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News Article | April 25, 2017
Site: www.prnewswire.com

"I am excited for this opportunity and look forward to working with the i2 team as we seek to optimize the value of the Company's unique and proprietary suite of transformative technologies and assets.  The breadth of i2's cutting edge discovery technologies allows me to utilize my antibody experience as well as the chance to forge new collaborations outside this space as well," Mr. Kubik added. Mark has extensive experience in the biopharmaceutical industry as a business development executive in roles of increasing impact in bioscience and drug discovery and development.  He has led negotiation of transformative and award-winning technology and product partnerships for leading therapeutics companies including global co-development agreements on behalf of Abgenix (now Amgen) with Immunex for Vectibix® (panitumab), on behalf of Seattle Genetics with Takeda for Adcetris® (brentuximab vedotin) and on behalf of MacroGenics with Gilead.  Mark graduated cum laude from the University of Colorado-Boulder (CU) in Molecular, Cellular and Developmental Biology (MCDB) and also holds an MBA in Finance from CU. About i2 Pharmaceuticals i2 Pharmaceuticals is a biopharmaceutical company focused on next generation discovery and development of  therapeutics with a focus on personalized cancer treatment.  i2 is unique in that it generates its pipeline of product candidates from its proprietary suite of transformative technologies including small molecules, antibodies and nucleic acid based therapeutics.  We are innovators coupling the power of cutting edge discovery technologies with ground breaking diagnostics to accelerate the development of more effective, safer therapeutics.  For more information please visit http://www.i2pharma.com. To view the original version on PR Newswire, visit:http://www.prnewswire.com/news-releases/i2-pharmaceuticals-appoints-chief-business-officer-300445633.html


News Article | November 23, 2016
Site: www.eurekalert.org

A biologist, an engineer and a computer scientist are among the newest members of the prestigious organization Three UC Santa Barbara faculty members have been elected to the American Association for the Advancement of Science (AAAS) for 2016. Biologist Kathleen Foltz, engineer Kaustav Banerjee and computer scientist Divyakant Agrawal have each been named fellows of the prestigious organization. Election as an AAAS Fellow is an honor bestowed upon AAAS members by their peers. The UCSB professors join 388 other newly elected members to AAAS for 2016. "It is a special honor to congratulate three of our colleagues on their election to the American Association for the Advancement of Science," said UCSB Chancellor Henry T. Yang. "Professors Agrawal, Banerjee, and Foltz join the ranks of distinguished fellows at one of the world's foremost scientific societies -- one with a strong tradition of promoting collaboration, defending scientific freedom, encouraging scientific responsibility and supporting scientific education. "This prestigious honor highlights their pioneering contributions, as recognized by peers in the same fields. We are immensely proud and honored to have them as scientific leaders and colleagues on our campus." Foltz, a professor in UCSB's Department of Molecular, Cellular and Developmental Biology, was cited among her peers in the association's section on biological sciences "for distinguished contributions to the developmental and cell biology of fertilization and egg activation, and in mentoring, outreach, education and undergraduate research in STEM fields." Foltz's research focuses on molecular- and cellular-level activity and signaling at the moment of fertilization and oocyte activation. She has been named a Searle Scholar and a National Science Foundation Faculty Fellow. She also is the recipient of UCSB's Plous Award, the Chancellor's Award for contributions to undergraduate research and the Distinguished Teaching Award. Foltz also holds an appointment at UCSB's Marine Science Institute, and is interim dean of the campus's College of Creative Studies. A professor in the Department of Electrical and Computer Engineering, Banerjee was recognized in AAAS's section on engineering "for distinguished contributions to nanoelectronics, particularly for pioneering devices and interconnects with nanomaterials, and innovating circuit and chip design concepts, all advancing toward ultra-energy-efficient electronics." The director of UCSB's Nanoelectronics Research Lab, Banerjee's research interests include nanometer-scale issues in complementary metal-oxide-semiconductor very large-scale integrated circuits as well as emerging nanotechnology. A fellow of the American Physical Society and the Institute of Electrical and Electronics Engineers (IEEE), he is the recipient of the IEEE Kiyo Tomiyasu Award and the Friedrich Wilhelm Bessel Research Award from the Humboldt Foundation. Banerjee is also affiliated with the California Nanosystems Institute and the Institute for Energy Efficiency at UCSB. Agrawal's "contributions to the design and development of scalable fault-tolerant infrastructures for large scale data and information" were cited by AAAS in its section on information, computing and communication. A professor of computer science, Agrawal focuses his research in the areas of database systems, distributed computing, data warehousing and large-scale information systems. His current interests include scalable data management and data analysis in cloud computing environments, and security and privacy of data in the cloud. Agrawal is a fellow of the Association of Computing Machinery and of the IEEE. He is the recipient of Best Paper awards from IEEE and serves on editorial boards of several journals and publications. He also is the recipient of a UCSB Graduate Mentor Award and is the director of Engineering Computing Infrastructure at UCSB's College of Engineering. Foltz, Banerjee and Agrawal will be presented with official certificates and gold and blue (representing science and engineering, respectively) rosette pins on Saturday, Feb. 18, during the 2017 AAAS Annual Meeting in Boston, Mass.


News Article | October 31, 2016
Site: www.eurekalert.org

October 31, 2016 Putting the squeeze on mitochondria: The final cut A new University of Colorado Boulder study shows for the first time the final stages of how mitochondria, the sausage-shaped, power-generating organelles found in nearly all living cells, regularly divide and propagate. In 2011, CU Boulder Associate Professor Gia Voeltz and her colleagues surprisingly found that endoplasmic reticulum (ER), another cell organelle, branches through cytoplasm like a spider web, wrapping around other organelles including mitochondria. They discovered that once an ER tentacle touches a single mitochondrion and initiates constriction, a cell protein called a dynamin-related protein, or Drp1, is recruited to further constrict the mitochondria at the spot of ER contact. Here is the new twist: Voeltz's team has now shown that once the squeeze is on the mitochondria by the Drp1 protein, a second protein - called Dynamin-2, or Dyn2 - is recruited to finish the job in a process called fission, splitting the organelle in two. Shaped like tiny springs, the dynamin proteins encircle the mitochondria and squeeze, somewhat like a person squeezing and twisting an elongated balloon into two halves. Both proteins are required for mitochondrial fission to occur since Drp1 is only strong enough to squeeze the mitochondria down to a certain size, and Dyn2 can only finish what Drp1 started after the constriction band is sufficiently shrunk. "Our findings change what everyone has believed about mitochondrial division," said postdoctoral fellow Jason Lee, first author on the study. "Now we know that it takes at least three different constriction steps in order to ultimately divide mitochondria." A paper on the subject was published online in Nature on Oct. 31. In addition to Voeltz and Lee, other CU Boulder paper contributors include postdoctoral fellow Laura Westrate, graduate student Haoxi Wu and researcher Cynthia Page. All study authors are in the Department of Molecular, Cellular and Developmental Biology. Floating around in almost all living cells, mitochondria vary in number from dozens to several thousand. Muscle cells, for example, have large numbers of mitochondria because of their high energy needs. New mitochondria are created when cells signal the need for more energy. Mitochondria also carry a small amount of DNA material passed down maternally. Mitochondria are important for a host of reasons. They generate energy in cells, they can play a role in longevity and they are crucial for blood sugar maintenance and fat loss. Damaged mitochondria can cause problems in cells of the brain, liver, heart, skeletal muscles and respiratory systems. The new study was funded by grants from the National Institutes of Health. The study results are important because a better understanding of mitochondrial division is a step closer to understanding what might change in cells under pathological conditions like cancer, said Wu. "The ability of our cells to efficiently convert nutrients into energy is rooted in the cell's ability to manage the shape, number and positioning of mitochondria through a balance of fusion and division," said Lee. "This balance goes awry in cancer and neurodegeneration."


News Article | November 1, 2016
Site: www.sciencedaily.com

A new University of Colorado Boulder study shows for the first time the final stages of how mitochondria, the sausage-shaped, power-generating organelles found in nearly all living cells, regularly divide and propagate. In 2011, CU Boulder Associate Professor Gia Voeltz and her colleagues surprisingly found that endoplasmic reticulum (ER), another cell organelle, branches through cytoplasm like a spider web, wrapping around other organelles including mitochondria. They discovered that once an ER tentacle touches a single mitochondrion and initiates constriction, a cell protein called a dynamin-related protein, or Drp1, is recruited to further constrict the mitochondria at the spot of ER contact. Here is the new twist: Voeltz's team has now shown that once the squeeze is on the mitochondria by the Drp1 protein, a second protein -- called Dynamin-2, or Dyn2 -- is recruited to finish the job in a process called fission, splitting the organelle in two. Shaped like tiny springs, the dynamin proteins encircle the mitochondria and squeeze, somewhat like a person squeezing and twisting an elongated balloon into two halves. Both proteins are required for mitochondrial fission to occur since Drp1 is only strong enough to squeeze the mitochondria down to a certain size, and Dyn2 can only finish what Drp1 started after the constriction band is sufficiently shrunk. "Our findings change what everyone has believed about mitochondrial division," said postdoctoral fellow Jason Lee, first author on the study. "Now we know that it takes at least three different constriction steps in order to ultimately divide mitochondria." A paper on the subject was published online in Nature on Oct. 31. In addition to Voeltz and Lee, other CU Boulder paper contributors include postdoctoral fellow Laura Westrate, graduate student Haoxi Wu and researcher Cynthia Page. All study authors are in the Department of Molecular, Cellular and Developmental Biology. Floating around in almost all living cells, mitochondria vary in number from dozens to several thousand. Muscle cells, for example, have large numbers of mitochondria because of their high energy needs. New mitochondria are created when cells signal the need for more energy. Mitochondria also carry a small amount of DNA material passed down maternally. Mitochondria are important for a host of reasons. They generate energy in cells, they can play a role in longevity and they are crucial for blood sugar maintenance and fat loss. Damaged mitochondria can cause problems in cells of the brain, liver, heart, skeletal muscles and respiratory systems. The new study was funded by grants from the National Institutes of Health. The study results are important because a better understanding of mitochondrial division is a step closer to understanding what might change in cells under pathological conditions like cancer, said Wu. "The ability of our cells to efficiently convert nutrients into energy is rooted in the cell's ability to manage the shape, number and positioning of mitochondria through a balance of fusion and division," said Lee. "This balance goes awry in cancer and neurodegeneration."


News Article | February 23, 2017
Site: www.eurekalert.org

A potentially life-saving treatment for sepsis has been under our noses for decades in the non-steroidal anti-inflammatory drugs (NSAIDs) most people have in their medicine cabinets, a new University of Colorado Boulder study suggests. Each year more than 1 million people in the United States contract sepsis, an overwhelming immune response to infection. It kills as many as half of those who contract it, sometimes within days, according to the National Institutes of Health. As the number of cases rises, particularly in intensive care units, pharmaceutical companies have been scrambling to develop a drug to combat the condition. "NSAIDS like ibuprofen and aspirin are among the most prevalent pharmaceuticals worldwide, with over 30 billion doses taken annually in the United States alone. But their precise mechanisms of action are not entirely understood," said Hang Hubert Yin, a biochemistry professor at CU Boulder's BioFrontiers Institute and lead author of the new paper, published today in Cell Chemical Biology. "We provide the first evidence for a novel mechanism of action for NSAIDS, one we believe could have a direct impact on people's lives." Researchers have long known that NSAIDs work in part by inhibiting an enzyme called cyclooxygenase (COX). They've also known that these NSAIDs can come with serious side effects. Some NSAIDs have been removed from the market after showing they boosted risk of heart attack and stroke. But Yin's research found that a subgroup of NSAIDs also act strongly and independently on another family of enzymes, caspases, which reside deep within the cell and have recently been found to play a key role in aggressive immune responses, like sepsis. "For instance, some chemicals derived from bacteria actually penetrate the cell and trigger the caspase response, prompting the cell to commit suicide. This also is known as apoptosis," said Yin. "Such activation, in turn, potentially causes inflammation." After the disappointing failure of late-stage clinical trials of anti-sepsis drugs targeting an immune receptor called toll-like receptor 4 (TLR4), located on the surface of cells, Yin and other scientists began to wonder if the key to halting the disease was to develop an antiseptic therapy that simultaneously targets caspases. As a first step, his team screened 1,280 existing FDA-approved drugs for caspase-inhibiting activity. Of the 27 that lit up, half were NSAIDs. NSAIDs also comprised eight of the top 10 most potent caspase inhibitors. "It was a complete surprise," said Yin. He and study co-author Ding Xue, a professor in the department of Molecular Cellular and Developmental Biology, then used biochemical and biophysical assays in the lab, as well as experiments with roundworms to test the theory further. "We showed that NSAIDs were effective in delaying cell death in worms, presumably by blocking caspase activity." It remains questionable whether existing NSAIDs, perhaps in higher doses, could be used to treat sepsis. The risk of side effects may be too great, said Yin. But he is already working on follow-up studies looking at whether new sepsis drugs could be developed combining caspase-inhibiting NSAIDS and TLR4 inhibitors. NSAIDs could also potentially be repurposed to address other conditions, including rheumatoid arthritis and neuro-degenerative diseases. "To think about the wide potential applications of these NSAID drugs is very exciting," Yin said. He hopes the research will also help scientists better understand why NSAIDs cause serious side effects like liver, kidney and cardiovascular problems, so they can develop safer next-generations versions. The National Institutes of Health funded the study.


Paz I.,Technion - Israel Institute of Technology | Kosti I.,Technion - Israel Institute of Technology | Ares Jr. M.,Cellular and Developmental Biology | Cline M.,Center for Biomolecular Science and Engineering | Mandel-Gutfreund Y.,Technion - Israel Institute of Technology
Nucleic Acids Research | Year: 2014

Regulation of gene expression is executed in many cases by RNA-binding proteins (RBPs) that bind to mRNAs as well as to non-coding RNAs. RBPs recognize their RNA target via specific binding sites on the RNA. Predicting the binding sites of RBPs is known to be a major challenge. We present a new webserver, RBPmap, freely accessible through the website http://rbpmap.technion.ac.il/ for accurate prediction and mapping of RBP binding sites. RBPmap has been developed specifically for mapping RBPs in human, mouse and Drosophila melanogaster genomes, though it supports other organisms too. RBPmap enables the users to select motifs from a large database of experimentally defined motifs. In addition, users can provide any motif of interest, given as either a consensus or a PSSM. The algorithm for mapping the motifs is based on a Weighted-Rank approach, which considers the clustering propensity of the binding sites and the overall tendency of regulatory regions to be conserved. In addition, RBPmap incorporates a position-specific background model, designed uniquely for different genomic regions, such as splice sites, 5' and 3' UTRs, non-coding RNA and intergenic regions. RBPmap was tested on high-throughput RNA-binding experiments and was proved to be highly accurate. © 2014 The Author(s).


McManus C.J.,University of Connecticut Health Center | McManus C.J.,Carnegie Mellon University | Coolon J.D.,Cellular and Developmental Biology | Eipper-Mains J.,University of Connecticut Health Center | And 2 more authors.
Genome Research | Year: 2014

The proteome expanding effects of alternative pre-mRNA splicing have had a profound impact on eukaryotic evolution. The events that create this diversity can be placed into four major classes: exon skipping, intron retention, alternative 59 splice sites, and alternative 39 splice sites. Although the regulatory mechanisms and evolutionary pressures among alternative splicing classes clearly differ, how these differences affect the evolution of splicing regulation remains poorly characterized. We used RNA-seq to investigate splicing differences in D. simulans, D. sechellia, and three strains of D. melanogaster. Regulation of exon skipping and tandem alternative 39 splice sites (NAGNAGs) were more divergent than other splicing classes. Splicing regulation was most divergent in frame-preserving events and events in noncoding regions. We further determined the contributions of cis- and trans-acting changes in splicing regulatory networks by comparing allele-specific splicing in F1 interspecific hybrids, because differences in allele-specific splicing reflect changes in cis-regulatory element activity. We find that species-specific differences in intron retention and alternative splice site usage are primarily attributable to changes in cis-regulatory elements (median ~80% cis), whereas species-specific exon skipping differences are driven by both cis- and trans-regulatory divergence (median ~50% cis). These results help define the mechanisms and constraints that influence splicing regulatory evolution and show that networks regulating the four major classes of alternative splicing diverge through different genetic mechanisms. We propose a model in which differences in regulatory network architecture among classes of alternative splicing affect the evolution of splicing regulation. © 2014 Nagarajan et al.


Chapnick D.A.,Cellular and Developmental Biology | Warner L.,Cellular and Developmental Biology | Bernet J.,University of Colorado at Boulder | Rao T.,Cellular and Developmental Biology | Liu X.,Cellular and Developmental Biology
Cell and Bioscience | Year: 2011

The TGFβ and Ras-MAPK pathways play critical roles in cell development and cell cycle regulation, as well as in tumor formation and metastasis. In the absence of cellular transformation, these pathways operate in opposition to one another, where TGFβ maintains an undifferentiated cell state and suppresses proliferation, while Ras-MAPK pathways promote proliferation, survival and differentiation. However, in colorectal and pancreatic cancers, the opposing pathways' mechanisms are simultaneously activated in order to promote cancer progression and metastasis. Here, we highlight the roles of the TGFβ and Ras-MAPK pathways in normal and malignant states, and provide an explanation for how the concomitant activation of these pathways drives tumor biology. Finally, we survey potential therapeutic targets in these pathways. © 2011 Chapnick et al; licensee BioMed Central Ltd.


Warren C.M.,Cellular and Developmental Biology | Iruela-Arispe M.L.,Cellular and Developmental Biology | Iruela-Arispe M.L.,Molecular Biology Institute | Iruela-Arispe M.L.,University of California at Los Angeles
Current Opinion in Hematology | Year: 2010

PURPOSE OF REVIEW: In this mini-review, we have highlighted the recent breakthroughs in growth factor signaling that have made conceptual changes in our understanding of how blood vessels are formed. RECENT FINDINGS: Studies conducted over the past few years have focused on understanding the cell biology of vascular morphogenesis. The major themes include characterization of the different cell types that comprise a vascular sprout, as well as the regulatory influence of cell-cell and cell-matrix interactions on signaling outcomes. In addition, novel trends have emerged, including nonconventional ways in which vascular endothelial growth factor contributes to cell survival and metabolic balance. SUMMARY: The growth of new capillary sprouts from a preexisting vascular network requires a highly coordinated cellular response to both growth factors and morphogens. This response is sensed and triggered by cell surface receptors responsible for the activation of an intracellular cascade that efficiently initiates migration and proliferation programs. While the molecular players that coordinate these effects have been identified, recent findings have expanded our understanding of how context, in particular cell-cell and cell-matrix interactions, affects endothelial cell responses to growth factors. © 2010 Lippincott Williams & Wilkins, Inc.


Liu Y.,Cellular and Developmental Biology
Plant signaling & behavior | Year: 2013

Calreticulin (CRT) is a highly conserved chaperone-like lectin that regulates Ca(2+) homeostasis and participates in protein quality control in the endoplasmic reticulum (ER). Most of our CRT knowledge came from mammalian studies, but our understanding of plant CRTs is limited. Many plants contain more than two CRTs that form two distinct groups: CRT1/CRT2 and CRT3. Previous studies on plant CRTs were focused on their Ca(2+)-binding function, but recent studies revealed a crucial role for the Arabidopsis CRT3 in ER retention of a mutant brassinosteroid receptor, brassinosteroid-insensitive 1-9 (bri1-9) and in complete folding of a plant immunity receptor EF-Tu Receptor (EFR). However, little is known about the molecular basis of the functional specification of the CRTs. We have recently shown that the C-terminal domain of CRT3, which is rich in basic residues, is essential for retaining bri1-9 in the ER; however, its role in assisting EFR folding has not been studied. Here, we used an insertional mutant of CRT3, ebs2-8 (EMS mutagenized bri1 suppressor 2-8), in the bri1-9 background as a genetic system to investigate the functional importance of two basic residue clusters in the CRT3's C-terminal domain. Complementation experiments of ebs2-8 bri1-9 with mutant CRT3(M) transgenes showed that a highly conserved basic tetrapeptide Arg(392)Arg (393)Arg(394)Lys(395) is essential but a less conserved basic tetrapeptide Arg(401)Arg(402)Arg(403)Arg(404) is dispensable for the quality control function of CRT3 that retains bri1-9 in the ER and facilitates the complete folding of EFR.

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