were developed and implemented to ensure precise characterization, stability and release of this multiple antibody cocktail." Review the complete press release via GlobalNewsWire

New heart attack biomarker uncovered (Molecular & Cellular Proteomics)

Though they remain a leading killer, heart attacks can be effectively treated provided they can be rapidly diagnosed following initial onset of symptoms. In a study appearing in this month's Molecular and Cellular Proteomics, researchers have identified cardiac myosin-binding protein C (cMyBP-C) as a potential new diagnostic biomarker for heart attacks, one that may be particularly valuable for mild attacks in which traditional diagnostic proteins may not be abundant enough.

Currently, one of the gold-standards for diagnosis of heart attacks, or acute myocardial infarctions, is scanning for the presence of the proteins troponin I and troponin T, as they are produced specifically in the heart and are almost completely absent in the blood in healthy individuals.

However, even troponins are not ideal markers, since they are released somewhat slowly following a heart attack (peaking around 18 hours post-infarction) and remain in the blood for up to 10 days afterwards, hindering the diagnosis of any secondary heart attacks. In the quest for better biomarkers, a group of researchers at King's College London performed a proteomic analysis of all the proteins released by mouse hearts following induced heart attacks. They identified 320 proteins not released by normal hearts, including all the currently employed biomarkers. Visit the Molecular and Cellular Proteomics portal for complete details

Drosophila ORC localizes to open chromatin and marks sites of cohesin complex loading (Genome Research)

The origin recognition complex (ORC) is an essential DNA replication initiation factor conserved in all eukaryotes. In S. cerevisiae ORC binds to specific DNA elements; however, in higher eukaryotes, ORC exhibits little sequence specificity in vitro or in vivo. We investigated the genome-wide distribution of ORC in Drosophila and found that ORC localizes to specific chromosomal locations in the absence of any discernible simple motif. Open chromatin appears to be the underlying factor that is deterministic for ORC binding. ORC-associated sequences are enriched for the histone variant, H3.3, often at transcription start sites, and depleted for bulk nucleosomes.

Although no clear sequence motif emerged from the ORC binding sites, we were able to use machine learning approaches to accurately discriminate between ORC-associated sequences and ORC-free sequences based solely on primary sequence. The complex sequence features that define ORC binding sites are highly correlated with nucleosome positioning signals and likely represent a preferred nucleosomal landscape for ORC association. The density of ORC binding along the chromosome is reflected in the time at which a sequence replicates, with early replicating sequences having a high density of ORC binding. Finally, we found a high concordance between sites of ORC binding and cohesin loading, suggesting that in addition to DNA replication, ORC may be required for the loading of cohesin on DNA in Drosophila. Review the complete abstract or order this article via the Genome Research Journal portal

Immunomedics Announces Preclinical Results of Milatuzumab in B-Cell Malignancies

Immunomedics, Inc. at the 51st annual meeting of the American Society of Hematology announced results from 3 preclinical studies aimed at understanding the mechanism of action of its proprietary humanized anti-CD74 antibody, milatuzumab, which is currently in clinical development for multiple myeloma (MM), non-Hodgkin's lymphoma (NHL) and chronic lymphocytic leukemia (CLL).

The first study was on CLL, a progressive disease for which most patients require treatment. A team of researchers at the Ohio State University, Columbus, OH, led by Dr. John Byrd, demonstrated expression of CD74 on the surface of CLL cells, but no expression was found on T cells. Milatuzumab-induced cell death occurred very rapidly, with 57% cell survival at 4 hours and only 30% at 24 hours, which was superior to that observed with rituximab.

The mode of cell death induced by milatuzumab was found to be mediated directly through interaction with CD74 and its ensuing effects on signal transduction. Milatuzumab, when crosslinked, promotes the maintenance of CD74 on the cell surface and thereby prevents receptor internalization and subsequent signaling. Retention of the CD74 receptor on the surface of B cells can also be induced, without the presence of a crosslinking antibody, the investigators found, by incorporating milatuzumab into liposomes. The subject of the second study was mantle cell lymphoma (MCL), an incurable B-cell malignancy with limited therapeutic options. Despite the success of rituximab in treating B-cell lymphoma, its use as a single agent or in combination with chemotherapy in MCL has demonstrated modest activity. Since rituximab and milatuzumab target distinct antigens lacking known association, Dr. Byrd and his team at the Ohio State University, explored a combination strategy with these antibodies in MCL cell lines, patient samples, and in a preclinical model.

U-Iowa study helps advance heart-related research (PLoS)

Using a new mathematical model of heart cells, University of Iowa investigators have shown how activation of a critical enzyme, calmodulin kinase II (CaM kinase), disrupts the electrical activity of heart cells. The study, which also involved Columbia University, was published online Dec. 3 in the journal PLoS Computational Biology.

"Recently, researchers have developed great interest in calmodulin kinase II as a critical regulator of the heart's response to injury. By targeting this enzyme's activity, it may be possible to prevent or treat heart disease and associated electrical rhythm disturbances," said Thomas Hund, Ph.D., associate in internal medicine at the University of Iowa Roy J. and Lucille A. Carver College of Medicine and the paper's senior author.

"CaM kinase is activated when the heart experiences injury, for example, when an artery providing blood to the heart becomes blocked. In the short-term, this increase in activity may be the heart's attempt to increase blood flow," Hund said. "However, unfortunately, the initial response results in a vicious cycle that likely advances heart disease."

In this study, the team analyzed tissue from injured hearts from animals, in which a coronary artery had been blocked. They found a dramatic increase in the levels of oxidized CaM kinase in specific heart regions where potentially lethal electrical activity occurs. Using the mathematical model of the cardiac cell, the researchers were able to predict, through computer simulation, the effects of oxidized CaM kinase on cardiac electrical activity. Oxidation activates the enzyme by modifying key chemical groups. In heart disease, oxidation is overactive, and CaM kinase is turned on too much. Visit the PLoS portal to review the full research abstract

Fluidigm Releases Access Array™ System for 454 FLX Applicon Tagging

Fluidigm released its 48.48 Access Array™ integrated fluidic chip (IFC) for 454 FLX™ users active in Amplicon Tagging. This Access Array IFC automatically generates emPCR-ready libraries by simultaneously combining 48 samples and 48 primer sets to produce 48 uniquely-barcoded samples per chip for approximately $7 (U.S.) per sample.

Fluidigm’s Access Array IFC, when used with a 454 FLX sequencer, can capture up to 12 kb of sequence data per sample, or 576 kb per array. Upcoming applications on the Access Array system, such as long range PCR, will allow for users to target up to 480 kb of sequence data per sample, or 23MB per array.

“Fluidigm’s Access Array System has already been adopted by users around the world for targeted re-sequencing projects focused on research of cancer, miRNA, and population genetics, where the ability to inexpensively sequence large cohort studies is critical,” noted Mike Lee, Fluidigm’s Senior Director of Marketing. “The flexibility, ease of use, and cost effectiveness of our Access Array system will enable researchers to expand the scope of experiments on next generation sequencers,” he added.

Sequencing library preparation for next-generation sequencers is by far the most time and labor demanding component of the entire next-generation sequencing process. While necessary for whole genome sequencing studies, the process can be almost entirely eliminated for targeted re-sequencing projects through the use of amplicon tagging. By incorporating the adaptor sequences into the primer design, the final PCR product is ready to go into emPCR or onto the flowcell since it already contains the necessary capture sequences. The Fluidigm product portal has complete techncail and performance details

PerkinElmer Launches New AlphaScreen® SureFire® and AlphaLISA® “No Wash” Immunoassay and Cellular Pathway Mapping Kits

PerkinElmer announced the expansion of its “No Wash” ALPHA (Amplified Luminescent Proximity Homogeneous Assay) Technology portfolio by introducing 46 new highly sensitive cell signaling pathway and biomarker research assay kits. The new assays provide researchers with comprehensive tools for advancing studies in cancer, inflammatory, and neurodegenerative disorders.

PerkinElmer’s AlphaScreen®SureFire® assays enable researchers to save time by providing the ability to study key biological pathways using the same sample and conditions in a single experiment. In addition, the kits simplify complex protocols, increasing the ability to automate high-throughput screening processes and assisting researchers in the transition from time-consuming Western Blot or ELISA methods.

In addition, the Company’s AlphaLISA® “No Wash” immunoassay kits enable the study of biomarkers for multiple disease states. The latest assays include human and mouse biomarker targets, significantly broadening the applicability of the ELISA-alternative ALPHA technology portfolio.

“PerkinElmer continues to make great strides with the expansion of the ALPHA Technology portfolio, based on scientific demand for alternative ways to measure cell signaling pathways and biomarkers,” said Richard M. Eglen, PhD, president, Bio-discovery, PerkinElmer. “The new kits will help open new directions in research for diseases such as cancer, Alzheimer’s, cardiovascular and inflammatory conditions.” Th PE product portal provides comlpete techncial and performance details

Applied Biosystems Debuts Industry’s First Acoustic Flow Cytometer

Applied Biosystems, part of Life Technologies Corporation announced its entry into the flow cytometry instrumentation market with the debut of the Attune™ Acoustic Focusing Cytometer, a first of its kind cytometry system designed to use sound waves to precisely control the movement of cells. The company has built upon its expertise in instrumentation, as well as its position as a long-time leading provider of flow cytometry reagents, to create a technology that will offer customers enhanced sample throughput, sensitivity and accuracy for a range of cell biology applications.

Flow cytometry allows scientists to count and examine cells by passing them through a laser-based detection device. Thousands of cells per second may be counted, allowing rapid characterization of entire populations of cells. Cellular biologists engage in flow cytometry for a rapidly growing range of applications, including the study of proteins expressed by cells (immunophenotyping), quantifying the amount of DNA in cells, cell counting, among others.

Attune enables scientists to gather statistical data on a large number of heterogeneous cells to study parameters within a cell population, including size, complexity, phenotype and health. Attune’s proprietary technology allows scientists to achieve enhanced sensitivity, saves time by increasing throughput, and can be used with small sample sizes. In addition, it offers these enhanced capabilities with a reduced footprint due to the compact acoustic technology and the far smaller volume of consumables required to perform an experiment. These unique capabilities will enable scientific applications not previously possible on traditional cytometry systems, ranging from sample preparation to bead-based analyses. Visit Life Technologies' press room for complete solution details

Genome BC collaborates with Chile and Norway to sequence salmon genome

The economically important, environmentally sensitive Atlantic salmon species will have its genome fully sequenced, thanks to an international collaboration involving researchers, funding agencies and industry from Canada, Chile and Norway. Genome BC is partnering with the Chilean Economic Development Agency, InnovaChile, Norwegian Research Council, Norwegian Fishery and Aquaculture Industry Research Fund to form the International Cooperation to Sequence the Atlantic Salmon Genome (Cooperation).

The Cooperation will invest approximately US$6 million in phase one of a multi-phased project to produce a genome sequence that identifies and maps all of the genes in the Atlantic salmon genome and can act as a reference/guide sequence for the genomes of other salmonids (e.g. Pacific salmon, rainbow trout and more distantly related fish such as smelt and pike.)

With salmonid product exports from Norway, Chile and Canada valued at US$3.4 billion, US$2.3 billion and US$0.6 billion, respectively in 2007, the sequenced genome will be an important public resource that may lead to better management of wild fish stocks, breeding selection for commercially important traits, and elements of food quality, security and traceability. Visit the Genome British Columbia portal for complete details

Oxidized Calmodulin Kinase II Regulates Conduction Following Myocardial Infarction (PLoS)

Calmodulin kinase II (CaMKII) mediates critical signaling pathways responsible for divergent functions in the heart including calcium cycling, hypertrophy and apoptosis. Dysfunction in the CaMKII signaling pathway occurs in heart disease and is associated with increased susceptibility to life-threatening arrhythmia. Furthermore, CaMKII inhibition prevents cardiac arrhythmia and improves heart function following myocardial infarction. Recently, a novel mechanism for oxidative CaMKII activation was discovered in the heart. Here, we provide the first report of CaMKII oxidation state in a well-validated, large-animal model of heart disease. Specifically, we observe increased levels of oxidized CaMKII in the infarct border zone (BZ). These unexpected new data identify an alternative activation pathway for CaMKII in common cardiovascular disease.

To study the role of oxidation-dependent CaMKII activation in creating a pro-arrhythmia substrate following myocardial infarction, we developed a new mathematical model of CaMKII activity including both oxidative and autophosphorylation activation pathways. Computer simulations using a multicellular mathematical model of the cardiac fiber demonstrate that enhanced CaMKII activity in the infarct BZ, due primarily to increased oxidation, is associated with reduced conduction velocity, increased effective refractory period, and increased susceptibility to formation of conduction block at the BZ margin, a prerequisite for reentry. Furthermore, our model predicts that CaMKII inhibition improves conduction and reduces refractoriness in the BZ, thereby reducing vulnerability to conduction block and reentry. These results identify a novel oxidation-dependent pathway for CaMKII activation in the infarct BZ that may be an effective therapeutic target for improving conduction and reducing heterogeneity in the infarcted heart. Read the full abstract or order this article via the PLoS portal

Genome-wide dynamics of replication timing revealed by in vitro models of mouse embryogenesis (Genome Research)

Differentiation of mouse embryonic stem cells (mESCs) is accompanied by changes in replication timing. To explore the relationship between replication timing and cell fate transitions, we constructed genome-wide replication-timing profiles of 22 independent mouse cell lines representing 10 stages of early mouse development, and transcription profiles for seven of these stages. Replication profiles were cell-type specific, with 45% of the genome exhibiting significant changes at some point during development that were generally coordinated with changes in transcription. Comparison of early and late epiblast cell culture models revealed a set of lineage-independent early-to-late replication switches completed at a stage equivalent to the post-implantation epiblast, prior to germ layer specification and down-regulation of key pluripotency transcription factors (POU5F1/NANOG/SOX2) and coinciding with the emergence of compact chromatin near the nuclear periphery.

These changes were conserved in all subsequent lineages and involved a group of irreversibly down-regulated genes, at least some of which were repositioned closer to the nuclear periphery. Importantly, many genomic regions of partially reprogrammed induced pluripotent stem cells (piPSCs) failed to re-establish ESC-specific replication timing and transcription programs. These regions were enriched for lineage-independent early-to-late changes, which in female cells included the inactive X-chromosome. Taken together, we demonstrate that replication-timing changes are extensive during development. Moreover, a distinct set of lineage-independent, early-to-late changes completed in and stably maintained after the post-implantation epiblast stage is difficult to reprogram and therefore coincides with an epigenetic commitment to differentiation prior to germ layer specification. Visit the Genome Research portal for complete details

Rapid and sustained nuclear–cytoplasmic ERK oscillations induced by epidermal growth factor (EMSL)

Time-lapsed video of individual breast tissue cells reveals a never-before-seen event in the life of a cell: a protein that cycles between two major compartments in the cell. The results give researchers a more complete view of the internal signals that cause breast tissue cells to grow, events that go awry in cancer and are targets of drug development.

The protein ERK, which helps cells respond to growth factors, travels back and forth between the nucleus, where genes are turned on and off, and the cell proper, where proteins work together to keep the cell functioning. In the video, individual cells pulsate with green light as an engineered fluorescent ERK fills the nucleus, exits and re-enters again in cycles that take about 15 minutes. The researchers don't know if the oscillation affects the activity of other proteins in a regulatory fashion, they report in December 1 issue of Molecular Systems Biology, but find the oscillations to be regular and robust.

"True oscillations in biology are rare," said lead author Steve Wiley, chief biologist at EMSL, located at the Department of Energy's Pacific Northwest National Laboratory. "And that the oscillations of such a major growth regulator could go undiscovered for so long is extremely surprising." Review the complete study findings via Molecular Systems Biology: