Showing papers by "Case Western Reserve University published in 2007"

A second generation human haplotype map of over 3.1 million SNPs

Abstract: We describe the Phase II HapMap, which characterizes over 3.1 million human single nucleotide polymorphisms (SNPs) genotyped in 270 individuals from four geographically diverse populations and includes 25-35% of common SNP variation in the populations surveyed. The map is estimated to capture untyped common variation with an average maximum r2 of between 0.9 and 0.96 depending on population. We demonstrate that the current generation of commercial genome-wide genotyping products captures common Phase II SNPs with an average maximum r2 of up to 0.8 in African and up to 0.95 in non-African populations, and that potential gains in power in association studies can be obtained through imputation. These data also reveal novel aspects of the structure of linkage disequilibrium. We show that 10-30% of pairs of individuals within a population share at least one region of extended genetic identity arising from recent ancestry and that up to 1% of all common variants are untaggable, primarily because they lie within recombination hotspots. We show that recombination rates vary systematically around genes and between genes of different function. Finally, we demonstrate increased differentiation at non-synonymous, compared to synonymous, SNPs, resulting from systematic differences in the strength or efficacy of natural selection between populations.

Scientific aspects of polymer electrolyte fuel cell durability and degradation.

Abstract: Rod Borup is a Team Leader in the fuel cell program at Los Alamos National Lab in Los Alamos, New Mexico. He received his B.S.E. in Chemical Engineering from the University of Iowa in 1988 and his Ph.D. from the University of Washington in 1993. He has worked on fuel cell technology since 1994, working in the areas of hydrogen production and PEM fuel cell stack components. He has been awarded 12 U.S. patents, authored over 40 papers related to fuel cell technology, and presented over 50 oral papers at national meetings. His current main research area is related to water transport in PEM fuel cells and PEM fuel cell durability. Recently, he was awarded the 2005 DOE Hydrogen Program R&D Award for the most significant R&D contribution of the year for his team's work in fuel cell durability and was the Principal Investigator for the 2004 Fuel Cell Seminar (San Antonio, TX, USA) Best Poster Award. Jeremy Meyers is an Assistant Professor of materials science and engineering and mechanical engineering at the University of Texas at Austin, where his research focuses on the development of electrochemical energy systems and materials. Prior to joining the faculty at Texas, Jeremy workedmore » as manager of the advanced transportation technology group at UTC Power, where he was responsible for developing new system designs and components for automotive PEM fuel cell power plants. While at UTC Power, Jeremy led several customer development projects and a DOE-sponsored investigation into novel catalysts and membranes for PEM fuel cells. Jeremy has coauthored several papers on key mechanisms of fuel cell degradation and is a co-inventor of several patents. In 2006, Jeremy and several colleagues received the George Mead Medal, UTC's highest award for engineering achievement, and he served as the co-chair of the Gordon Research Conference on fuel cells. Jeremy received his Ph.D. in Chemical Engineering from the University of California at Berkeley and holds a Bachelor's Degree in Chemical Engineering from Stanford University. Bryan Pivovar received his B.S. in Chemical Engineering from the University of Wisconsin in 1994. He completed his Ph.D. in Chemical Engineering at the University of Minnesota in 2000 under the direction of Profs. Ed Cussler and Bill Smyrl, studying transport properties in fuel cell electrolytes. He continued working in the area of polymer electrolyte fuel cells at Los Alamos National Laboratory as a post-doc (2000-2001), as a technical staff member (2001-2005), and in his current position as a team leader (2005-present). In this time, Bryan's research has expanded to include further aspects of fuel cell operation, including electrodes, subfreezing effects, alternative polymers, hydroxide conductors, fuel cell interfaces, impurities, water transport, and high-temperature membranes. Bryan has served at various levels in national and international conferences and workshops, including organizing a DOE sponsored workshop on freezing effects in fuel cells and an ARO sponsored workshop on alkaline membrane fuel cells, and he was co-chair of the 2007 Gordon Research Conference on Fuel Cells. Minoru Inaba is a Professor at the Department of Molecular Science and Technology, Faculty of Engineering, Doshisha University, Japan. He received his B.Sc. from the Faculty of Engineering, Kyoto University, in 1984 and his M.Sc. in 1986 and his Dr. Eng. in 1995 from the Graduate School of Engineering, Kyoto University. He has worked on electrochemical energy conversion systems including fuel cells and lithium-ion batteries at Kyoto University (1992-2002) and at Doshisha University (2002-present). His primary research interest is the durability of polymer electrolyte fuel cells (PEFCs), in particular, membrane degradation, and he has been involved in NEDO R&D research projects on PEFC durability since 2001. He has authored over 140 technical papers and 30 review articles. Kenichiro Ota is a Professor of the Chemical Energy Laboratory at the Graduate School of Engineering, Yokohama National University, Japan. He received his B.S.E. in Applied Chemistry from the University of Tokyo in 1968 and his Ph.D. from the University of Tokyo in 1973. He has worked on hydrogen energy and fuel cells since 1974, working on materials science for fuel cells and water electrolysis. He has published more than 150 original papers, 70 review papers, and 50 scientific books. He is now the president of the Hydrogen Energy Systems Society of Japan, the chairman of the Fuel Cell Research Group of the Electrochemical Society of Japan, and the chairman of the National Committee for the Standardization of the Stationary Fuel Cells. ABSTRACT TRUNCATED« less

Adult mesenchymal stem cells for tissue engineering versus regenerative medicine.

Abstract: Adult mesenchymal stem cells (MSCs) can be isolated from bone marrow or marrow aspirates and because they are culture-dish adherent, they can be expanded in culture while maintaining their multipotency. The MSCs have been used in preclinical models for tissue engineering of bone, cartilage, muscle, marrow stroma, tendon, fat, and other connective tissues. These tissue-engineered materials show considerable promise for use in rebuilding damaged or diseased mesenchymal tissues. Unanticipated is the realization that the MSCs secrete a large spectrum of bioactive molecules. These molecules are immunosuppressive, especially for T-cells and, thus, allogeneic MSCs can be considered for therapeutic use. In this context, the secreted bioactive molecules provide a regenerative microenvironment for a variety of injured adult tissues to limit the area of damage and to mount a self-regulated regenerative response. This regenerative microenvironment is referred to as trophic activity and, therefore, MSCs appear to be valuable mediators for tissue repair and regeneration. The natural titers of MSCs that are drawn to sites of tissue injury can be augmented by allogeneic MSCs delivered via the bloodstream. Indeed, human clinical trials are now under way to use allogeneic MSCs for treatment of myocardial infarcts, graft-versus-host disease, Crohn's Disease, cartilage and meniscus repair, stroke, and spinal cord injury. This review summarizes the biological basis for the in vivo functioning of MSCs through development and aging.

Review of progress in shape-memory polymers

Abstract: Shape-memory polymers (SMPs) have attracted significant attention from both industrial and academic researchers due to their useful and fascinating functionality. This review thoroughly examines progress in shape-memory polymers, including the very recent past, achieved by numerous groups around the world and our own research group. Considering all of the shape-memory polymers reviewed, we identify a classification scheme wherein nearly all SMPs may be associated with one of four classes in accordance with their shape fixing and recovering mechanisms and as dictated by macromolecular details. We discuss how the described shape-memory polymers show great potential for diverse applications, including in the medical arena, sensors, and actuators.

Genome-wide detection and characterization of positive selection in human populations

Abstract: With the advent of dense maps of human genetic variation, it is now possible to detect positive natural selection across the human genome. Here we report an analysis of over 3 million polymorphisms from the International HapMap Project Phase 2 (HapMap2). We used 'long-range haplotype' methods, which were developed to identify alleles segregating in a population that have undergone recent selection, and we also developed new methods that are based on cross-population comparisons to discover alleles that have swept to near-fixation within a population. The analysis reveals more than 300 strong candidate regions. Focusing on the strongest 22 regions, we develop a heuristic for scrutinizing these regions to identify candidate targets of selection. In a complementary analysis, we identify 26 non-synonymous, coding, single nucleotide polymorphisms showing regional evidence of positive selection. Examination of these candidates highlights three cases in which two genes in a common biological process have apparently undergone positive selection in the same population:LARGE and DMD, both related to infection by the Lassa virus, in West Africa;SLC24A5 and SLC45A2, both involved in skin pigmentation, in Europe; and EDAR and EDA2R, both involved in development of hair follicles, in Asia.

Evolving the lock to fit the key to create a family of G protein-coupled receptors potently activated by an inert ligand

Abstract: We evolved muscarinic receptors in yeast to generate a family of G protein-coupled receptors (GPCRs) that are activated solely by a pharmacologically inert drug-like and bioavailable compound (clozapine-N-oxide) Subsequent screening in human cell lines facilitated the creation of a family of muscarinic acetylcholine GPCRs suitable for in vitro and in situ studies We subsequently created lines of telomerase-immortalized human pulmonary artery smooth muscle cells stably expressing all five family members and found that each one faithfully recapitulated the signaling phenotype of the parent receptor We also expressed a Gi-coupled designer receptor in hippocampal neurons (hM4D) and demonstrated its ability to induce membrane hyperpolarization and neuronal silencing We have thus devised a facile approach for designing families of GPCRs with engineered ligand specificities Such reverse-engineered GPCRs will prove to be powerful tools for selectively modulating signal-transduction pathways in vitro and in vivo

Relating protein pharmacology by ligand chemistry

Abstract: The identification of protein function based on biological information is an area of intense research. Here we consider a complementary technique that quantitatively groups and relates proteins based on the chemical similarity of their ligands. We began with 65,000 ligands annotated into sets for hundreds of drug targets. The similarity score between each set was calculated using ligand topology. A statistical model was developed to rank the significance of the resulting similarity scores, which are expressed as a minimum spanning tree to map the sets together. Although these maps are connected solely by chemical similarity, biologically sensible clusters nevertheless emerged. Links among unexpected targets also emerged, among them that methadone, emetine and loperamide (Imodium) may antagonize muscarinic M3, α2 adrenergic and neurokinin NK2 receptors, respectively. These predictions were subsequently confirmed experimentally. Relating receptors by ligand chemistry organizes biology to reveal unexpected relationships that may be assayed using the ligands themselves.

Global Challenge of Multidrug-Resistant Acinetobacter baumannii

Abstract: We may soon be facing the end of the “antibiotic era.” The initial and seemingly unstoppable success of antibiotics, the fruit of human ingenuity, has been countered by an escalation of resistance mechanisms in bacteria. This crisis has been described as an “unwinnable war” (www.wellcome.org). The statistics compiled as a result of surveillance efforts illustrate the emergence of many genera of bacteria that are resistant to all antibiotics (57, 60). The genus Acinetobacter epitomizes this trend and deserves close attention. Acinetobacter spp. display mechanisms of resistance to all existing antibiotic classes as well as a prodigious capacity to acquire new determinants of resistance (7). The increasing recovery in the clinic of multidrug-resistant (MDR) Acinetobacter baumannii is a frightening reality (112). This review summarizes the worldwide emergence of antibiotic-resistant A. baumannii as a nosocomial pathogen and focuses on its mechanisms of resistance against selected antibiotics. It concludes with a summary of current strategies in the treatment of MDR A. baumannii and offers perspectives on the control of this global public health threat.

The neuronal sortilin-related receptor SORL1 is genetically associated with Alzheimer disease

Abstract: The recycling of the amyloid precursor protein (APP) from the cell surface via the endocytic pathways plays a key role in the generation of amyloid beta peptide (Abeta) in Alzheimer disease. We report here that inherited variants in the SORL1 neuronal sorting receptor are associated with late-onset Alzheimer disease. These variants, which occur in at least two different clusters of intronic sequences within the SORL1 gene (also known as LR11 or SORLA) may regulate tissue-specific expression of SORL1. We also show that SORL1 directs trafficking of APP into recycling pathways and that when SORL1 is underexpressed, APP is sorted into Abeta-generating compartments. These data suggest that inherited or acquired changes in SORL1 expression or function are mechanistically involved in causing Alzheimer disease.

Interferons at age 50: past, current and future impact on biomedicine.

Abstract: The family of interferon (IFN) proteins has now more than reached the potential envisioned by early discovering virologists: IFNs are not only antivirals with a spectrum of clinical effectiveness against both RNA and DNA viruses, but are also the prototypic biological response modifiers for oncology, and show effectiveness in suppressing manifestations of multiple sclerosis. Studies of IFNs have resulted in fundamental insights into cellular signalling mechanisms, gene transcription and innate and acquired immunity. Further elucidation of the multitude of IFN-induced genes, as well as drug development strategies targeting IFN production via the activation of the Toll-like receptors (TLRs), will almost certainly lead to newer and more efficacious therapeutics. Our goal is to offer a molecular and clinical perspective that will enable IFNs or their TLR agonist inducers to reach their full clinical potential.

Predicting the Outcome of Salvage Radiation Therapy for Recurrent Prostate Cancer After Radical Prostatectomy

Abstract: Purpose An increasing serum prostate-specific antigen (PSA) level is the initial sign of recurrent prostate cancer among patients treated with radical prostatectomy. Salvage radiation therapy (SRT) may eradicate locally recurrent cancer, but studies to distinguish local from systemic recurrence lack adequate sensitivity and specificity. We developed a nomogram to predict the probability of cancer control at 6 years after SRT for PSA-defined recurrence. Patients and Methods Using multivariable Cox regression analysis, we constructed a model to predict the probability of disease progression after SRT in a multi-institutional cohort of 1,540 patients. Results The 6-year progression-free probability was 32% (95% CI, 28% to 35%) overall. Forty-eight percent (95% CI, 40% to 56%) of patients treated with SRT alone at PSA levels of 0.50 ng/mL or lower were disease free at 6 years, including 41% (95% CI, 31% to 51%) who also had a PSA doubling time of 10 months or less or poorly differentiated (Gleason grade 8 to 10) cancer. Significant variables in the model were PSA level before SRT (P .001), prostatectomy Gleason grade (P .001), PSA doubling time (P .001), surgical margins (P .001), androgen-deprivation therapy before or during SRT (P .001), and lymph node metastasis (P .019). The resultant nomogram was internally validated and had a concordance index of 0.69. Conclusion Nearly half of patients with recurrent prostate cancer after radical prostatectomy have a long-term PSA response to SRT when treatment is administered at the earliest sign of recurrence. The nomogram we developed predicts the outcome of SRT and should prove valuable for medical decision making for patients with a rising PSA level. J Clin Oncol 25:2035-2041. © 2007 by American Society of Clinical Oncology

Effectiveness of Adjunctive Antidepressant Treatment for Bipolar Depression

Abstract: �Background Episodes of depression are the most frequent cause of disability among patients with bipolar disorder. The effectiveness and safety of standard antidepressant agents for depressive episodes associated with bipolar disorder (bipolar depression) have not been well studied. Our study was designed to determine whether adjunctive antidepressant therapy reduces symptoms of bipolar depression without increasing the risk of mania. Methods In this double-blind, placebo-controlled study, we randomly assigned subjects with bipolar depression to receive up to 26 weeks of treatment with a mood stabilizer plus adjunctive antidepressant therapy or a mood stabilizer plus a matching placebo, under conditions generalizable to routine clinical care. A standardized clinical monitoring form adapted from the mood-disorder modules of the Structured Clinical Interview for the Diagnostic and Statistical Manual of Mental Disorders, fourth edition, was used at all follow-up visits. The primary outcome was the percentage of subjects in each treatment group meeting the criterion for a durable recovery (8 consecutive weeks of euthymia). Secondary effectiveness outcomes and rates of treatment-emergent affective switch (a switch to mania or hypomania early in the course of treatment) were also examined. Results Forty-two of the 179 subjects (23.5%) receiving a mood stabilizer plus adjunctive antidepressant therapy had a durable recovery, as did 51 of the 187 subjects (27.3%) receiving a mood stabilizer plus a matching placebo (P = 0.40). Modest nonsignificant trends favoring the group receiving a mood stabilizer plus placebo were observed across the secondary outcomes. Rates of treatment-emergent affective switch were similar in the two groups. Conclusions The use of adjunctive, standard antidepressant medication, as compared with the use of mood stabilizers, was not associated with increased efficacy or with increased risk of treatment-emergent affective switch. Longer-term outcome studies are needed to fully assess the benefits and risks of antidepressant therapy for bipolar disorder. (ClinicalTrials.gov number, NCT00012558.)

The Fifth Data Release of the Sloan Digital Sky Survey

Abstract: This paper describes the Fifth Data Release (DR5) of the Sloan Digital Sky Survey (SDSS). DR5 includes all survey quality data taken through 2005 June and represents the completion of the SDSS-I project (whose successor, SDSS-II, will continue through mid-2008). It includes five-band photometric data for 217 million objects selected over 8000 deg^2 and 1,048,960 spectra of galaxies, quasars, and stars selected from 5713 deg^2 of that imaging data. These numbers represent a roughly 20% increment over those of the Fourth Data Release; all the data from previous data releases are included in the present release. In addition to "standard" SDSS observations, DR5 includes repeat scans of the southern equatorial stripe, imaging scans across M31 and the core of the Perseus Cluster of galaxies, and the first spectroscopic data from SEGUE, a survey to explore the kinematics and chemical evolution of the Galaxy. The catalog database incorporates several new features, including photometric redshifts of galaxies, tables of matched objects in overlap regions of the imaging survey, and tools that allow precise computations of survey geometry for statistical investigations.

Correlation of the highest-energy cosmic rays with nearby extragalactic objects.

Abstract: Using data collected at the Pierre Auger Observatory during the past 3.7 years, we demonstrate that there is a correlation between the arrival directions of cosmic rays with energy above {approx} 6 x 10{sup 19} eV and the positions of active galactic nuclei (AGN) lying within {approx} 75 Mpc. We reject the hypothesis of an isotropic distribution of these cosmic rays at over 99% confidence level from a prescribed a priori test. The correlation we observe is compatible with the hypothesis that the highest energy particles originate from nearby extragalactic sources whose flux has not been significantly reduced by interaction with the cosmic background radiation. AGN or objects having a similar spatial distribution are possible sources.

Surgical versus Nonsurgical Treatment for Lumbar Degenerative Spondylolisthesis

Abstract: We enrolled 304 patients in the randomized cohort and 303 in the observational cohort. The baseline characteristics of the two cohorts were similar. The one-year crossover rates were high in the randomized cohort (approximately 40% in each direction) but moderate in the observational cohort (17% crossover to surgery and 3% crossover to nonsurgical care). The intention-to-treat analysis for the randomized cohort showed no statistically significant effects for the primary outcomes. The as-treated analysis for both cohorts combined showed a significant advantage for surgery at 3 months that increased at 1 year and diminished only slightly at 2 years. The treatment effects at 2 years were 18.1 for bodily pain (95% confidence interval [CI], 14.5 to 21.7), 18.3 for physical function (95% CI, 14.6 to 21.9), and −16.7 for the Oswestry Disability Index (95% CI, −19.5 to −13.9). There was little evidence of harm from either treatment. CONCLUSIONS In nonrandomized as-treated comparisons with careful control for potentially confounding baseline factors, patients with degenerative spondylolisthesis and spinal stenosis treated surgically showed substantially greater improvement in pain and function during a period of 2 years than patients treated nonsurgically. (ClinicalTrials. gov number, NCT00000409.)

Underdiagnosis of hypertension in children and adolescents

Abstract: ContextPediatric hypertension is increasing in prevalence with the pediatric obesity epidemic. Diagnosis of hypertension in children is complicated because normal and abnormal blood pressure values vary with age, sex, and height and are therefore difficult to remember.ObjectivesTo determine the frequency of undiagnosed hypertension and prehypertension and to identify patient factors associated with this underdiagnosis.Design, Setting, and ParticipantsA cohort study of 14 187 children and adolescents aged 3 to 18 years who were observed at least 3 times for well-child care between June 1999 and September 2006 in the outpatient clinics in a large academic urban medical system in northeast Ohio. For children and adolescents who met criteria for hypertension or prehypertension at 3 or more well-child care visits, the proportion with a hypertension-related International Classification of Diseases, Ninth Revision code in the diagnoses list, problem list, or past medical history list of any visit was determined.Main Outcome MeasuresProportion of children and adolescents with 3 or more elevated age-adjusted and height-adjusted blood pressure measurements at well-child care visits and with a diagnosis of hypertension or prehypertension documented in the electronic medical record. Multivariate logistic regression identified patient factors associated with a correct diagnosis.ResultsOf 507 children and adolescents (3.6%) who had hypertension, 131 (26%) had a diagnosis of hypertension or elevated blood pressure documented in the electronic medical record. Patient factors that increased the adjusted odds of a correct diagnosis were a 1-year increase in age over age 3 (odds ratio [OR], 1.09; 95% confidence interval [CI], 1.03-1.16), number of elevated blood pressure readings beyond 3 (OR, 1.77; 95% CI, 1.21-2.57), increase of 1% in height-for-age percentile (OR, 1.02; 95% CI, 1.01-1.03), having an obesity-related diagnosis (OR, 2.61; 95% CI, 1.49-4.55), and number of blood pressure readings in the stage 2 hypertension range (OR, 1.68; 95% CI, 1.29-2.19). Of 485 children and adolescents (3.4%) who had prehypertension, 55 (11%) had an appropriate diagnosis documented in the electronic medical record. Patient factors that increased the adjusted odds of being diagnosed with prehypertension included a 1-year increase in age over age 3 (OR, 1.21; 95% CI, 1.09-1.34) and number of elevated blood pressure readings beyond 3 (OR, 3.07; 95% CI, 2.20-4.28).ConclusionsHypertension and prehypertension were frequently undiagnosed in this pediatric population. Patient age, height, obesity-related diagnoses, and magnitude and frequency of abnormal blood pressure readings all increased the odds of diagnosis.

Non-coding RNAs: lessons from the small nuclear and small nucleolar RNAs

Abstract: Recent advances have fuelled rapid growth in our appreciation of the tremendous number, diversity and biological importance of non-coding (nc)RNAs. Because ncRNAs typically function as ribonucleoprotein (RNP) complexes and not as naked RNAs, understanding their biogenesis is crucial to comprehending their regulation and function. The small nuclear and small nucleolar RNPs are two well studied classes of ncRNPs with elaborate assembly and trafficking pathways that provide paradigms for understanding the biogenesis of other ncRNPs.

Hydroxyl radical-mediated modification of proteins as probes for structural proteomics.

Abstract: ion of hydrogen from the γ-(C-4) carbon of aliphatic side chains in the presence of oxygen can yield C-2 -C-3 dehydropeptides, via the formation of peroxyl radicals from the γ-carbon-centered radical. 208,210 For example, in the oxidation of the Glu side chain, the γ-carbon peroxyl radical may undergo subsequent reactions leading to the formation of side chain modification products with a mass shift of -30 Da due to decarboxylation; 209,211+14 and+16 Da products; or an unsaturated product, a C-2 -C-3 dehydropeptide (Scheme 4). The dehydropeptide behaves like an oxygenated enol species, which readily undergoes tautomerism to the keto form. This species is easily hydrolyzed to yield two protein fragments: a new amide and a keto acid. 210 Oxidation of aspartic acid seems similar to the case of Glu and may also result in the cleavage of the protein backbone 212 or decarboxylation of a side chain carboxyl group, 211 except at a lower rate than that for Glu. 211 3.2.4. Main Chain Cleavage via Radical Transfer from the â-Carbon at Side Chains Initial hydroxyl radical attack at theâ-carbon (C-3) position can lead to the formation of R-carbon radicals and subsequent main chain rupture. 213,214 In this case, alkoxyl radicals are generated after initial H-abstraction to produce carbon-centered radicals and subsequent reaction with O 2 o give peroxyl radicals (Scheme 5). A number of different pathways may generate alkoxyl radical from different precursors, including termination reactions of the peroxyl species with other radicals and decomposition of the intermediate hydroperoxides. 215,216The alkoxyl radicals can undergoâ-scission at a rate >107 s-1, leading to the loss of a side chain and/or generation of R-carbon radicals and subsequent backbone cleavage. 213,214 The â-scission reaction of alkoxyl radicals appears to be common for aliphatic side chains such as Val, Leu, and Asp,214 resulting in the release of a family of carbonyls including formaldehyde, acetone, isobutyraldehyde, and glyoxylic acids. The rate of suchâ-scission reactions is affected by the nature of the substituents, R and R ′, with the rate of fragmentation increased by the presence of electron releasing alkyl groups and substituents that can stabilize the incipient radical center. The R-carbon radicals generated by the â-scission reaction of alkoxyl radicals are stable due to the delocalization of unpaired electrons onto the neighboring carbonyl and amide functions and relief of steric strain in the alkoxyl radical. 217 Scheme 3. Backbone Cleavage and Side Chain Modification of Pro Hydroxyl Radical-Mediated Modification of Proteins Chemical Reviews, 2007, Vol. 107, No. 8 3527

MicroRNA inhibition of translation initiation in vitro by targeting the cap-binding complex eIF4F

Abstract: MicroRNAs (miRNAs) play an important role in gene regulatory networks in animals. Yet, the mechanistic details of their function in translation inhibition or messenger RNA (mRNA) destabilization remain controversial. To directly examine the earliest events in this process, we have developed an in vitro translation system using mouse Krebs-2 ascites cell-free extract that exhibits an authentic miRNA response. We show here that translation initiation, specifically the 5' cap recognition process, is repressed by endogenous let-7 miRNAs within the first 15 minutes of mRNA exposure to the extract when no destabilization of the transcript is observed. Our results indicate that inhibition of translation initiation is the earliest molecular event effected by miRNAs. Other mechanisms, such as mRNA degradation, may subsequently consolidate mRNA silencing.

Forecasting the Effects of Global Warming on Biodiversity

Abstract: The demand for accurate forecasting of the effects of global warming on biodiversity is growing, but current methods for forecasting have limitations. In this article, we compare and discuss the different uses of four forecasting methods: (1) models that consider species individually, (2) niche-theory models that group species by habitat (more specifically, by environmental conditions under which a species can persist or does persist), (3) general circulation models and coupled ocean–atmosphere–biosphere models, and (4) species–area curve models that consider all species or large aggregates of species. After outlining the different uses and limitations of these methods, we make eight primary suggestions for improving forecasts. We find that greater use of the fossil record and of modern genetic studies would improve forecasting methods. We note a Quaternary conundrum: While current empirical and theoretical ecological results suggest that many species could be at risk from global warming, during t...

Unphosphorylated STAT3 accumulates in response to IL-6 and activates transcription by binding to NFκB

Abstract: Signal transducer and activator of transcription 3 (STAT3), one of seven STAT family members, is activated in response to interleukin-6 (IL-6) (Akira et al. 1994). Many cytokines use the common gp130 receptor to activate the phosphorylation of STAT3 on tyrosine residue 705, leading to the formation of dimers through reciprocal phosphotyrosine–SH2 domain interactions. Several growth factors also stimulate STAT3 activation. STAT3 dimers bind to specific γ-interferon activation sequence (GAS) elements (TTCNNNGAA) in the promoters of the induced genes (Seidel et al. 1995). Constitutive activation of STAT3 is observed in many types of tumors. Thus, STAT3 is an oncogene, promoting cell proliferation and survival (Haura et al. 2005; Hodge et al. 2005). STAT3 is persistently phosphorylated in many human cancer cell lines and primary tumors, including hepatocellular carcinomas, breast cancers, prostate cancers, and head and neck cancers, and also in several hematological malignancies. Furthermore, STAT3 is necessary for v-src-induced transformation, and a constitutively active mutant of STAT3 can transform fibroblasts in cooperation with other transcription factors (Joo et al. 2004). Genes encoding proteins that regulate cell survival, including Bcl-2, Bcl-xL, mcl-1, and Fas, are direct targets of STAT3, as are genes encoding the cell cycle regulatory proteins cyclin D1, cyclin E1, and p21. In addition, other transcription factors, including c-Myc, c-Jun, and c-Fos, are themselves STAT3 targets (Hirano et al. 2000). STAT3 also functions as a transcriptional repressor of p53 expression: Blocking STAT3 in cancer cells up-regulates the expression of p53, leading to p53-mediated apoptosis (Niu et al. 2005). Major mechanisms of STAT3 activation in tumor cells are autocrine production of IL-6 and paracrine activation by IL-6 from stroma and infiltrating inflammatory cells. Indeed, circulating IL-6 levels are usually high in cancer patients (Giannitrapani et al. 2002). STAT3 activation provides an important link between inflammation and cancer. For example, Tebbutt et al. (2002) generated gp130757F/F mice, which carry a Y757F point mutation that disrupts the binding of the negative regulators SOCS3 and SHP2 to gp130. As a result, these mice show hyperactivation of STAT3, resulting in chronic gastric inflammation and distal stomach tumors. There are several reports that STAT3 and NF-κB interact with each other (Battle and Frank 2002). For example, Hagihara et al. (2005) demonstrated that STAT3 forms a complex with the p65 subunit of NFκB following stimulation of cells with IL-1 plus IL-6, and that the bound STAT3 interacts with nonconsensus sequences near the κB element of the SAA promoter. Moreover, they showed that a complex that includes STAT3, p65, and p300 is essential for the synergistic induction of the SAA gene by IL-1 plus IL-6. Yu et al. (2002) reported a physical and functional interaction between STAT3 and p65 that inhibits transcriptional activation of the iNOS gene. Yoshida et al. (2004) showed that STAT3 and p65 physically interact in vivo and that p65 homodimers can cooperate with unphosphorylated STAT3 (U-STAT3) when bound to a specific type of κB motif. Reciprocally, this interaction appears to inhibit the function of GAS-binding sites for STAT3. In contrast, the p50 subunit of NFκB can cooperate with phosphorylated STAT3 (P-STAT3) bound to GAS sites (Yoshida et al. 2004). Previous work from this laboratory has shown that STAT1 can drive gene expression even in the absence of tyrosine phosphorylation. For example, Chatterjee-Kishore et al. (2000) showed that unphosphorylated STAT1 binds to IRF1, forming a complex that activates a half GAS-half ICS element in the LMP2 promoter. In the case of STAT3, our recent work (Yang et al. 2005) showed that its high-level expression drives the transcription of many genes in the complete absence of tyrosine phosphorylation, a function quite distinct from the role of P-STAT3 in driving inducible gene expression. This activity of STAT3 is likely to have important physiological functions, since the STAT3 gene has a GAS element that drives a major increase in the concentration of STAT3 protein in response to signal-dependent tyrosine phosphorylation of STAT3 (Kojima et al. 1996; Narimatsu et al. 2001). We now address the mechanism through which U-STAT3 regulates gene expression, showing that, for many genes, it does so through its ability to interact with NFκB. To understand how U-STAT3 functions, we expressed the Y705F mutant of STAT3, which cannot be phosphorylated on residue 705, at a high level in untransformed human mammary epithelial hTERT-HME1 cells and used coimmunoprecipitation and chromatin immunoprecipitation (ChIP) assays to identify cofactors and DNA elements to which Y705F-STAT3 binds. Our data reveal that Y705F-STAT3 forms a complex with unphosphorylated NFκB (U-NFκB), binding to the κB elements of promoters, such as that of the RANTES (CCL5) gene, to induce their transcription.