Visualizing Endogenous Synaptic Proteins in Living Neurons

The recently published method is based on the generation of disulfide-free “intrabodies”, a structure from the 10th fibronectin type III domain known as FingRs. These affinity molecules were fused to GFP for direct fluorescence miscroscopy. The FingRs do not need di-sulfite bonds and are therefore better folders in mammalian cells. Specifically, a library was screened with in vitro display to identify FingRs that bind two synaptic proteins, Gephyrin and PSD95. After the initial selection, the researchers from USC secondarily screened binders using a cellular localization assay to identify potential FingRs that bind at high affinity in an intracellular environment. As it turned out, only 10-20% of the original positive clones bind well inside the cells, suggesting this type of further screening was a critical step.

The expression of intrabody is transcriptionally regulated by the target protein through a ZFN-repressor fusion. This transcriptional control system matches the expression of the intrabody to that of the target protein regardless of the target’s expression level. This design virtually eliminates unbound FingR, resulting in very low background that allows unobstructed visualization of the target proteins. As result, the FingRs presented in this study enabled live cell visualization of excitatory and inhibitory synapses, and apparently without affecting neuronal function.

Technically, the reason to use in vitro mRNA display was required by the need to use a large library (>10exp12, beyond the limit of the more commonly used phase display) to find good binders. A similar visualization system can be established using more potent affinity domains such as the VHH single-domain antibodies that have only one, sometimes dispensable, di-sulfite bond. The VHH domain nanobodies can be more easily isolated from camelid animals. Another improvement to the visualization system can be made by using stronger, superresolution-ready FPs such as mNeonGreen or mMaple to enable single molecule imaging, which is particularly interesting for studying synapses and applied to the BRAIN initiative.

Gross et al. Neuron, June 2013, http://www.ncbi.nlm.nih.gov/pubmed/23791193

Tags: alpaca antibodies, BRAIN, FingR, fluorescent protein tag, intrabodies, mNeonGreen, nAb, nanobodies, neuron, single domain, Synapses, VHH, VHH antibodies

Allele Biotech Receives $200,000 Grant to Update Its mRNA Reprogramming Commercial Products and Services

On June 10, 2013 Allele received an SBIR award from the National Institute of Drug Abuse (NIDA/NIH) entitled “Revolutionary Technology for Efficient Derivation of Human iPSCs with Messenger RNA”. The goal of the proposed project is to provide to the biomedical research market an advanced reagent kit and services for highly efficient reprogramming of high quality human induced pluripotent stem cells (iPSCs). At the core of this kit is the Allele team’s recent development transcribed messenger RNA (mRNA). Compared to other reprogramming methods, such as lentivirus, Sendai virus, protein, small molecules or any combinations of these reagents, our new generation of the mRNA method often requires less than half the time while sometimes achieving “bulk conversion” efficiency.

While the Allele reprogramming technology was designed for clinical use as the process is feeder-free, xeno-free, chromosome integration-free, as well as without the need for cell splitting, PI, Dr. Jiwu Wang states, “Our purpose of executing the NIH-funded research it to make our method so easy that any researcher can integrate iPSC into his or her projects.” In addition to the extremely high efficiency, mRNA-generated iPSCs should also be more stable because there are no genetic alterations, more uniform among all clones as there is no clonal event, and ultimately suitable for future autologous cell therapy now that creating iPSCs from patient tissue cells should no longer be the rate-limiting steps.

Allele’s business model is to provide cGMP-grade iPSCs to pharmaceutical companies and perform large scale reprogramming by partnering first with university-affiliated hospitals. Great progress has been made in both directions, which has prompted the initiation of a cGMP unit within Allele’s newly acquired building in San Diego.

Tags: cell therapy, feeder-free, footprint free, iPSC, mRNA iPSC, pluripotent, stem cells, tissue regeneration, xeno-free

NIDA Branch Chief, Jonathan D. Pollock, Ph.D., Encourages SBIR/STTR Grants on Reagent Kits Including iPSC

“We’re interested in areas of genetics, in terms of smoking cessation, pharmacogenomics, treatment of substance abuse, and particularly right now, issues related to prescription substance abuse,” Jonathan D. Pollock, Ph.D., chief of the Genetics and Molecular Neurobiology Research Branch at NIDA’s Division of Basic Neuroscience and Behavioral Research, told GEN.

In addition to that solicitation, Dr. Pollock said, the branch is interested in supporting commercialization and development of products, resources, and services through SBIR/STTR relevant to brain research. They include protein capture reagents, proteomics, genomics, pharmacogenomics, molecular diagnostics, nanotechnology, gene delivery and viral vectors, identification of RNA and DNA sequences in formalin fixed nervous tissue, shRNA, microfluidics, epigenetics diagnostics, therapeutics, and tools to detect epigenetic modifications.

The branch is also looking to support commercialization and development of biomarkers, optogenetics, reagents for iPS and neural stem cells, technologies to uniquely barcode cell types, improved super resolution microscopy methods, in vivo gene expression imaging, automated sectioning, image acquisition and 3D reconstruction of electron micrographic sections, genetically encoded markers for electron microscopy, and “big” genomic and proteomic data, including data visualization, data contextualization, and data analysis.

“What we’re really looking for is products that you could basically commercialize coming out of research. These can be things that are either products or services. I think that there are opportunities, particularly for groups of individuals that have an idea, IP, and want to have a startup company.”

SBIR/STTR grants account for 2.8% of NIDA’s roughly $1 billion annual budget. NIDA spent $26.679 million on SBIR and STTR in fiscal year 2012, which ended September 30—up from $26.497 million in FY 2011. The number of SBIR/STTR research projects grants rose to 56 in FY 2012 from 44 a year earlier, according to the GEN article.

Allele Biotech’s CEO, Jiwu Wang, Ph.D., has worked with Dr. Pollock on a previous, VHH nanobody-related project under the NIDA SBIR program. He has just submitted a SBIR grant application based on Allele’s recently published mRNA-based reprogramming technology, after discussion with Dr. Pollock.

Tags: capture regent, iPSC, NIDA, RNAi, shRNA

The NIH is one step closer to be short of $260 million from its 2011 budget

The National Institutes of Health (NIH) 2011 budget will be cut by $260 million in the budget that the House has just passed based on the last minute pact reached last Friday to avoid federal government shut down.

The NIH’s 2011 budget will be $30.7 billion, down 0.8% from its 2010 budget of $30.9 billion, according to news releases that can be found from various sources. Previously, the President proposed a $32.1 billion budget for the NIH and the House of Representatives allocated $29.4 billion to the agency. President Obama asked for a $1 billion increase for the NIH in 2012, which will be in new debate to start immediately. Chances are the 2012 budget for the agency will be less than what the administration wanted.

Combined with “the cliff effect” from the ending of the stimulus money the NIH has epically managed since 2009 to fund extra research projects, the negative growth of the NIH budget could mean less academic positions and tighter lab budgets ahead. Cutting-edge technology and cost effectiveness will be the key for survival of the fittest in the biomedical research jungle.

Promotion of the week: Save 10% on any purchase of feeder cells. Email brianahasey@allelebiotech.com with offer code : FDST11

New Product of the week: Damage-free cloning kit for difficult cloning projects—get recombined plasmids or failed ligation? Your DNA is damaged by purification bugger and/or UV, ask us how to deal with it oligo@allelebiotech.com

Tags: 2011 budget, budget, congressional republicans, federal budget, NIH, President Obama, research budget

NIH Announces SHIFT SBIR Grants to Help Academic Researchers Get Jobs in Biotech

The National Institutes of Health (NIH) just announced a new type of Small Business Innovative Research (SBIR) grants. Called SHIFT SBIR, these grants are designed to “(1) to foster research that is translational in nature and (2) to transform academic scientific discoveries into commercial products and services,” according to the NIH announcement, and to also facilitate licensing of intellectual properties from academic institutions as well as promote better access to academic resources. The PI transitioning from the academic institution must be primarily employed by his/her research institution at the time of application and must be primarily employed (more than 50% time) by the company by or at the time of award.

One very attractive aspect of these grants is that they mean more money than standard SBIR grants. Up to $200,000 total costs per year and time periods up to 2 years may be requested for Phase I. Well-justified budgets up to $750,000 total costs per year and time periods up to 3 years may be requested for Phase II. That is sufficient for a good researcher to build a team to do research in one direction within pretty much any small company setting.

A little background about SBIR grants: SBIR programs sponsored by federal funding agencies including the NIH, NSF, DOE, FDA, the military departments, etc. have been a major source of funding for many biotech companies like Allele Biotech during their startup phases. SBIR grants can also be used to facilitate continued research and help business expansion even as the company grows. As an example of the effects of SBIR grants, Allele Biotech obtained 5 such grants from 2000 to 2003 and built a company from just ideas to one with a patent in RNAi, an out-licensing deal with Promega, a product line in oligo synthesis, and a structure that helped launch currently ~1,500 products since 2004. We then carried out 2 more SBIR contracts for the NIH from 2007 to now, which moved us into the field of special antigen production, iPS using Bacmam systems, viral packaging services, and hopefully more advanced antibodies in the pipeline.

The link to the full NIH announcement is here.

To read more blogs on SBIR related topics, click here.

The current topics of SHIFT SBIR solicitation is listed below for Allele Blog viewers’ convenience:

• Applying opportunities in genomics and other high throughput technologies to understand fundamental biology, and to uncover the causes of specific diseases
• Translating basic science discoveries into new and better treatments
• Development of diagnostics, preventative strategies and therapeutic tools
• Development and clinical evaluation of biomarkers for alcohol exposure and alcohol-induced tissue injury
• Therapeutic development for alcoholism treatment
• Diagnostic assessment and treatment of alcohol use disorders and comorbidity
• Alcohol biosensors and data analysis systems
• Prevention, diagnosis, and treatment of fetal alcohol spectrum disorder and alcohol-related birth defects
• Minimal dose post-exposure vaccine for rabies
• Immunotherapy to kill HIV-infected cells
• Asthma therapeutic vaccine
• Novel antifibrotic therapies for progressive liver failure
• Diagnostic measurement devices or methods for assessment of urinary leakage and incontinence
• Therapeutics for diabetic wound healing
• Pediatric formulations
• Robust diagnostic biosensors for infants
• mHealth tools for assessing and addressing health in children and families
• Wearable diagnostic and therapeutic devices for physiologic monitoring and interventions
• Wearable biosensors for persons with genetic sensitivity to environmental factors
• Therapeutic interventions for persons with physical and developmental disabilities
• Advancement of novel botanical therapies for effective symptom management of non-life-threatening conditions
• Development of interactive technologies to improve and expand delivery of mind/body interventions
• Discovery of improved methodology for the characterization of plants and their secondary metabolites
• Development of standardized, objective methods to assess patient adherence to specific CAM treatment interventions;
• Development of devices/tools to assess consistency and fidelity of practitioner approaches and other aspects of protocol implementation
• Virtual settings or online tools for clinician training and implementation of fidelity monitors
• Development and validation of enhanced patient-reported outcome assessment tools for CAM (e.g. new user (clinician, researcher, and/or patient/study volunteer)–friendly interfaces, methods to improve compatibility with research and health informatics systems currently in use)
• Development of measurement tools for assessing expectancy for effects of CAM mind-body medicine, acupuncture, and manual therapy interventions
• Novel technologies that enhance/track/monitor “real time” adherence to drug abuse (and HIV+) treatment regimens
• Technology to improve the efficacy of substance abuse treatment, treatment adherence, and reduce recidivism among criminally-involved patients
• Mobile and/or internet technology based treatment interventions to augment traditional substance use disorder (SUD) treatments and their outcome
• Technologies and/or devices to boost medication adherence for SUD patients
• Technology-based treatment platforms to standardize interventions and to make them more community-friendly
• Integrate item response theory and computer adaptive testing in measures of addiction liability.
• Brief screening tools to assess relapse risks in and out drug treatment settings
• Use of the internet to link community based outreach and HIV testing services to facilitate access by drug users and their sex partners in neighborhood settings.
• Development of novel therapeutics, diagnostics, and devices for treating heart, lung, blood and sleep diseases and disorders
• New or improved measures, analytical methods, and instruments for gene expression in individuals with heart, lung, blood, and sleep disorders and diseases
• Health-care systems and outcomes research, including development of new quality measures for evidence-based heart, lung, blood, and sleep health care
• Models of behavior modification and other approaches to behavior change related to heart, lung, blood, and sleep diseases and disorders
• Devices and technologies to prevent cardiac ischemia/reperfusion injury
• Vaccines for the prevention or treatment of heart, lung, and blood diseases
• Non-invasive methods to diagnose DVT and PE
• Technologies and strategies to advance cellular therapies for heart, lung and non-malignant blood diseases
• Therapies to treat hematologic diseases and cytopenic states
• Technologies for in vitro reduction, inactivation or removal of microorganisms and other infectious moieties from blood, blood components, and plasma derivatives
• Development of products, technologies and services to diagnose, treat and/or prevent skin and rheumatic diseases, muscle disorders, and joint and bone diseases

Tags: biotech industry jobs, career in biotech, NIH grants, SBIR, start up, translational research