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Sample records for molecular signature multiplicity

  1. Systems Analysis of Immunity to Influenza Vaccination across Multiple Years and in Diverse Populations Reveals Shared Molecular Signatures.

    PubMed

    Nakaya, Helder I; Hagan, Thomas; Duraisingham, Sai S; Lee, Eva K; Kwissa, Marcin; Rouphael, Nadine; Frasca, Daniela; Gersten, Merril; Mehta, Aneesh K; Gaujoux, Renaud; Li, Gui-Mei; Gupta, Shakti; Ahmed, Rafi; Mulligan, Mark J; Shen-Orr, Shai; Blomberg, Bonnie B; Subramaniam, Shankar; Pulendran, Bali

    2015-12-15

    Systems approaches have been used to describe molecular signatures driving immunity to influenza vaccination in humans. Whether such signatures are similar across multiple seasons and in diverse populations is unknown. We applied systems approaches to study immune responses in young, elderly, and diabetic subjects vaccinated with the seasonal influenza vaccine across five consecutive seasons. Signatures of innate immunity and plasmablasts correlated with and predicted influenza antibody titers at 1 month after vaccination with >80% accuracy across multiple seasons but were not associated with the longevity of the response. Baseline signatures of lymphocyte and monocyte inflammation were positively and negatively correlated, respectively, with antibody responses at 1 month. Finally, integrative analysis of microRNAs and transcriptomic profiling revealed potential regulators of vaccine immunity. These results identify shared vaccine-induced signatures across multiple seasons and in diverse populations and might help guide the development of next-generation vaccines that provide persistent immunity against influenza.

  2. Are there molecular signatures?

    SciTech Connect

    Bennett, W.P.

    1995-10-01

    This report describes molecular signatures and mutational spectrum analysis. The mutation spectrum is defined as the type and location of DNA base change. There are currently about five well documented cases. Mutations and radon-associated tumors are discussed.

  3. Raman spectroscopy explores molecular structural signatures of hidden materials in depth: Universal Multiple Angle Raman Spectroscopy

    PubMed Central

    Sil, Sanchita; Umapathy, Siva

    2014-01-01

    Non-invasive 3D imaging in materials and medical research involves methodologies such as X-ray imaging, MRI, fluorescence and optical coherence tomography, NIR absorption imaging, etc., providing global morphological/density/absorption changes of the hidden components. However, molecular information of such buried materials has been elusive. In this article we demonstrate observation of molecular structural information of materials hidden/buried in depth using Raman scattering. Typically, Raman spectroscopic observations are made at fixed collection angles, such as, 90°, 135°, and 180°, except in spatially offset Raman scattering (SORS) (only back scattering based collection of photons) and transmission techniques. Such specific collection angles restrict the observations of Raman signals either from or near the surface of the materials. Universal Multiple Angle Raman Spectroscopy (UMARS) presented here employs the principle of (a) penetration depth of photons and then diffuse propagation through non-absorbing media by multiple scattering and (b) detection of signals from all the observable angles. PMID:24930768

  4. Signature molecular descriptor : advanced applications.

    SciTech Connect

    Visco, Donald Patrick, Jr.

    2010-04-01

    In this work we report on the development of the Signature Molecular Descriptor (or Signature) for use in the solution of inverse design problems as well as in highthroughput screening applications. The ultimate goal of using Signature is to identify novel and non-intuitive chemical structures with optimal predicted properties for a given application. We demonstrate this in three studies: green solvent design, glucocorticoid receptor ligand design and the design of inhibitors for Factor XIa. In many areas of engineering, compounds are designed and/or modified in incremental ways which rely upon heuristics or institutional knowledge. Often multiple experiments are performed and the optimal compound is identified in this brute-force fashion. Perhaps a traditional chemical scaffold is identified and movement of a substituent group around a ring constitutes the whole of the design process. Also notably, a chemical being evaluated in one area might demonstrate properties very attractive in another area and serendipity was the mechanism for solution. In contrast to such approaches, computer-aided molecular design (CAMD) looks to encompass both experimental and heuristic-based knowledge into a strategy that will design a molecule on a computer to meet a given target. Depending on the algorithm employed, the molecule which is designed might be quite novel (re: no CAS registration number) and/or non-intuitive relative to what is known about the problem at hand. While CAMD is a fairly recent strategy (dating to the early 1980s), it contains a variety of bottlenecks and limitations which have prevented the technique from garnering more attention in the academic, governmental and industrial institutions. A main reason for this is how the molecules are described in the computer. This step can control how models are developed for the properties of interest on a given problem as well as how to go from an output of the algorithm to an actual chemical structure. This report

  5. Schizophrenia-associated methylomic variation: molecular signatures of disease and polygenic risk burden across multiple brain regions

    PubMed Central

    Viana, Joana; Hannon, Eilis; Dempster, Emma; Pidsley, Ruth; Macdonald, Ruby; Knox, Olivia; Spiers, Helen; Troakes, Claire; Al-Saraj, Safa; Turecki, Gustavo; Schalkwyk, Leonard C.

    2017-01-01

    Abstract Genetic association studies provide evidence for a substantial polygenic component to schizophrenia, although the neurobiological mechanisms underlying the disorder remain largely undefined. Building on recent studies supporting a role for developmentally regulated epigenetic variation in the molecular aetiology of schizophrenia, this study aimed to identify epigenetic variation associated with both a diagnosis of schizophrenia and elevated polygenic risk burden for the disease across multiple brain regions. Genome-wide DNA methylation was quantified in 262 post-mortem brain samples, representing tissue from four brain regions (prefrontal cortex, striatum, hippocampus and cerebellum) from 41 schizophrenia patients and 47 controls. We identified multiple disease-associated and polygenic risk score-associated differentially methylated positions and regions, which are not enriched in genomic regions identified in genetic studies of schizophrenia and do not reflect direct genetic effects on DNA methylation. Our study represents the first analysis of epigenetic variation associated with schizophrenia across multiple brain regions and highlights the utility of polygenic risk scores for identifying molecular pathways associated with aetiological variation in complex disease. PMID:28011714

  6. Molecular signatures of major depression.

    PubMed

    Cai, Na; Chang, Simon; Li, Yihan; Li, Qibin; Hu, Jingchu; Liang, Jieqin; Song, Li; Kretzschmar, Warren; Gan, Xiangchao; Nicod, Jerome; Rivera, Margarita; Deng, Hong; Du, Bo; Li, Keqing; Sang, Wenhu; Gao, Jingfang; Gao, Shugui; Ha, Baowei; Ho, Hung-Yao; Hu, Chunmei; Hu, Jian; Hu, Zhenfei; Huang, Guoping; Jiang, Guoqing; Jiang, Tao; Jin, Wei; Li, Gongying; Li, Kan; Li, Yi; Li, Yingrui; Li, Youhui; Lin, Yu-Ting; Liu, Lanfen; Liu, Tiebang; Liu, Ying; Liu, Yuan; Lu, Yao; Lv, Luxian; Meng, Huaqing; Qian, Puyi; Sang, Hong; Shen, Jianhua; Shi, Jianguo; Sun, Jing; Tao, Ming; Wang, Gang; Wang, Guangbiao; Wang, Jian; Wang, Linmao; Wang, Xueyi; Wang, Xumei; Yang, Huanming; Yang, Lijun; Yin, Ye; Zhang, Jinbei; Zhang, Kerang; Sun, Ning; Zhang, Wei; Zhang, Xiuqing; Zhang, Zhen; Zhong, Hui; Breen, Gerome; Wang, Jun; Marchini, Jonathan; Chen, Yiping; Xu, Qi; Xu, Xun; Mott, Richard; Huang, Guo-Jen; Kendler, Kenneth; Flint, Jonathan

    2015-05-04

    Adversity, particularly in early life, can cause illness. Clues to the responsible mechanisms may lie with the discovery of molecular signatures of stress, some of which include alterations to an individual's somatic genome. Here, using genome sequences from 11,670 women, we observed a highly significant association between a stress-related disease, major depression, and the amount of mtDNA (p = 9.00 × 10(-42), odds ratio 1.33 [95% confidence interval [CI] = 1.29-1.37]) and telomere length (p = 2.84 × 10(-14), odds ratio 0.85 [95% CI = 0.81-0.89]). While both telomere length and mtDNA amount were associated with adverse life events, conditional regression analyses showed the molecular changes were contingent on the depressed state. We tested this hypothesis with experiments in mice, demonstrating that stress causes both molecular changes, which are partly reversible and can be elicited by the administration of corticosterone. Together, these results demonstrate that changes in the amount of mtDNA and telomere length are consequences of stress and entering a depressed state. These findings identify increased amounts of mtDNA as a molecular marker of MD and have important implications for understanding how stress causes the disease.

  7. Molecular Signatures of Major Depression

    PubMed Central

    Cai, Na; Chang, Simon; Li, Yihan; Li, Qibin; Hu, Jingchu; Liang, Jieqin; Song, Li; Kretzschmar, Warren; Gan, Xiangchao; Nicod, Jerome; Rivera, Margarita; Deng, Hong; Du, Bo; Li, Keqing; Sang, Wenhu; Gao, Jingfang; Gao, Shugui; Ha, Baowei; Ho, Hung-Yao; Hu, Chunmei; Hu, Jian; Hu, Zhenfei; Huang, Guoping; Jiang, Guoqing; Jiang, Tao; Jin, Wei; Li, Gongying; Li, Kan; Li, Yi; Li, Yingrui; Li, Youhui; Lin, Yu-Ting; Liu, Lanfen; Liu, Tiebang; Liu, Ying; Liu, Yuan; Lu, Yao; Lv, Luxian; Meng, Huaqing; Qian, Puyi; Sang, Hong; Shen, Jianhua; Shi, Jianguo; Sun, Jing; Tao, Ming; Wang, Gang; Wang, Guangbiao; Wang, Jian; Wang, Linmao; Wang, Xueyi; Wang, Xumei; Yang, Huanming; Yang, Lijun; Yin, Ye; Zhang, Jinbei; Zhang, Kerang; Sun, Ning; Zhang, Wei; Zhang, Xiuqing; Zhang, Zhen; Zhong, Hui; Breen, Gerome; Wang, Jun; Marchini, Jonathan; Chen, Yiping; Xu, Qi; Xu, Xun; Mott, Richard; Huang, Guo-Jen; Kendler, Kenneth; Flint, Jonathan

    2015-01-01

    Summary Adversity, particularly in early life, can cause illness. Clues to the responsible mechanisms may lie with the discovery of molecular signatures of stress, some of which include alterations to an individual’s somatic genome. Here, using genome sequences from 11,670 women, we observed a highly significant association between a stress-related disease, major depression, and the amount of mtDNA (p = 9.00 × 10−42, odds ratio 1.33 [95% confidence interval [CI] = 1.29–1.37]) and telomere length (p = 2.84 × 10−14, odds ratio 0.85 [95% CI = 0.81–0.89]). While both telomere length and mtDNA amount were associated with adverse life events, conditional regression analyses showed the molecular changes were contingent on the depressed state. We tested this hypothesis with experiments in mice, demonstrating that stress causes both molecular changes, which are partly reversible and can be elicited by the administration of corticosterone. Together, these results demonstrate that changes in the amount of mtDNA and telomere length are consequences of stress and entering a depressed state. These findings identify increased amounts of mtDNA as a molecular marker of MD and have important implications for understanding how stress causes the disease. PMID:25913401

  8. Molecular signatures of vaccine adjuvants.

    PubMed

    Olafsdottir, Thorunn; Lindqvist, Madelene; Harandi, Ali M

    2015-09-29

    Mass vaccination has saved millions of human lives and improved the quality of life in both developing and developed countries. The emergence of new pathogens and inadequate protection conferred by some of the existing vaccines such as vaccines for tuberculosis, influenza and pertussis especially in certain age groups have resulted in a move from empirically developed vaccines toward more pathogen tailored and rationally engineered vaccines. A deeper understanding of the interaction of innate and adaptive immunity at molecular level enables the development of vaccines that selectively target certain type of immune responses without excessive reactogenicity. Adjuvants constitute an imperative element of modern vaccines. Although a variety of candidate adjuvants have been evaluated in the past few decades, only a limited number of vaccine adjuvants are currently available for human use. A better understanding of the mode of action of adjuvants is pivotal to harness the potential of existing and new adjuvants in shaping a desired immune response. Recent advancement in systems biology powered by the emerging cutting edge omics technology has led to the identification of molecular signatures rapidly induced after vaccination in the blood that correlate and predict a later protective immune response or vaccine safety. This can pave ways to prospectively determine the potency and safety of vaccines and adjuvants. This review is intended to highlight the importance of big data analysis in advancing our understanding of the mechanisms of actions of adjuvants to inform rational development of future human vaccines.

  9. Quantum broadcasting multiple blind signature with constant size

    NASA Astrophysics Data System (ADS)

    Xiao, Min; Li, Zhenli

    2016-09-01

    Using quantum homomorphic signature in quantum network, we propose a quantum broadcasting multiple blind signature scheme. Different from classical signature and current quantum signature schemes, the multi-signature proposed in our scheme is not generated by simply putting the individual signatures together, but by aggregating the individual signatures based on homomorphic property. Therefore, the size of the multi-signature is constant. Furthermore, based on a wide range of investigation for the security of existing quantum signature protocols, our protocol is designed to resist possible forgery attacks against signature and message from the various attack sources and disavowal attacks from participants.

  10. Molecular signature in HCV-positive lymphomas.

    PubMed

    De Re, Valli; Caggiari, Laura; Garziera, Marica; De Zorzi, Mariangela; Repetto, Ombretta

    2012-01-01

    Hepatitis C virus (HCV) is a positive, single-stranded RNA virus, which has been associated to different subtypes of B-cell non-Hodgkin lymphoma (B-NHL). Cumulative evidence suggests an HCV-related antigen driven process in the B-NHL development. The underlying molecular signature associated to HCV-related B-NHL has to date remained obscure. In this review, we discuss the recent developments in this field with a special mention to different sets of genes whose expression is associated with BCR coupled to Blys signaling which in turn was found to be linked to B-cell maturation stages and NF-κb transcription factor. Even if recent progress on HCV-B-NHL signature has been made, the precise relationship between HCV and lymphoma development and phenotype signature remain to be clarified.

  11. Does radiation cause molecular signatures?

    SciTech Connect

    Bennett, W.P.

    1997-03-01

    Several classes of genes are mutated during the progression to cancer. The oncogenes include ras, myc and c-erbB-2; suppressor genes include p53, Rb, p16, and APC; and cancer susceptibility genes include hMSH2. Germline mutations in many of these genes produce cancer syndromes such as retinoblastoma, Li-Fraumeni Sydrome, familial adenomatous polyposis, or HNPCC (hereditary non-polyposis colon cancer). Sporadic tumors frequently contain somatic mutations in the same genes. Analysis of the mutational spectrum of sporadic and inherited tumors can provide clues to etiology and insight into molecular pathogenesis. The character and distribution of mutations comprise a mutational spectrum. Mutations of the p53 tumor suppressor gene occur commonly in human cancer, and nearly 5000 have been reported to date. The p53 mutational spectrum is dominated by missense point mutations (84%) and complemented by insertions/deletions (10%) and non-sense mutations (7%). Most mutations occur within evolutionarily conserved residues within the DNA-binding domain, and the pattern of mutational hotspots provided the first clue to p53 function: it is a transcription factor that binds to a DNA consensus sequence. Elucidation of the crystal structure of the central DNA-binding domain has uncovered the significance of the mutational hotspots. These insights suggest strategies for rational drug design, for example, constructing `restoring` compounds that complete the wild type hydrogen bonds missing in the mutant p53 protein. Mutational spectrum analysis is a new tool for probing cancer etiology and pathogensis. Using current technology, the p53 tumor suppressor gene is the most informative target sequence, but the next generation of rapid sequencing technologies will expand the range of testable cancer genes and fill new mutational databases.

  12. [Molecular signatures of breast cancer: What clinical utility?].

    PubMed

    Delaloge, Suzette; Saghatchian, Mahasti; Ghouadni, Amal; Fekih, Mahmoud; André, Fabrice

    2015-06-01

    The role of molecular signatures in the adjuvant management of breast cancer remains a debated topic. Discussions should take into account the level of scientific validation, the impact on practice, the expected benefits and financing issues. This article presents the key points for a rational use of commercial molecular signatures.

  13. A Systems Biological Approach Reveals Multiple Crosstalk Mechanism between Gram-Positive and Negative Bacterial Infections: An Insight into Core Mechanism and Unique Molecular Signatures

    PubMed Central

    Thangam, Berla; Ahmed, Shiek S. S. J.

    2014-01-01

    Background Bacterial infections remain a major threat and a leading cause of death worldwide. Most of the bacterial infections are caused by gram-positive and negative bacteria, which are recognized by Toll-like receptor (TLR) 2 and 4, respectively. Activation of these TLRs initiates multiple pathways that subsequently lead to effective immune response. Although, both the TLRs share common signaling mechanism yet they may exhibit specificity as well, resulting in the release of diverse range of inflammatory mediators which could be used as candidate biomolecules for bacterial infections. Results We adopted systems biological approach to identify signaling pathways mediated by TLRs to determine candidate molecules associated with bacterial infections. We used bioinformatics concepts, including literature mining to construct protein-protein interaction network, prioritization of TLRs specific nodes using microarray data and pathway analysis. Our constructed PPI network for TLR 2 (nodes: 4091 and edges: 66068) and TLR 4 (node: 4076 and edges: 67898) showed 3207 common nodes, indicating that both the TLRs might share similar signaling events that are attributed to cell migration, MAPK pathway and several inflammatory cascades. Our results propose the potential collaboration between the shared signaling pathways of both the receptors may enhance the immune response against invading pathogens. Further, to identify candidate molecules, the TLRs specific nodes were prioritized using microarray differential expressed genes. Of the top prioritized TLR 2 molecules, 70% were co-expressed. A similar trend was also observed within TLR 4 nodes. Further, most of these molecules were preferentially found in blood plasma for feasible diagnosis. Conclusions The analysis reveals the common and unique mechanism regulated by both the TLRs that provide a broad perspective of signaling events in bacterial infections. Further, the identified candidate biomolecules could potentially aid

  14. Reactive oxygen species–associated molecular signature predicts survival in patients with sepsis

    PubMed Central

    Zhou, Tong; Wang, Ting; Slepian, Marvin J.; Garcia, Joe G. N.; Hecker, Louise

    2016-01-01

    Abstract Sepsis-related multiple organ dysfunction syndrome is a leading cause of death in intensive care units. There is overwhelming evidence that oxidative stress plays a significant role in the pathogenesis of sepsis-associated multiple organ failure; however, reactive oxygen species (ROS)–associated biomarkers and/or diagnostics that define mortality or predict survival in sepsis are lacking. Lung or peripheral blood gene expression analysis has gained increasing recognition as a potential prognostic and/or diagnostic tool. The objective of this study was to identify ROS-associated biomarkers predictive of survival in patients with sepsis. In-silico analyses of expression profiles allowed the identification of a 21-gene ROS-associated molecular signature that predicts survival in sepsis patients. Importantly, this signature performed well in a validation cohort consisting of sepsis patients aggregated from distinct patient populations recruited from different sites. Our signature outperforms randomly generated signatures of the same signature gene size. Our findings further validate the critical role of ROSs in the pathogenesis of sepsis and provide a novel gene signature that predicts survival in sepsis patients. These results also highlight the utility of peripheral blood molecular signatures as biomarkers for predicting mortality risk in patients with sepsis, which could facilitate the development of personalized therapies. PMID:27252846

  15. A broadcasting multiple blind signature scheme based on quantum GHZ entanglement

    NASA Astrophysics Data System (ADS)

    Tian, Yuan; Chen, Hong; Gao, Yan; Zhuang, Honglin; Lian, Haigang; Han, Zhengping; Yu, Peng; Kong, Xiangze; Wen, Xiaojun

    2014-09-01

    Using the correlation of the GHZ triplet states, a broadcasting multiple blind signature scheme is proposed. Different from classical multiple signature and current quantum signature schemes, which could only deliver either multiple signature or unconditional security, our scheme guarantees both by adopting quantum key preparation, quantum encryption algorithm and quantum entanglement. Our proposed scheme has the properties of multiple signature, blindness, non-disavowal, non-forgery and traceability. To the best of our knowledge, we are the first to propose the broadcasting multiple blind signature of quantum cryptography.

  16. Novel risk stratification of patients with neuroblastoma by genomic signature, which is independent of molecular signature.

    PubMed

    Tomioka, N; Oba, S; Ohira, M; Misra, A; Fridlyand, J; Ishii, S; Nakamura, Y; Isogai, E; Hirata, T; Yoshida, Y; Todo, S; Kaneko, Y; Albertson, D G; Pinkel, D; Feuerstein, B G; Nakagawara, A

    2008-01-17

    Human neuroblastoma remains enigmatic because it often shows spontaneous regression and aggressive growth. The prognosis of advanced stage of sporadic neuroblastomas is still poor. Here, we investigated whether genomic and molecular signatures could categorize new therapeutic risk groups in primary neuroblastomas. We conducted microarray-based comparative genomic hybridization (array-CGH) with a DNA chip carrying 2464 BAC clones to examine genomic aberrations of 236 neuroblastomas and used in-house cDNA microarrays for gene-expression profiling. Array-CGH demonstrated three major genomic groups of chromosomal aberrations: silent (GGS), partial gains and/or losses (GGP) and whole gains and/or losses (GGW), which well corresponded with the patterns of chromosome 17 abnormalities. They were further classified into subgroups with different outcomes. In 112 sporadic neuroblastomas, MYCN amplification was frequent in GGS (22%) and GGP (53%) and caused serious outcomes in patients. Sporadic tumors with a single copy of MYCN showed the 5-year cumulative survival rates of 89% in GGS, 53% in GGP and 85% in GGW. Molecular signatures also segregated patients into the favorable and unfavorable prognosis groups (P=0.001). Both univariate and multivariate analyses revealed that genomic and molecular signatures were mutually independent, powerful prognostic indicators. Thus, combined genomic and molecular signatures may categorize novel risk groups and confer new clues for allowing tailored or even individualized medicine to patients with neuroblastoma.

  17. Molecular signatures for the Crenarchaeota and the Thaumarchaeota.

    PubMed

    Gupta, Radhey S; Shami, Ali

    2011-02-01

    Crenarchaeotes found in mesophilic marine environments were recently placed into a new phylum of Archaea called the Thaumarchaeota. However, very few molecular characteristics of this new phylum are currently known which can be used to distinguish them from the Crenarchaeota. In addition, their relationships to deep-branching archaeal lineages are unclear. We report here detailed analyses of protein sequences from Crenarchaeota and Thaumarchaeota that have identified many conserved signature indels (CSIs) and signature proteins (SPs) (i.e., proteins for which all significant blast hits are from these groups) that are specific for these archaeal groups. Of the identified signatures 6 CSIs and 13 SPs are specific for the Crenarchaeota phylum; 6 CSIs and >250 SPs are uniquely found in various Thaumarchaeota (viz. Cenarchaeum symbiosum, Nitrosopumilus maritimus and a number of uncultured marine crenarchaeotes) and 3 CSIs and ~10 SPs are found in both Thaumarchaeota and Crenarchaeota species. Some of the molecular signatures are also present in Korarchaeum cryptofilum, which forms the independent phylum Korarchaeota. Although some of these molecular signatures suggest a distant shared ancestry between Thaumarchaeota and Crenarchaeota, our identification of large numbers of Thaumarchaeota-specific proteins and their deep branching between the Crenarchaeota and Euryarchaeota phyla in phylogenetic trees shows that they are distinct from both Crenarchaeota and Euryarchaeota in both genetic and phylogenetic terms. These observations support the placement of marine mesophilic archaea into the separate phylum Thaumarchaeota. Additionally, many CSIs and SPs have been found that are specific for different orders within Crenarchaeota (viz. Sulfolobales-3 CSIs and 169 SPs, Thermoproteales-5 CSIs and 25 SPs, Desulfurococcales-4 SPs, and Sulfolobales and Desulfurococcales-2 CSIs and 18 SPs). The signatures described here provide novel means for distinguishing the Crenarchaeota and

  18. A Molecular Signature of Proteinuria in Glomerulonephritis

    PubMed Central

    Reich, Heather N.; Tritchler, David; Cattran, Daniel C.; Eichinger, Felix; Boucherot, Anissa; Henger, Anna; Berthier, Celine C.; Nair, Viji; Cohen, Clemens D.

    2010-01-01

    Proteinuria is the most important predictor of outcome in glomerulonephritis and experimental data suggest that the tubular cell response to proteinuria is an important determinant of progressive fibrosis in the kidney. However, it is unclear whether proteinuria is a marker of disease severity or has a direct effect on tubular cells in the kidneys of patients with glomerulonephritis. Accordingly we studied an in vitro model of proteinuria, and identified 231 “albumin-regulated genes” differentially expressed by primary human kidney tubular epithelial cells exposed to albumin. We translated these findings to human disease by studying mRNA levels of these genes in the tubulo-interstitial compartment of kidney biopsies from patients with IgA nephropathy using microarrays. Biopsies from patients with IgAN (n = 25) could be distinguished from those of control subjects (n = 6) based solely upon the expression of these 231 “albumin-regulated genes.” The expression of an 11-transcript subset related to the degree of proteinuria, and this 11-mRNA subset was also sufficient to distinguish biopsies of subjects with IgAN from control biopsies. We tested if these findings could be extrapolated to other proteinuric diseases beyond IgAN and found that all forms of primary glomerulonephritis (n = 33) can be distinguished from controls (n = 21) based solely on the expression levels of these 11 genes derived from our in vitro proteinuria model. Pathway analysis suggests common regulatory elements shared by these 11 transcripts. In conclusion, we have identified an albumin-regulated 11-gene signature shared between all forms of primary glomerulonephritis. Our findings support the hypothesis that albuminuria may directly promote injury in the tubulo-interstitial compartment of the kidney in patients with glomerulonephritis. PMID:20976140

  19. Molecular signatures for sex in the Placozoa

    PubMed Central

    Signorovitch, Ana Y.; Dellaporta, Stephen L.; Buss, Leo W.

    2005-01-01

    Placozoans, the simplest free-living animals, have never been observed to reproduce sexually. Here, we describe molecular evidence for sexual reproduction within one clade of the Placozoa. In a population sample of 10 individuals, within-individual and overall nucleotide diversity were similar to each other and consistent with levels observed in sexually reproducing species. Intergenic recombination as well as the sharing of alleles between heterozygous and homozygous individuals was also observed. These hallmarks of sexual reproduction establish that sex is indeed present in this phylum. PMID:16230622

  20. Metabolomic signatures associated with disease severity in multiple sclerosis

    PubMed Central

    Alonso, Cristina; Agirrezabal, Ion; Kotelnikova, Ekaterina; Zubizarreta, Irati; Pulido-Valdeolivas, Irene; Saiz, Albert; Comabella, Manuel; Montalban, Xavier; Villar, Luisa; Alvarez-Cermeño, Jose Carlos; Fernández, Oscar; Alvarez-Lafuente, Roberto; Arroyo, Rafael; Castro, Azucena

    2017-01-01

    Objective: To identify differences in the metabolomic profile in the serum of patients with multiple sclerosis (MS) compared to controls and to identify biomarkers of disease severity. Methods: We studied 2 cohorts of patients with MS: a retrospective longitudinal cohort of 238 patients and 74 controls and a prospective cohort of 61 patients and 41 controls with serial serum samples. Patients were stratified into active or stable disease based on 2 years of prospective assessment accounting for presence of clinical relapses or changes in disability measured with the Expanded Disability Status Scale (EDSS). Metabolomic profiling (lipids and amino acids) was performed by ultra-high-performance liquid chromatography coupled to mass spectrometry in serum samples. Data analysis was performed using parametric methods, principal component analysis, and partial least square discriminant analysis for assessing the differences between cases and controls and for subgroups based on disease severity. Results: We identified metabolomics signatures with high accuracy for classifying patients vs controls as well as for classifying patients with medium to high disability (EDSS >3.0). Among them, sphingomyelin and lysophosphatidylethanolamine were the metabolites that showed a more robust pattern in the time series analysis for discriminating between patients and controls. Moreover, levels of hydrocortisone, glutamic acid, tryptophan, eicosapentaenoic acid, 13S-hydroxyoctadecadienoic acid, lysophosphatidylcholines, and lysophosphatidylethanolamines were associated with more severe disease (non-relapse-free or increase in EDSS). Conclusions: We identified metabolomic signatures composed of hormones, lipids, and amino acids associated with MS and with a more severe course. PMID:28180139

  1. Transcriptional networks inferred from molecular signatures of breast cancer.

    PubMed

    Tongbai, Ron; Idelman, Gila; Nordgard, Silje H; Cui, Wenwu; Jacobs, Jonathan L; Haggerty, Cynthia M; Chanock, Stephen J; Børresen-Dale, Anne-Lise; Livingston, Gary; Shaunessy, Patrick; Chiang, Chih-Hung; Kristensen, Vessela N; Bilke, Sven; Gardner, Kevin

    2008-02-01

    Global genomic approaches in cancer research have provided new and innovative strategies for the identification of signatures that differentiate various types of human cancers. Computational analysis of the promoter composition of the genes within these signatures may provide a powerful method for deducing the regulatory transcriptional networks that mediate their collective function. In this study we have systematically analyzed the promoter composition of gene classes derived from previously established genetic signatures that recently have been shown to reliably and reproducibly distinguish five molecular subtypes of breast cancer associated with distinct clinical outcomes. Inferences made from the trends of transcription factor binding site enrichment in the promoters of these gene groups led to the identification of regulatory pathways that implicate discrete transcriptional networks associated with specific molecular subtypes of breast cancer. One of these inferred pathways predicted a role for nuclear factor-kappaB in a novel feed-forward, self-amplifying, autoregulatory module regulated by the ERBB family of growth factor receptors. The existence of this pathway was verified in vivo by chromatin immunoprecipitation and shown to be deregulated in breast cancer cells overexpressing ERBB2. This analysis indicates that approaches of this type can provide unique insights into the differential regulatory molecular programs associated with breast cancer and will aid in identifying specific transcriptional networks and pathways as potential targets for tumor subtype-specific therapeutic intervention.

  2. Transcriptional Networks Inferred from Molecular Signatures of Breast Cancer

    PubMed Central

    Tongbai, Ron; Idelman, Gila; Nordgard, Silje H.; Cui, Wenwu; Jacobs, Jonathan L.; Haggerty, Cynthia M.; Chanock, Stephen J.; Børresen-Dale, Anne-Lise; Livingston, Gary; Shaunessy, Patrick; Chiang, Chih-Hung; Kristensen, Vessela N.; Bilke, Sven; Gardner, Kevin

    2008-01-01

    Global genomic approaches in cancer research have provided new and innovative strategies for the identification of signatures that differentiate various types of human cancers. Computational analysis of the promoter composition of the genes within these signatures may provide a powerful method for deducing the regulatory transcriptional networks that mediate their collective function. In this study we have systematically analyzed the promoter composition of gene classes derived from previously established genetic signatures that recently have been shown to reliably and reproducibly distinguish five molecular subtypes of breast cancer associated with distinct clinical outcomes. Inferences made from the trends of transcription factor binding site enrichment in the promoters of these gene groups led to the identification of regulatory pathways that implicate discrete transcriptional networks associated with specific molecular subtypes of breast cancer. One of these inferred pathways predicted a role for nuclear factor-κB in a novel feed-forward, self-amplifying, autoregulatory module regulated by the ERBB family of growth factor receptors. The existence of this pathway was verified in vivo by chromatin immunoprecipitation and shown to be deregulated in breast cancer cells overexpressing ERBB2. This analysis indicates that approaches of this type can provide unique insights into the differential regulatory molecular programs associated with breast cancer and will aid in identifying specific transcriptional networks and pathways as potential targets for tumor subtype-specific therapeutic intervention. PMID:18187569

  3. AuNPs for identification of molecular signatures of resistance

    PubMed Central

    Veigas, Bruno; Fernandes, Alexandra R.; Baptista, Pedro V.

    2014-01-01

    The increasing levels of drug resistance are one of biggest threats to overcome microbial infection. The ability to rapidly and accurately detect a given pathogen and its drug resistance profile is essential for the appropriate treatment of patients and for preventing further spread of drug-resistant strains. The predictive and informative value of these molecular markers needs to be translated into robust surveillance tools that correlate to the target and extent of resistance, monitor multiresistance and provide real time assessment at point-of-need. Rapid molecular assays for the detection of drug-resistance signatures in clinical specimens are based on the detection of specific nucleotide sequences and/or mutations within pre-selected biomarkers in the genome, indicative of the presence of the pathogen and/or associated with drug resistance. DNA and/or RNA based assays offer advantages over phenotypic assays, such as specificity and time from collection to result. Nanotechnology has provided new and robust tools for the detection of pathogens and more crucially to the fast and sensitive characterisation of molecular signatures of drug resistance. Amongst the plethora of nanotechnology based approaches, gold nanoparticles have prompt for the development of new strategies and platforms capable to provide valuable data at point-of-need with increased versatility but reduced costs. Gold nanoparticles, due to their unique spectral, optical and electrochemical properties, are one of the most widely used nanotechnology systems for molecular diagnostics. This review will focus on the use of gold nanoparticles for screening molecular signatures of drug resistance that have been reported thus far, and provide a critical evaluation of current and future developments of these technologies assisting pathogen identification and characterisation. PMID:25221547

  4. Molecular classification of prostate cancer using curated expression signatures.

    PubMed

    Markert, Elke K; Mizuno, Hideaki; Vazquez, Alexei; Levine, Arnold J

    2011-12-27

    High Gleason score is currently the best prognostic indicator for poor prognosis in prostate cancer. However, a significant number of patients with low Gleason scores develop aggressive disease as well. In an effort to understand molecular signatures associated with poor outcome in prostate cancer, we analyzed a microarray dataset characterizing 281 prostate cancers from a Swedish watchful-waiting cohort. Patients were classified on the basis of their mRNA microarray signature profiles indicating embryonic stem cell expression patterns (stemness), inactivation of the tumor suppressors p53 and PTEN, activation of several oncogenic pathways, and the TMPRSS2-ERG fusion. Unsupervised clustering identified a subset of tumors manifesting stem-like signatures together with p53 and PTEN inactivation, which had very poor survival outcome, a second group with intermediate survival outcome, characterized by the TMPRSS2-ERG fusion, and three groups with benign outcome. The stratification was validated on a second independent dataset of 150 tumor and metastatic samples from a clinical cohort at Memorial Sloan-Kettering Cancer Center. This classification is independent of Gleason score and therefore provides useful unique molecular profiles for prostate cancer prognosis, helping to predict poor outcome in patients with low or average Gleason scores.

  5. Dynamical signatures of molecular symmetries in nonequilibrium quantum transport.

    PubMed

    Thingna, Juzar; Manzano, Daniel; Cao, Jianshu

    2016-06-17

    Symmetries play a crucial role in ubiquitous systems found in Nature. In this work, we propose an elegant approach to detect symmetries by measuring quantum currents. Our detection scheme relies on initiating the system in an anti-symmetric initial condition, with respect to the symmetric sites, and using a probe that acts like a local noise. Depending on the position of the probe the currents exhibit unique signatures such as a quasi-stationary plateau indicating the presence of metastability and multi-exponential decays in case of multiple symmetries. The signatures are sensitive to the characteristics of the probe and vanish completely when the timescale of the coherent system dynamics is much longer than the timescale of the probe. These results are demonstrated using a 4-site model and an archetypal example of the para-benzene ring and are shown to be robust under a weak disorder.

  6. Dynamical signatures of molecular symmetries in nonequilibrium quantum transport

    NASA Astrophysics Data System (ADS)

    Thingna, Juzar; Manzano, Daniel; Cao, Jianshu

    2016-06-01

    Symmetries play a crucial role in ubiquitous systems found in Nature. In this work, we propose an elegant approach to detect symmetries by measuring quantum currents. Our detection scheme relies on initiating the system in an anti-symmetric initial condition, with respect to the symmetric sites, and using a probe that acts like a local noise. Depending on the position of the probe the currents exhibit unique signatures such as a quasi-stationary plateau indicating the presence of metastability and multi-exponential decays in case of multiple symmetries. The signatures are sensitive to the characteristics of the probe and vanish completely when the timescale of the coherent system dynamics is much longer than the timescale of the probe. These results are demonstrated using a 4-site model and an archetypal example of the para-benzene ring and are shown to be robust under a weak disorder.

  7. Dynamical signatures of molecular symmetries in nonequilibrium quantum transport

    PubMed Central

    Thingna, Juzar; Manzano, Daniel; Cao, Jianshu

    2016-01-01

    Symmetries play a crucial role in ubiquitous systems found in Nature. In this work, we propose an elegant approach to detect symmetries by measuring quantum currents. Our detection scheme relies on initiating the system in an anti-symmetric initial condition, with respect to the symmetric sites, and using a probe that acts like a local noise. Depending on the position of the probe the currents exhibit unique signatures such as a quasi-stationary plateau indicating the presence of metastability and multi-exponential decays in case of multiple symmetries. The signatures are sensitive to the characteristics of the probe and vanish completely when the timescale of the coherent system dynamics is much longer than the timescale of the probe. These results are demonstrated using a 4-site model and an archetypal example of the para-benzene ring and are shown to be robust under a weak disorder. PMID:27311717

  8. Molecular signatures of mammalian hibernation: comparisons with alternative phenotypes

    PubMed Central

    2013-01-01

    Background Mammalian hibernators display phenotypes similar to physiological responses to calorie restriction and fasting, sleep, cold exposure, and ischemia-reperfusion in non-hibernating species. Whether biochemical changes evident during hibernation have parallels in non-hibernating systems on molecular and genetic levels is unclear. Results We identified the molecular signatures of torpor and arousal episodes during hibernation using a custom-designed microarray for the Arctic ground squirrel (Urocitellus parryii) and compared them with molecular signatures of selected mouse phenotypes. Our results indicate that differential gene expression related to metabolism during hibernation is associated with that during calorie restriction and that the nuclear receptor protein PPARα is potentially crucial for metabolic remodeling in torpor. Sleep-wake cycle-related and temperature response genes follow the same expression changes as during the torpor-arousal cycle. Increased fatty acid metabolism occurs during hibernation but not during ischemia-reperfusion injury in mice and, thus, might contribute to protection against ischemia-reperfusion during hibernation. Conclusions In this study, we systematically compared hibernation with alternative phenotypes to reveal novel mechanisms that might be used therapeutically in human pathological conditions. PMID:23957789

  9. A Urinary Metabolic Signature for Multiple Sclerosis and Neuromyelitis Optica.

    PubMed

    Gebregiworgis, Teklab; Nielsen, Helle H; Massilamany, Chandirasegaran; Gangaplara, Arunakumar; Reddy, Jay; Illes, Zsolt; Powers, Robert

    2016-02-05

    Urine is a metabolite-rich biofluid that reflects the body's effort to maintain chemical and osmotic homeostasis. Clinical diagnosis routinely relies on urine samples because the collection process is easy and noninvasive. Despite these advantages, urine is an under-investigated source of biomarkers for multiple sclerosis (MS). Nuclear magnetic resonance spectroscopy (NMR) has become a common approach for analyzing urinary metabolites for disease diagnosis and biomarker discovery. For illustration of the potential of urinary metabolites for diagnosing and treating MS patients, and for differentiating between MS and other illnesses, 38 urine samples were collected from healthy controls, MS patients, and neuromyelitis optica-spectrum disorder (NMO-SD) patients and analyzed with NMR, multivariate statistics, one-way ANOVA, and univariate statistics. Urine from MS patients exhibited a statistically distinct metabolic signature from healthy and NMO-SD controls. A total of 27 metabolites were differentially altered in the urine from MS and NMO-SD patients and were associated with synthesis and degradation of ketone bodies, amino acids, propionate and pyruvate metabolism, tricarboxylic acid cycle, and glycolysis. Metabolites altered in urine from MS patients were shown to be related to known pathogenic processes relevant to MS, including alterations in energy and fatty acid metabolism, mitochondrial activity, and the gut microbiota.

  10. Molecular signatures of neural connectivity in the olfactory cortex

    PubMed Central

    Diodato, Assunta; Ruinart de Brimont, Marion; Yim, Yeong Shin; Derian, Nicolas; Perrin, Sandrine; Pouch, Juliette; Klatzmann, David; Garel, Sonia; Choi, Gloria B; Fleischmann, Alexander

    2016-01-01

    The ability to target subclasses of neurons with defined connectivity is crucial for uncovering neural circuit functions. The olfactory (piriform) cortex is thought to generate odour percepts and memories, and odour information encoded in piriform is routed to target brain areas involved in multimodal sensory integration, cognition and motor control. However, it remains unknown if piriform outputs are spatially organized, and if distinct output channels are delineated by different gene expression patterns. Here we identify genes selectively expressed in different layers of the piriform cortex. Neural tracing experiments reveal that these layer-specific piriform genes mark different subclasses of neurons, which project to distinct target areas. Interestingly, these molecular signatures of connectivity are maintained in reeler mutant mice, in which neural positioning is scrambled. These results reveal that a predictive link between a neuron's molecular identity and connectivity in this cortical circuit is determined independent of its spatial position. PMID:27426965

  11. Extracellular matrix proteomics identifies molecular signature of symptomatic carotid plaques

    PubMed Central

    Langley, Sarah R.; Willeit, Karin; Didangelos, Athanasios; Matic, Ljubica Perisic; Skroblin, Philipp; Barallobre-Barreiro, Javier; Lengquist, Mariette; Rungger, Gregor; Kapustin, Alexander; Kedenko, Ludmilla; Molenaar, Chris; Lu, Ruifang; Barwari, Temo; Suna, Gonca; Iglseder, Bernhard; Paulweber, Bernhard; Willeit, Peter; Pasterkamp, Gerard; Davies, Alun H.; Monaco, Claudia; Hedin, Ulf; Shanahan, Catherine M.; Willeit, Johann; Kiechl, Stefan

    2017-01-01

    BACKGROUND. The identification of patients with high-risk atherosclerotic plaques prior to the manifestation of clinical events remains challenging. Recent findings question histology- and imaging-based definitions of the “vulnerable plaque,” necessitating an improved approach for predicting onset of symptoms. METHODS. We performed a proteomics comparison of the vascular extracellular matrix and associated molecules in human carotid endarterectomy specimens from 6 symptomatic versus 6 asymptomatic patients to identify a protein signature for high-risk atherosclerotic plaques. Proteomics data were integrated with gene expression profiling of 121 carotid endarterectomies and an analysis of protein secretion by lipid-loaded human vascular smooth muscle cells. Finally, epidemiological validation of candidate biomarkers was performed in two community-based studies. RESULTS. Proteomics and at least one of the other two approaches identified a molecular signature of plaques from symptomatic patients that comprised matrix metalloproteinase 9, chitinase 3-like-1, S100 calcium binding protein A8 (S100A8), S100A9, cathepsin B, fibronectin, and galectin-3-binding protein. Biomarker candidates measured in 685 subjects in the Bruneck study were associated with progression to advanced atherosclerosis and incidence of cardiovascular disease over a 10-year follow-up period. A 4-biomarker signature (matrix metalloproteinase 9, S100A8/S100A9, cathepsin D, and galectin-3-binding protein) improved risk prediction and was successfully replicated in an independent cohort, the SAPHIR study. CONCLUSION. The identified 4-biomarker signature may improve risk prediction and diagnostics for the management of cardiovascular disease. Further, our study highlights the strength of tissue-based proteomics for biomarker discovery. FUNDING. UK: British Heart Foundation (BHF); King’s BHF Center; and the National Institute for Health Research Biomedical Research Center based at Guy’s and St

  12. Signature properties of water: Their molecular electronic origins

    PubMed Central

    Jones, Andrew P.; Cipcigan, Flaviu S.; Crain, Jason; Martyna, Glenn J.

    2015-01-01

    Water challenges our fundamental understanding of emergent materials properties from a molecular perspective. It exhibits a uniquely rich phenomenology including dramatic variations in behavior over the wide temperature range of the liquid into water’s crystalline phases and amorphous states. We show that many-body responses arising from water’s electronic structure are essential mechanisms harnessed by the molecule to encode for the distinguishing features of its condensed states. We treat the complete set of these many-body responses nonperturbatively within a coarse-grained electronic structure derived exclusively from single-molecule properties. Such a “strong coupling” approach generates interaction terms of all symmetries to all orders, thereby enabling unique transferability to diverse local environments such as those encountered along the coexistence curve. The symmetries of local motifs that can potentially emerge are not known a priori. Consequently, electronic responses unfiltered by artificial truncation are then required to embody the terms that tip the balance to the correct set of structures. Therefore, our fully responsive molecular model produces, a simple, accurate, and intuitive picture of water’s complexity and its molecular origin, predicting water’s signature physical properties from ice, through liquid–vapor coexistence, to the critical point. PMID:25941394

  13. Blind separation of multiple vehicle signatures in frequency domain

    NASA Astrophysics Data System (ADS)

    Azimi-Sadjadi, M. R.; Srinivasan, S.

    2005-05-01

    This paper considers the problem of classifying ground vehicles using their acoustic signatures recorded by unattended passive acoustic sensors. Using these sensors, acoustic signatures of a wide variety of sources such as trucks, tanks, personnel, and airborne targets can be recorded. Additionally, interference sources such as wind noise and ambient noise are typically present. The proposed approach in this paper relies on the blind source separation of the recorded signatures of various sources. Two different frequency domain source separation methods have been employed to separate the vehicle signatures that overlap both spectrally and temporally. These methods rely on the frequency domain extension of the independent component analysis (ICA) method and a joint diagonalization of the time varying spectra. Spectral and temporal-dependent features are then extracted from the separated sources using a new feature extraction method and subsequently used for target classification using a three-layer neural network. The performance of the developed algorithms are demonstrated on a subset of a real acoustic signature database acquired from the US Army TACOM-ARDEC, Picatinny Arsenal, NJ.

  14. Molecular signatures associated with cognitive deficits in schizophrenia: a study of biopsied olfactory neural epithelium

    PubMed Central

    Horiuchi, Y; Kondo, M A; Okada, K; Takayanagi, Y; Tanaka, T; Ho, T; Varvaris, M; Tajinda, K; Hiyama, H; Ni, K; Colantuoni, C; Schretlen, D; Cascella, N G; Pevsner, J; Ishizuka, K; Sawa, A

    2016-01-01

    Cognitive impairment is a key feature of schizophrenia (SZ) and determines functional outcome. Nonetheless, molecular signatures in neuronal tissues that associate with deficits are not well understood. We conducted nasal biopsy to obtain olfactory epithelium from patients with SZ and control subjects. The neural layers from the biopsied epithelium were enriched by laser-captured microdissection. We then performed an unbiased microarray expression study and implemented a systematic neuropsychological assessment on the same participants. The differentially regulated genes in SZ were further filtered based on correlation with neuropsychological traits. This strategy identified the SMAD 5 gene, and real-time quantitative PCR analysis also supports downregulation of the SMAD pathway in SZ. The SMAD pathway has been important in multiple tissues, including the role for neurodevelopment and bone formation. Here the involvement of the pathway in adult brain function is suggested. This exploratory study establishes a strategy to better identify neuronal molecular signatures that are potentially associated with mental illness and cognitive deficits. We propose that the SMAD pathway may be a novel target in addressing cognitive deficit of SZ in future studies. PMID:27727244

  15. Gene-expression signature of benign monoclonal gammopathy evident in multiple myeloma is linked to good prognosis

    PubMed Central

    Zhan, Fenghuang; Barlogie, Bart; Arzoumanian, Varant; Huang, Yongsheng; Williams, David R.; Hollmig, Klaus; Pineda-Roman, Mauricio; Tricot, Guido; van Rhee, Frits; Zangari, Maurizio; Dhodapkar, Madhav; Shaughnessy, John D.

    2007-01-01

    Monoclonal gammopathy of undetermined significance (MGUS) can progress to multiple myeloma (MM). Although these diseases share many of the same genetic features, it is still unclear whether global gene-expression profiling might identify prior genomic signatures that distinguish them. Through significance analysis of microarrays, 52 genes involved in important pathways related to cancer were differentially expressed in the plasma cells of healthy subjects (normal plasma-cell [NPC]; n = 22) and patients with stringently defined MGUS/smoldering MM (n = 24) and symptomatic MM (n = 351) (P < .001). Unsupervised hierarchical clustering of 351 patients with MM, 44 with MGUS (24 + 20), and 16 with MM from MGUS created 2 major cluster branches, one containing 82% of the MGUS patients and the other containing 28% of the MM patients, termed MGUS-like MM (MGUS-L MM). Using the same clustering approach on an independent cohort of 214 patients with MM, 27% were found to be MGUS-L. This molecular signature, despite its association with a lower incidence of complete remission (P = .006), was associated with low-risk clinical and molecular features and superior survival (P < .01). The MGUS-L signature was also seen in plasma cells from 15 of 20 patients surviving more than 10 years after autotransplantation. These data provide insight into the molecular mechanisms of plasma-cell dyscrasias. PMID:17023574

  16. Molecular signatures in response to Isoliquiritigenin in lymphoblastoid cell lines

    SciTech Connect

    Lee, Jae-Eun; Hong, Eun-Jung; Nam, Hye-Young; Hwang, Meeyul; Kim, Ji-Hyun; Han, Bok-Ghee; Jeon, Jae-Pil

    2012-10-19

    Highlights: Black-Right-Pointing-Pointer We identified the inhibitory effect of ISL on cell proliferation of LCLs. Black-Right-Pointing-Pointer We found ISL-induced genes and miRNAs through microarray approach. Black-Right-Pointing-Pointer ISL-treated LCLs represented gene expression changes in cell cycle and p53 pathway. Black-Right-Pointing-Pointer We revealed 12 putative mRNA-miRNA functional pairs associated with ISL effect. -- Abstract: Isoliquiritigenin (ISL) has been known to induce cell cycle arrest and apoptosis of various cancer cells. However, genetic factors regulating ISL effects remain unclear. The aim of this study was to identify the molecular signatures involved in ISL-induced cell death of EBV-transformed lymphoblastoid cell lines (LCLs) using microarray analyses. For gene expression and microRNA (miRNA) microarray experiments, each of 12 LCL strains was independently treated with ISL or DMSO as a vehicle control for a day prior to total RNA extraction. ISL treatment inhibited cell proliferation of LCLs in a dose-dependent manner. Microarray analysis showed that ISL-treated LCLs represented gene expression changes in cell cycle and p53 signaling pathway, having a potential as regulators in LCL survival and sensitivity to ISL-induced cytotoxicity. In addition, 36 miRNAs including five miRNAs with unknown functions were differentially expressed in ISL-treated LCLs. The integrative analysis of miRNA and gene expression profiles revealed 12 putative mRNA-miRNA functional pairs. Among them, miR-1207-5p and miR-575 were negatively correlated with p53 pathway- and cell cycle-associated genes, respectively. In conclusion, our study suggests that miRNAs play an important role in ISL-induced cytotoxicity in LCLs by targeting signaling pathways including p53 pathway and cell cycle.

  17. Revealing the molecular signatures of host-pathogen interactions

    PubMed Central

    2011-01-01

    Advances in sequencing technology and genome-wide association studies are now revealing the complex interactions between hosts and pathogen through genomic variation signatures, which arise from evolutionary co-existence. PMID:22011345

  18. Transcriptome analysis and molecular signature of human retinal pigment epithelium

    PubMed Central

    Strunnikova, N.V.; Maminishkis, A.; Barb, J.J.; Wang, F.; Zhi, C.; Sergeev, Y.; Chen, W.; Edwards, A.O.; Stambolian, D.; Abecasis, G.; Swaroop, A.; Munson, P.J.; Miller, S.S.

    2010-01-01

    Retinal pigment epithelium (RPE) is a polarized cell layer critical for photoreceptor function and survival. The unique physiology and relationship to the photoreceptors make the RPE a critical determinant of human vision. Therefore, we performed a global expression profiling of native and cultured human fetal and adult RPE and determined a set of highly expressed ‘signature’ genes by comparing the observed RPE gene profiles to the Novartis expression database (SymAtlas: http://wombat.gnf.org/index.html) of 78 tissues. Using stringent selection criteria of at least 10-fold higher expression in three distinct preparations, we identified 154 RPE signature genes, which were validated by qRT-PCR analysis in RPE and in an independent set of 11 tissues. Several of the highly expressed signature genes encode proteins involved in visual cycle, melanogenesis and cell adhesion and Gene ontology analysis enabled the assignment of RPE signature genes to epithelial channels and transporters (ClCN4, BEST1, SLCA20) or matrix remodeling (TIMP3, COL8A2). Fifteen RPE signature genes were associated with known ophthalmic diseases, and 25 others were mapped to regions of disease loci. An evaluation of the RPE signature genes in a recently completed AMD genomewide association (GWA) data set revealed that TIMP3, GRAMD3, PITPNA and CHRNA3 signature genes may have potential roles in AMD pathogenesis and deserve further examination. We propose that RPE signature genes are excellent candidates for retinal diseases and for physiological investigations (e.g. dopachrome tautomerase in melanogenesis). The RPE signature gene set should allow the validation of RPE-like cells derived from human embryonic or induced pluripotent stem cells for cell-based therapies of degenerative retinal diseases. PMID:20360305

  19. Signatures of multiple stellar populations in unresolved extragalactic globular/young massive star clusters

    SciTech Connect

    Peacock, Mark B.; Zepf, Stephen E.; Finzell, Thomas

    2013-06-01

    We present an investigation of potential signatures of the formation of multiple stellar populations in recently formed extragalactic star clusters. All of the Galactic globular clusters for which good samples of individual stellar abundances are available show evidence for multiple populations. This appears to require that multiple episodes of star formation and light element enrichment are the norm in the history of a globular cluster. We show that there are detectable observational signatures of multiple formation events in the unresolved spectra of massive, young extragalactic star clusters. We present the results of a pilot program to search for one of the cleanest signatures that we identify—the combined presence of emission lines from a very recently formed population and absorption lines from a somewhat older population. A possible example of such a system is identified in the Antennae galaxies. This source's spectrum shows evidence of two stellar populations with ages of 8 Myr and 80 Myr. Further investigation shows that these populations are in fact physically separated, but only by a projected distance of 59 pc. We show that the clusters are consistent with being bound and discuss the possibility that their coalescence could result in a single globular cluster hosting multiple stellar populations. While not the prototypical system proposed by most theories of the formation of multiple populations in clusters, the detection of this system in a small sample is both encouraging and interesting. Our investigation suggests that expanded surveys of massive young star clusters should detect more clusters with such signatures.

  20. Identification of characteristic molecular signature for volatile organic compounds in peripheral blood of rat

    SciTech Connect

    Kim, Jeong Kyu; Jung, Kwang Hwa; Noh, Ji Heon; Eun, Jung Woo; Bae, Hyun Jin; Xie, Hong Jian; Jang, Ja-June; Ryu, Jae Chun; Park, Won Sang; Lee, Jung Young; Nam, Suk Woo

    2011-01-15

    In a previous report we demonstrated that the transcriptomic response of liver tissue was specific to toxicants, and a characteristic molecular signature could be used as an early prognostic biomarker in rats. It is necessary to determine the transcriptomic response to toxicants in peripheral blood for application to the human system. Volatile organic compounds (VOCs) comprise a major group of pollutants which significantly affect the chemistry of the atmosphere and human health. In this study we identified and validated the specific molecular signatures of toxicants in rat whole blood as early predictors of environmental toxicants. VOCs (dichloromethane, ethylbenzene, and trichloroethylene) were administered to 11-week-old SD male rats after 48 h of exposure, peripheral whole blood was subjected to expression profiling analysis. Unsupervised gene expression analysis resulted in a characteristic molecular signature for each toxicant, and supervised analysis identified 1,217 outlier genes as distinct molecular signatures discerning VOC exposure from healthy controls. Further analysis of multi-classification suggested 337 genes as early detective molecular markers for three VOCs with 100% accuracy. A large-scale gene expression analysis of a different VOC exposure animal model suggested that characteristic expression profiles exist in blood cells and multi-classification of this VOC-specific molecular signature can discriminate each toxicant at an early exposure time. This blood expression signature can thus be used as discernable surrogate marker for detection of biological responses to VOC exposure in an environment.

  1. Improvement of a quantum broadcasting multiple blind signature scheme based on quantum teleportation

    NASA Astrophysics Data System (ADS)

    Zhang, Wei; Qiu, Daowen; Zou, Xiangfu

    2016-06-01

    Recently, a broadcasting multiple blind signature scheme based on quantum teleportation has been proposed for the first time. It is claimed to have unconditional security and properties of quantum multiple signature and quantum blind signature. In this paper, we analyze the security of the protocol and show that each signatory can learn the signed message by a single-particle measurement and the signed message can be modified at random by any attacker according to the scheme. Furthermore, there are some participant attacks and external attacks existing in the scheme. Finally, we present an improved scheme and show that it can resist all of the mentioned attacks. Additionally, the secret keys can be used again and again, making it more efficient and practical.

  2. A DYNAMICAL SIGNATURE OF MULTIPLE STELLAR POPULATIONS IN 47 TUCANAE

    SciTech Connect

    Richer, Harvey B.; Heyl, Jeremy; Anderson, Jay; Kalirai, Jason S.; Shara, Michael M.; Dotter, Aaron; Fahlman, Gregory G.; Rich, R. Michael E-mail: heyl@phas.ubc.ca E-mail: jkalarai@stsci.edu E-mail: aaron.dotter@gmail.com E-mail: rmr@astro.ucla.edu

    2013-07-01

    Based on the width of its main sequence, and an actual observed split when viewed through particular filters, it is widely accepted that 47 Tucanae contains multiple stellar populations. In this contribution, we divide the main sequence of 47 Tuc into four color groups, which presumably represent stars of various chemical compositions. The kinematic properties of each of these groups are explored via proper motions, and a strong signal emerges of differing proper-motion anisotropies with differing main-sequence color; the bluest main-sequence stars exhibit the largest proper-motion anisotropy which becomes undetectable for the reddest stars. In addition, the bluest stars are also the most centrally concentrated. A similar analysis for Small Magellanic Cloud stars, which are located in the background of 47 Tuc on our frames, yields none of the anisotropy exhibited by the 47 Tuc stars. We discuss implications of these results for possible formation scenarios of the various populations.

  3. Molecular signature of erythroblast enucleation in human embryonic stem cells.

    PubMed

    Rouzbeh, Shaghayegh; Kobari, Ladan; Cambot, Marie; Mazurier, Christelle; Hebert, Nicolas; Faussat, Anne-Marie; Durand, Charles; Douay, Luc; Lapillonne, Hélène

    2015-08-01

    While enucleation is a critical step in the terminal differentiation of human red blood cells, the molecular mechanisms underlying this unique process remain unclear. To investigate erythroblast enucleation, we studied the erythroid differentiation of human embryonic stem cells (hESCs), which provide a unique model for deeper understanding of the development and differentiation of multiple cell types. First, using a two-step protocol, we demonstrated that terminal erythroid differentiation from hESCs is directly dependent on the age of the embryoid bodies. Second, by choosing hESCs in two extreme conditions of erythroid culture, we obtained an original differentiation model which allows one to study the mechanisms underlying the enucleation of erythroid cells by analyzing the gene and miRNA (miR) expression profiles of cells from these two culture conditions. Third, using an integrated analysis of mRNA and miR expression profiles, we identified five miRs potentially involved in erythroblast enucleation. Finally, by selective knockdown of these five miRs we found miR-30a to be a regulator of erythroblast enucleation in hESCs.

  4. Molecular signature of anastasis for reversal of apoptosis

    PubMed Central

    Tang, Ho Man; Talbot Jr, C. Conover; Fung, Ming Chiu; Tang, Ho Lam

    2017-01-01

    Anastasis (Greek for "rising to life") is a cell recovery phenomenon that rescues dying cells from the brink of cell death. We recently discovered anastasis to occur after the execution-stage of apoptosis in vitro and in vivo. Promoting anastasis could in principle preserve injured cells that are difficult to replace, such as cardiomyocytes and neurons. Conversely, arresting anastasis in dying cancer cells after cancer therapies could improve treatment efficacy. To develop new therapies that promote or inhibit anastasis, it is essential to identify the key regulators and mediators of anastasis – the therapeutic targets. Therefore, we performed time-course microarray analysis to explore the molecular mechanisms of anastasis during reversal of ethanol-induced apoptosis in mouse primary liver cells. We found striking changes in transcription of genes involved in multiple pathways, including early activation of pro-cell survival, anti-oxidation, cell cycle arrest, histone modification, DNA-damage and stress-inducible responses, and at delayed times, angiogenesis and cell migration. Validation with RT-PCR confirmed similar changes in the human liver cancer cell line, HepG2, during anastasis. Here, we present the time-course whole-genome gene expression dataset revealing gene expression profiles during the reversal of apoptosis. This dataset provides important insights into the physiological, pathological, and therapeutic implications of anastasis. PMID:28299189

  5. Uncovering the Hidden Molecular Signatures of Breast Cancer

    DTIC Science & Technology

    2012-05-01

    aromatase   inhibitor ...is  more   natural  for  samples  to  display  a  range  of  activation  levels  for  a  given  signature.  This...more   natural   for   human   breast   tumors   to   display   a   range   in   signal  activation  levels  or

  6. The molecular signature of selection underlying human adaptations.

    PubMed

    Harris, Eugene E; Meyer, Diogo

    2006-01-01

    In the last decade, advances in human population genetics and comparative genomics have resulted in important contributions to our understanding of human genetic diversity and genetic adaptation. For the first time, we are able to reliably detect the signature of natural selection from patterns of DNA polymorphism. Identifying the effects of natural selection in this way provides a crucial piece of evidence needed to support hypotheses of human adaptation. This review provides a detailed description of the theory and analytical approaches used to detect signatures of natural selection in the human genome. We discuss these methods in relation to four classic human traits--skin color, the Duffy blood group, bitter-taste sensation, and lactase persistence. By highlighting these four traits we are able to discuss the ways in which analyses of DNA polymorphism can lead to inferences regarding past histories of selection. Specifically, we can infer the importance of specific regimes of selection (i.e. directional selection, balancing selection, and purifying selection) in the evolution of a trait because these different types of selection leave different patterns of DNA polymorphism. In addition, we demonstrate how these types of data can be used to estimate the time frame in which selection operated on a trait. As the field has advanced, a general issue that has come to the forefront is how specific demographic events in human history, such as population expansions, bottlenecks, and subdivision of populations, have also left a signature across the genome that can interfere with our detection of the footprint of selection at particular genes. Therefore, we discuss this general problem with respect to the four traits reviewed here, and describe the ways in which the signature of selection can be teased from a background signature of demographic history. Finally, we move from a discussion of analyses of selection motivated by a "candidate-gene" approach, in which a priori

  7. Instance influence estimation for hyperspectral target signature characterization using extended functions of multiple instances

    NASA Astrophysics Data System (ADS)

    Zou, Sheng; Zare, Alina

    2016-05-01

    The Extended Functions of Multiple Instances (eFUMI) algorithm1 is a generalization of Multiple Instance Learning (MIL). In eFUMI, only bag level (i.e. set level) labels are needed to estimate target signatures from mixed data. The training bags in eFUMI are labeled positive if any data point in a bag contains or represents any proportion of the target signature and are labeled as a negative bag if all data points in the bag do not represent any target. From these imprecise labels, eFUMI has been shown to be effective at estimating target signatures in hyperspectral subpixel target detection problems. One motivating scenario for the use of eFUMI is where an analyst circles objects/regions of interest in a hyperspectral scene such that the target signatures of these objects can be estimated and be used to determine whether other instances of the object appear elsewhere in the image collection. The regions highlighted by the analyst serve as the imprecise labels for eFUMI. Often, an analyst may want to iteratively refine their imprecise labels. In this paper, we present an approach for estimating the influence on the estimated target signature if the label for a particular input data point is modified. This instance influence estimation guides an analyst to focus on (re-)labeling the data points that provide the largest change in the resulting estimated target signature and, thus, reduce the amount of time an analyst needs to spend refining the labels for a hyperspectral scene. Results are shown on real hyperspectral sub-pixel target detection data sets.

  8. Multi-Tissue Microarray Analysis Identifies a Molecular Signature of Regeneration

    PubMed Central

    Mercer, Sarah E.; Cheng, Chia-Ho; Atkinson, Donald L.; Krcmery, Jennifer; Guzman, Claudia E.; Kent, David T.; Zukor, Katherine; Marx, Kenneth A.; Odelberg, Shannon J.; Simon, Hans-Georg

    2012-01-01

    The inability to functionally repair tissues that are lost as a consequence of disease or injury remains a significant challenge for regenerative medicine. The molecular and cellular processes involved in complete restoration of tissue architecture and function are expected to be complex and remain largely unknown. Unlike humans, certain salamanders can completely regenerate injured tissues and lost appendages without scar formation. A parsimonious hypothesis would predict that all of these regenerative activities are regulated, at least in part, by a common set of genes. To test this hypothesis and identify genes that might control conserved regenerative processes, we performed a comprehensive microarray analysis of the early regenerative response in five regeneration-competent tissues from the newt Notophthalmus viridescens. Consistent with this hypothesis, we established a molecular signature for regeneration that consists of common genes or gene family members that exhibit dynamic differential regulation during regeneration in multiple tissue types. These genes include members of the matrix metalloproteinase family and its regulators, extracellular matrix components, genes involved in controlling cytoskeleton dynamics, and a variety of immune response factors. Gene Ontology term enrichment analysis validated and supported their functional activities in conserved regenerative processes. Surprisingly, dendrogram clustering and RadViz classification also revealed that each regenerative tissue had its own unique temporal expression profile, pointing to an inherent tissue-specific regenerative gene program. These new findings demand a reconsideration of how we conceptualize regenerative processes and how we devise new strategies for regenerative medicine. PMID:23300656

  9. Molecular Signatures of Obstructive Sleep Apnea in Adults: A Review and Perspective

    PubMed Central

    Arnardottir, Erna S.; Mackiewicz, Miroslaw; Gislason, Thorarinn; Teff, Karen L.; Pack, Allan I.

    2009-01-01

    The consequences of obstructive sleep apnea (OSA) are largely mediated by chronic intermittent hypoxia and sleep fragmentation. The primary molecular domains affected are sympathetic activity, oxidative stress and inflammation. Other affected domains include adipokines, adhesion molecules and molecules that respond to endoplasmic reticulum stress. Changes in molecular domains affected by OSA, assessed in blood and/or urine, can provide a molecular signature for OSA that could potentially be used diagnostically and to predict who is likely to develop different OSA-related comorbidities. High-throughput discovery strategies such as microarrays, assessing changes in gene expression in circulating blood cells, have the potential to find new candidates and pathways thereby expanding the molecular signatures for OSA. More research is needed to fully understand the pathophysiological significance of these molecular signatures and their relationship with OSA comorbidities. Many OSA subjects are obese, and obesity is an independent risk factor for many comorbidities associated with OSA. Moreover, obesity affects the same molecular pathways as OSA. Thus, a challenge to establishing a molecular signature for OSA is to separate the effects of OSA from obesity. We propose that the optimal strategy is to evaluate the temporal changes in relevant molecular pathways during sleep and, in particular, the alterations from before to after sleep when assessed in blood and/or urine. Such changes will be at least partly a consequence of chronic intermittent hypoxia and sleep fragmentation that occurs during sleep. Citation: Arnardottir ES; Mackiewicz M; Gislason T; Teff KL; Pack AI. Molecular signatures of obstructive sleep apnea in adults: A review and perspective. SLEEP 2009;32(4):447–470. PMID:19413140

  10. Molecular signatures of lung cancer: defining new diagnostic and therapeutic paradigms.

    PubMed

    Balko, Justin M; Arteaga, Carlos L

    2012-02-01

    Molecular profiling holds great promise for improving our ability to diagnose, prognosticate, and select individualized treatments for lung cancer patients. However, using multidimensional data and novel technologies to derive these profiles is limited by our ability to employ the assay in a clinical scenario where it can impact the course of disease. Although many molecular signatures have been reported in lung cancer, as of yet, few have been sufficiently validated for widespread clinical use. Recently, several novel signatures have been reported, which address critical aspects of patient care and/or demonstrate improved efforts for appropriate clinical validation. Here, we present our opinion on the current state of the field of molecular signatures in lung cancer.

  11. Estimation of the Performance of Multiple Active Neutron Interrogation Signatures for Detecting Shielded HEU

    SciTech Connect

    David L. Chichester; Scott J. Thompson; Scott M. Watson; James T. Johnson; Edward H. Seabury

    2012-10-01

    A comprehensive modeling study has been carried out to evaluate the utility of multiple active neutron interrogation signatures for detecting shielded highly enriched uranium (HEU). The modeling effort focused on varying HEU masses from 1 kg to 20 kg; varying types of shields including wood, steel, cement, polyethylene, and borated polyethylene; varying depths of the HEU in the shields, and varying engineered shields immediately surrounding the HEU including steel, tungsten, and cadmium. Neutron and gamma-ray signatures were the focus of the study and false negative detection probabilities versus measurement time were used as a performance metric. To facilitate comparisons among different approaches an automated method was developed to generate receiver operating characteristic (ROC) curves for different sets of model variables for multiple background count rate conditions. This paper summarizes results or the analysis, including laboratory benchmark comparisons between simulations and experiments. The important impact engineered shields can play towards degrading detectability and methods for mitigating this will be discussed.

  12. Micro-Doppler analysis of multiple frequency continuous wave radar signatures

    NASA Astrophysics Data System (ADS)

    Anderson, Michael G.; Rogers, Robert L.

    2007-04-01

    Micro-Doppler refers to Doppler scattering returns produced by non rigid-body motion. Micro-Doppler gives rise to many detailed radar image features in addition to those associated with bulk target motion. Targets of different classes (for example, humans, animals, and vehicles) produce micro-Doppler images that are often distinguishable even by nonexpert observers. Micro-Doppler features have great potential for use in automatic target classification algorithms. Although the potential benefit of using micro-Doppler in classification algorithms is high, relatively little experimental (non-synthetic) micro-Doppler data exists. Much of the existing experimental data comes from highly cooperative targets (human or vehicle targets directly approaching the radar). This research involved field data collection and analysis of micro-Doppler radar signatures from non-cooperative targets. The data was collected using a low cost Xband multiple frequency continuous wave (MFCW) radar with three transmit frequencies. The collected MFCW radar signatures contain data from humans, vehicles, and animals. The presented data includes micro-Doppler signatures previously unavailable in the literature such as crawling humans and various animal species. The animal micro-Doppler signatures include deer, dog, and goat datasets. This research focuses on the analysis of micro-Doppler from noncooperative targets approaching the radar at various angles, maneuvers, and postures.

  13. Phylogeny and molecular signatures for the phylum Fusobacteria and its distinct subclades.

    PubMed

    Gupta, Radhey S; Sethi, Mohit

    2014-08-01

    The members of the phylum Fusobacteria and its two families, Fusobacteriaceae and Leptotrichiaceae, are distinguished at present mainly on the basis of their branching in the 16S rRNA gene trees and analysis of the internal transcribed spacer sequences in the 16S-23S rDNA. However, no biochemical or molecular characteristics are known that are uniquely shared by all of most members of these groups of bacteria. We report here detailed phylogenetic and comparative analyses on 45 sequenced Fusobacteria genomes to examine their evolutionary relationships and to identify molecular markers that are specific for the members of this phylum. In phylogenetic trees based on 16S rRNA gene sequences or concatenated sequences for 17 conserved proteins, members of the families Fusobacteriaceae and Leptotrichiaceae formed strongly supported clades and were clearly distinguished. In these trees, the species from the genus Fusobacterium also formed a number of well-supported clades. In parallel, comparative analyses on Fusobacteria genomes have identified 44 conserved signature indels (CSIs) in proteins involved in a broad range of functions that are either specific for the phylum Fusobacteria or a number of distinct subclades within this phylum. Seven of these CSIs in important proteins are uniquely present in the protein homologs of all sequenced Fusobacteria and they provide potential molecular markers for this phylum. Six and three other CSIs in other protein sequences are specific for members of the families Fusobacteriaceae and Leptotrichiaceae, respectively, and they provide novel molecular means for distinguishing members of these two families. Fourteen additional CSIs in different proteins, which are specific for either members of the genera Fusobacterium or Leptotrichia, or a number of other well-supported clades of Fusobacteria at multiple phylogenetic levels, provide molecular markers for these groups and information regarding the evolutionary relationships among the

  14. Molecular Signatures of Membrane Protein Complexes Underlying Muscular Dystrophy*

    PubMed Central

    Turk, Rolf; Hsiao, Jordy J.; Smits, Melinda M.; Ng, Brandon H.; Pospisil, Tyler C.; Jones, Kayla S.; Campbell, Kevin P.; Wright, Michael E.

    2016-01-01

    Mutations in genes encoding components of the sarcolemmal dystrophin-glycoprotein complex (DGC) are responsible for a large number of muscular dystrophies. As such, molecular dissection of the DGC is expected to both reveal pathological mechanisms, and provides a biological framework for validating new DGC components. Establishment of the molecular composition of plasma-membrane protein complexes has been hampered by a lack of suitable biochemical approaches. Here we present an analytical workflow based upon the principles of protein correlation profiling that has enabled us to model the molecular composition of the DGC in mouse skeletal muscle. We also report our analysis of protein complexes in mice harboring mutations in DGC components. Bioinformatic analyses suggested that cell-adhesion pathways were under the transcriptional control of NFκB in DGC mutant mice, which is a finding that is supported by previous studies that showed NFκB-regulated pathways underlie the pathophysiology of DGC-related muscular dystrophies. Moreover, the bioinformatic analyses suggested that inflammatory and compensatory mechanisms were activated in skeletal muscle of DGC mutant mice. Additionally, this proteomic study provides a molecular framework to refine our understanding of the DGC, identification of protein biomarkers of neuromuscular disease, and pharmacological interrogation of the DGC in adult skeletal muscle https://www.mda.org/disease/congenital-muscular-dystrophy/research. PMID:27099343

  15. Identification of a common Wnt-associated genetic signature across multiple cell types in pulmonary arterial hypertension.

    PubMed

    West, James D; Austin, Eric D; Gaskill, Christa; Marriott, Shennea; Baskir, Rubin; Bilousova, Ganna; Jean, Jyh-Chang; Hemnes, Anna R; Menon, Swapna; Bloodworth, Nathaniel C; Fessel, Joshua P; Kropski, Johnathan A; Irwin, David; Ware, Lorraine B; Wheeler, Lisa; Hong, Charles C; Meyrick, Barbara; Loyd, James E; Bowman, Aaron B; Ess, Kevin C; Klemm, Dwight J; Young, Pampee P; Merryman, W David; Kotton, Darrell; Majka, Susan M

    2014-09-01

    Understanding differences in gene expression that increase risk for pulmonary arterial hypertension (PAH) is essential to understanding the molecular basis for disease. Previous studies on patient samples were limited by end-stage disease effects or by use of nonadherent cells, which are not ideal to model vascular cells in vivo. These studies addressed the hypothesis that pathological processes associated with PAH may be identified via a genetic signature common across multiple cell types. Expression array experiments were initially conducted to analyze cell types at different stages of vascular differentiation (mesenchymal stromal and endothelial) derived from PAH patient-specific induced pluripotent stem (iPS) cells. Molecular pathways that were altered in the PAH cell lines were then compared with those in fibroblasts from 21 patients, including those with idiopathic and heritable PAH. Wnt was identified as a target pathway and was validated in vitro using primary patient mesenchymal and endothelial cells. Taken together, our data suggest that the molecular lesions that cause PAH are present in all cell types evaluated, regardless of origin, and that stimulation of the Wnt signaling pathway was a common molecular defect in both heritable and idiopathic PAH.

  16. A new molecular signature method for prediction of driver cancer pathways from transcriptional data

    PubMed Central

    Rykunov, Dmitry; Beckmann, Noam D.; Li, Hui; Uzilov, Andrew; Schadt, Eric E.; Reva, Boris

    2016-01-01

    Assigning cancer patients to the most effective treatments requires an understanding of the molecular basis of their disease. While DNA-based molecular profiling approaches have flourished over the past several years to transform our understanding of driver pathways across a broad range of tumors, a systematic characterization of key driver pathways based on RNA data has not been undertaken. Here we introduce a new approach for predicting the status of driver cancer pathways based on signature functions derived from RNA sequencing data. To identify the driver cancer pathways of interest, we mined DNA variant data from TCGA and nominated driver alterations in seven major cancer pathways in breast, ovarian and colon cancer tumors. The activation status of these driver pathways were then characterized using RNA sequencing data by constructing classification signature functions in training datasets and then testing the accuracy of the signatures in test datasets. The signature functions differentiate well tumors with nominated pathway activation from tumors with no signs of activation: average AUC equals to 0.83. Our results confirm that driver genomic alterations are distinctively displayed at the transcriptional level and that the transcriptional signatures can generally provide an alternative to DNA sequencing methods in detecting specific driver pathways. PMID:27098033

  17. A new molecular signature method for prediction of driver cancer pathways from transcriptional data.

    PubMed

    Rykunov, Dmitry; Beckmann, Noam D; Li, Hui; Uzilov, Andrew; Schadt, Eric E; Reva, Boris

    2016-06-20

    Assigning cancer patients to the most effective treatments requires an understanding of the molecular basis of their disease. While DNA-based molecular profiling approaches have flourished over the past several years to transform our understanding of driver pathways across a broad range of tumors, a systematic characterization of key driver pathways based on RNA data has not been undertaken. Here we introduce a new approach for predicting the status of driver cancer pathways based on signature functions derived from RNA sequencing data. To identify the driver cancer pathways of interest, we mined DNA variant data from TCGA and nominated driver alterations in seven major cancer pathways in breast, ovarian and colon cancer tumors. The activation status of these driver pathways were then characterized using RNA sequencing data by constructing classification signature functions in training datasets and then testing the accuracy of the signatures in test datasets. The signature functions differentiate well tumors with nominated pathway activation from tumors with no signs of activation: average AUC equals to 0.83. Our results confirm that driver genomic alterations are distinctively displayed at the transcriptional level and that the transcriptional signatures can generally provide an alternative to DNA sequencing methods in detecting specific driver pathways.

  18. Identification of a Unique TGF-β Dependent Molecular and Functional Signature in Microglia

    PubMed Central

    Butovsky, Oleg; Jedrychowski, Mark P.; Moore, Craig S.; Cialic, Ron; Lanser, Amanda J.; Gabriely, Galina; Koeglsperger, Thomas; Dake, Ben; Wu, Pauline M.; Doykan, Camille E.; Fanek, Zain; Liu, LiPing; Chen, Zhuoxun; Rothstein, Jeffrey D.; Ransohoff, Richard M.; Gygi, Steven P.; Antel, Jack P.; Weiner, Howard L.

    2014-01-01

    Microglia are myeloid cells of the central nervous system (CNS) that participate both in normal CNS function and disease. We investigated the molecular signature of microglia and identified 239 genes and 8 microRNAs that were uniquely or highly expressed in microglia vs. myeloid and other immune cells. Out of 239 genes, 106 were enriched in microglia as compared to astrocytes, oligodendrocytes and neurons. This microglia signature was not observed in microglial lines or in monocytes recruited to the CNS and was also observed in human microglia. Based on this signature, we found a crucial role for TGF-β in microglial biology that included: 1) the requirement of TGF-β for the in vitro development of microglia that express the microglial molecular signature characteristic of adult microglia; and 2) the absence of microglia in CNS TGF-β1 deficient mice. Our results identify a unique microglial signature that is dependent on TGF-β signaling which provides insights into microglial biology and the possibility of targeting microglia for the treatment of CNS disease. PMID:24316888

  19. Gene signatures in wound tissue as evidenced by molecular profiling in the chick embryo model

    PubMed Central

    2010-01-01

    Background Modern functional genomic approaches may help to better understand the molecular events involved in tissue morphogenesis and to identify molecular signatures and pathways. We have recently applied transcriptomic profiling to evidence molecular signatures in the development of the normal chicken chorioallantoic membrane (CAM) and in tumor engrafted on the CAM. We have now extended our studies by performing a transcriptome analysis in the "wound model" of the chicken CAM, which is another relevant model of tissue morphogenesis. Results To induce granulation tissue (GT) formation, we performed wounding of the chicken CAM and compared gene expression to normal CAM at the same stage of development. Matched control samples from the same individual were used. We observed a total of 282 genes up-regulated and 44 genes down-regulated assuming a false-discovery rate at 5% and a fold change > 2. Furthermore, bioinformatics analysis lead to the identification of several categories that are associated to organismal injury, tissue morphology, cellular movement, inflammatory disease, development and immune system. Endothelial cell data filtering leads to the identification of several new genes with an endothelial cell signature. Conclusions The chick chorioallantoic wound model allows the identification of gene signatures and pathways involved in GT formation and neoangiogenesis. This may constitute a fertile ground for further studies. PMID:20840761

  20. Circulating miRNAs revealed as surrogate molecular signatures for the early detection of breast cancer.

    PubMed

    Mishra, Sanjay; Srivastava, Amit Kumar; Suman, Shankar; Kumar, Vijay; Shukla, Yogeshwer

    2015-12-01

    The miRNAs have well studied roles in cancer. Here, we identified altered miRNA expression by global miRNA profiling in peripheral blood mononuclear cells (PBMCs) of breast cancer (n = 15) and healthy subjects (n = 15), and further validated the selected miRNAs in PBMCs (n = 45), blood plasma (n = 45) and breast tissue samples (n = 09). The expression of altered miRNAs was also evaluated in PBMCs among early stage (n = 32), advanced stage (n = 13), triple positive (n = 5) and triple negative (n = 5) breast cancer patients. Results showed differential pattern of expressions of these miRNAs in multiple cohorts, however in early stage breast cancer, miR-106a-5p and miR-454-3p were upregulated (p < 0.05), miR-195-5p and miR-495 were downregulated (p < 0.05) in PBMCs. In addition, these miRNAs were also significantly associated with cancer and ErbB signaling pathways. Multiple regression analysis and receiver-operative curve (ROC) analysis of miR-195-5p and miR-495 with area under curve (AUC) of 0.901 showed best discriminating combination for early stage breast cancer detection. In summary, the present study delineated the importance of miR-195-5p and miR-495 miRNAs as prospective circulating surrogate molecular signatures for early detection of breast cancer.

  1. Characteristic molecular and proteomic signatures of drug-induced liver injury in a rat model.

    PubMed

    Eun, Jung Woo; Bae, Hyun Jin; Shen, Qingyu; Park, Se Jin; Kim, Hyung Seok; Shin, Woo Chan; Yang, Hee Doo; Jin, Chan Young; You, Jueng Soo; Kang, Hyun Joo; Kim, Hoguen; Ahn, Young Min; Park, Won Sang; Lee, Jung Young; Nam, Suk Woo

    2015-02-01

    Drug-induced liver injury (DILI) is a major safety concern during drug development and remains one of the main reasons for withdrawal of drugs from the market. Although it is crucial to develop methods that will detect potential hepatotoxicity of drug candidates as early and as quickly as possible, there is still a lack of sensitive and specific biomarkers for DILI that consequently leads to a scarcity of reliable hepatotoxic data. Hence, in this study, we assessed characteristic molecular signatures in rat liver treated with drugs (pyrazinamide, ranitidine, enalapril, carbamazepine and chlorpromazine) that are known to cause DILI in humans. Unsupervised hierarchical clustering analysis of transcriptome changes induced by DILI-causing drugs resulted in three different subclusters on dendrogram, i.e., hepatocellular, cholestatic and mixed type of DILI at early time points (2 days), and multiclassification analysis suggested 31 genes as discernible markers for each DILI pattern. Further analysis for characteristic molecular signature of each DILI pattern provided a molecular basis for different modes of DILI action. A proteomics study of the same rat livers was used to confirm the results, and the two sets of data showed 60 matching classifiers. In conclusion, the data of different DILI-causing drug treatments from genomic analysis in a rat model suggest that DILI-specific molecular signatures can discriminate different patterns of DILI at an early exposure time point, and that they provide useful information for mechanistic studies that may lead to a better understanding of the molecular basis of DILI.

  2. The molecular and gene regulatory signature of a neuron

    PubMed Central

    Hobert, Oliver; Carrera, Inés; Stefanakis, Nikolaos

    2010-01-01

    Neuron-type specific gene batteries define the morphological and functional diversity of cell types in the nervous system. Here, we discuss the composition of neuron-type specific gene batteries and illustrate gene regulatory strategies employed by distinct organisms from C.elegans to higher vertebrates, which are instrumental in determining the unique gene expression profile and molecular composition of individual neuronal cell types. Based on principles learned from prokaryotic gene regulation, we argue that neuronal, terminal gene batteries are functionally grouped into parallel acting “regulons”. The theoretical concepts discussed here provide testable hypotheses for future experimental analysis into the exact gene regulatory mechanisms that are employed in the generation of neuronal diversity and identity. PMID:20663572

  3. CONTRACTION SIGNATURES TOWARD DENSE CORES IN THE PERSEUS MOLECULAR CLOUD

    SciTech Connect

    Campbell, J. L.; Friesen, R. K.; Martin, P. G.; Caselli, P.; Pineda, J. E.; Kauffmann, J.

    2016-03-10

    We report the results of an HCO{sup +} (3–2) and N{sub 2}D{sup +} (3–2) molecular line survey performed toward 91 dense cores in the Perseus molecular cloud using the James Clerk Maxwell Telescope, to identify the fraction of starless and protostellar cores with systematic radial motions. We quantify the HCO{sup +} asymmetry using a dimensionless asymmetry parameter δ{sub v}, and identify 20 cores with significant blue or red line asymmetries in optically thick emission indicative of collapsing or expanding motions, respectively. We separately fit the HCO{sup +} profiles with an analytic collapse model and determine contraction (expansion) speeds toward 22 cores. Comparing the δ{sub v} and collapse model results, we find that δ{sub v} is a good tracer of core contraction if the optically thin emission is aligned with the model-derived systemic velocity. The contraction speeds range from subsonic (0.03 km s{sup −1}) to supersonic (0.4 km s{sup −1}), where the supersonic contraction speeds may trace global rather than local core contraction. Most cores have contraction speeds significantly less than their free-fall speeds. Only 7 of 28 starless cores have spectra well-fit by the collapse model, which more than doubles (15 of 28) for protostellar cores. Starless cores with masses greater than the Jeans mass (M/M{sub J} > 1) are somewhat more likely to show contraction motions. We find no trend of optically thin non-thermal line width with M/M{sub J}, suggesting that any undetected contraction motions are small and subsonic. Most starless cores in Perseus are either not in a state of collapse or expansion, or are in a very early stage of collapse.

  4. Contraction Signatures toward Dense Cores in the Perseus Molecular Cloud

    NASA Astrophysics Data System (ADS)

    Campbell, J. L.; Friesen, R. K.; Martin, P. G.; Caselli, P.; Kauffmann, J.; Pineda, J. E.

    2016-03-01

    We report the results of an HCO+ (3-2) and N2D+ (3-2) molecular line survey performed toward 91 dense cores in the Perseus molecular cloud using the James Clerk Maxwell Telescope, to identify the fraction of starless and protostellar cores with systematic radial motions. We quantify the HCO+ asymmetry using a dimensionless asymmetry parameter δv, and identify 20 cores with significant blue or red line asymmetries in optically thick emission indicative of collapsing or expanding motions, respectively. We separately fit the HCO+ profiles with an analytic collapse model and determine contraction (expansion) speeds toward 22 cores. Comparing the δv and collapse model results, we find that δv is a good tracer of core contraction if the optically thin emission is aligned with the model-derived systemic velocity. The contraction speeds range from subsonic (0.03 km s-1) to supersonic (0.4 km s-1), where the supersonic contraction speeds may trace global rather than local core contraction. Most cores have contraction speeds significantly less than their free-fall speeds. Only 7 of 28 starless cores have spectra well-fit by the collapse model, which more than doubles (15 of 28) for protostellar cores. Starless cores with masses greater than the Jeans mass (M/MJ > 1) are somewhat more likely to show contraction motions. We find no trend of optically thin non-thermal line width with M/MJ, suggesting that any undetected contraction motions are small and subsonic. Most starless cores in Perseus are either not in a state of collapse or expansion, or are in a very early stage of collapse.

  5. Expression profiling elucidates a molecular gene signature for pulmonary hypertension in sarcoidosis

    PubMed Central

    Singla, Sunit; Zhou, Tong; Javaid, Kamran; Abbasi, Taimur; Casanova, Nancy; Zhang, Wei; Ma, Shwu-Fan; Wade, Michael S.; Noth, Imre; Sweiss, Nadera J.; Garcia, Joe G. N.

    2016-01-01

    Abstract Pulmonary hypertension (PH), when it complicates sarcoidosis, carries a poor prognosis, in part because it is difficult to detect early in patients with worsening respiratory symptoms. Pathogenesis of sarcoidosis occurs via incompletely characterized mechanisms that are distinct from the mechanisms of pulmonary vascular remodeling well known to occur in conjunction with other chronic lung diseases. To address the need for a biomarker to aid in early detection as well as the gap in knowledge regarding the mechanisms of PH in sarcoidosis, we used genome-wide peripheral blood gene expression analysis and identified an 18-gene signature capable of distinguishing sarcoidosis patients with PH (n = 8), sarcoidosis patients without PH (n = 17), and healthy controls (n = 45). The discriminative accuracy of this 18-gene signature was 100% in separating sarcoidosis patients with PH from those without it. If validated in a large replicate cohort, this signature could potentially be used as a diagnostic molecular biomarker for sarcoidosis-associated PH. PMID:28090288

  6. Clonogenic Multiple Myeloma Cells have Shared stemness Signature Associated with Patient Survival

    PubMed Central

    Reghunathan, Renji; Bi, Chonglei; Liu, Shaw Cheng; Loong, Koh Tze; Chung, Tae-Hoon; Huang, Gaofeng; Chng, Wee Joo

    2013-01-01

    Multiple myeloma is the abnormal clonal expansion of post germinal B cells in the bone marrow. It was previously reported that clonogenic myeloma cells are CD138−. Human MM cell lines RPMI8226 and NCI H929 contained 2-5% of CD138− population. In this study, we showed that CD138− cells have increased ALDH1 activity, a hallmark of normal and neoplastic stem cells. CD138−ALDH+ cells were more clonogenic than CD138+ALDH− cells and only CD138− cells differentiated into CD138+ population. In vivo tumor initiation and clonogenic potentials of the CD138− population was confirmed using NOG mice. We derived a gene expression signature from functionally validated and enriched CD138− clonogenic population from MM cell lines and validated these in patient samples. This data showed that CD138− cells had an enriched expression of genes that are expressed in normal and malignant stem cells. Differentially expressed genes included components of the polycomb repressor complex (PRC) and their targets. Inhibition of PRC by DZNep showed differential effect on CD138− and CD138+ populations. The ‘stemness’ signature derived from clonogenic CD138− cells overlap significantly with signatures of common progenitor cells, hematopoietic stem cells, and Leukemic stem cells and is associated with poorer survival in different clinical datasets. PMID:23985559

  7. Specific molecular signatures predict decitabine response in chronic myelomonocytic leukemia.

    PubMed

    Meldi, Kristen; Qin, Tingting; Buchi, Francesca; Droin, Nathalie; Sotzen, Jason; Micol, Jean-Baptiste; Selimoglu-Buet, Dorothée; Masala, Erico; Allione, Bernardino; Gioia, Daniela; Poloni, Antonella; Lunghi, Monia; Solary, Eric; Abdel-Wahab, Omar; Santini, Valeria; Figueroa, Maria E

    2015-05-01

    Myelodysplastic syndromes and chronic myelomonocytic leukemia (CMML) are characterized by mutations in genes encoding epigenetic modifiers and aberrant DNA methylation. DNA methyltransferase inhibitors (DMTis) are used to treat these disorders, but response is highly variable, with few means to predict which patients will benefit. Here, we examined baseline differences in mutations, DNA methylation, and gene expression in 40 CMML patients who were responsive or resistant to decitabine (DAC) in order to develop a molecular means of predicting response at diagnosis. While somatic mutations did not differentiate responders from nonresponders, we identified 167 differentially methylated regions (DMRs) of DNA at baseline that distinguished responders from nonresponders using next-generation sequencing. These DMRs were primarily localized to nonpromoter regions and overlapped with distal regulatory enhancers. Using the methylation profiles, we developed an epigenetic classifier that accurately predicted DAC response at the time of diagnosis. Transcriptional analysis revealed differences in gene expression at diagnosis between responders and nonresponders. In responders, the upregulated genes included those that are associated with the cell cycle, potentially contributing to effective DAC incorporation. Treatment with CXCL4 and CXCL7, which were overexpressed in nonresponders, blocked DAC effects in isolated normal CD34+ and primary CMML cells, suggesting that their upregulation contributes to primary DAC resistance.

  8. Molecular signature of organic nitrogen in septic-impacted groundwater

    USGS Publications Warehouse

    Arnold, William A.; Longnecker, Krista; Kroeger, Kevin D.; Kujawinski, Elizabeth B.

    2014-01-01

    Dissolved inorganic and organic nitrogen levels are elevated in aquatic systems due to anthropogenic activities. Dissolved organic nitrogen (DON) arises from various sources, and its impact could be more clearly constrained if specific sources were identified and if the molecular-level composition of DON were better understood. In this work, the pharmaceutical carbamazepine was used to identify septic-impacted groundwater in a coastal watershed. Using ultrahigh resolution mass spectrometry data, the nitrogen-containing features of the dissolved organic matter in septic-impacted and non-impacted samples were compared. The septic-impacted groundwater samples have a larger abundance of nitrogen-containing formulas. Impacted samples have additional DON features in the regions ascribed as ‘protein-like’ and ‘lipid-like’ in van Krevelen space and have more intense nitrogen-containing features in a specific region of a carbon versus mass plot. These features are potential indicators of dissolved organic nitrogen arising from septic effluents, and this work suggests that ultrahigh resolution mass spectrometry is a valuable tool to identify and characterize sources of DON.

  9. Spectroscopic signatures of molecular orbitals in transition metal oxides with a honeycomb lattice

    NASA Astrophysics Data System (ADS)

    Pchelkina, Z. V.; Streltsov, S. V.; Mazin, I. I.

    2016-11-01

    A tendency to form benzenelike molecular orbitals has recently been shown to be a common feature of the 4 d and 5 d transition metal oxides with a honeycomb lattice. This tendency competes with other interactions such as the spin-orbit coupling and Hubbard correlations and can be partially or completely suppressed. In the calculations, SrRu2O6 presents the cleanest case of well-formed molecular orbitals so far; however, direct experimental evidence for or against this proposition has been missing. In this paper, we show that combined photoemission and optical studies can be used to identify molecular orbitals in SrRu2O6 . Symmetry-driven election selection rules suppress optical transitions between certain molecular orbitals, while photoemission and inverse photoemission measurements are insensitive to them. Comparing the photoemission and optical conductivity spectra, one should be able to observe clear signatures of molecular orbitals.

  10. Linking the Molecular Signature of Heteroatomic Dissolved Organic Matter to Watershed Characteristics in World Rivers.

    PubMed

    Wagner, Sasha; Riedel, Thomas; Niggemann, Jutta; Vähätalo, Anssi V; Dittmar, Thorsten; Jaffé, Rudolf

    2015-12-01

    Large world rivers are significant sources of dissolved organic matter (DOM) to the oceans. Watershed geomorphology and land use can drive the quality and reactivity of DOM. Determining the molecular composition of riverine DOM is essential for understanding its source, mobility and fate across landscapes. In this study, DOM from the main stem of 10 global rivers covering a wide climatic range and land use features was molecularly characterized via ultrahigh-resolution Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR-MS). FT-ICR mass spectral data revealed an overall similarity in molecular components among the rivers. However, when focusing specifically on the contribution of nonoxygen heteroatomic molecular formulas (CHON, CHOS, CHOP, etc.) to the bulk molecular signature, patterns relating DOM composition and watershed land use became apparent. Greater abundances of N- and S-containing molecular formulas were identified as unique to rivers influenced by anthropogenic inputs, whereas rivers with primarily forested watersheds had DOM signatures relatively depleted in heteroatomic content. A strong correlation between cropland cover and dissolved black nitrogen was established when focusing specifically on the pyrogenic class of compounds. This study demonstrated how changes in land use directly affect downstream DOM quality and could impact C and nutrient cycling on a global scale.

  11. Molecularly targeted therapies in multiple myeloma.

    PubMed

    de la Puente, Pilar; Muz, Barbara; Azab, Feda; Luderer, Micah; Azab, Abdel Kareem

    2014-01-01

    Multiple myeloma (MM) is a hematological malignancy that remains incurable because most patients will eventually relapse or become refractory to the treatments. Although the treatments have improved, the major problem in MM is the resistance to therapy. Novel agents are currently in development for the treatment of relapsed/refractory MM, including immunomodulatory drugs, proteasome inhibitors, monoclonal antibodies, cell signaling targeted therapies, and strategies targeting the tumor microenvironment. We have previously reviewed in detail the contemporary immunomodulatory drugs, proteasome inhibitors, and monoclonal antibodies therapies for MM. Therefore, in this review, we focused on the role of molecular targeted therapies in the treatment of relapsed/refractory multiple myeloma, including cell signaling targeted therapies (HDAC, PI3K/AKT/mTOR, p38 MAPK, Hsp90, Wnt, Notch, Hedgehog, and cell cycle) and strategies targeting the tumor microenvironment (hypoxia, angiogenesis, integrins, CD44, CXCR4, and selectins). Although these novel agents have improved the therapeutic outcomes for MM patients, further development of new therapeutic agents is warranted.

  12. Molecular signature of MT1-MMP: transactivation of the downstream universal gene network in cancer.

    PubMed

    Rozanov, Dmitri V; Savinov, Alexei Y; Williams, Roy; Liu, Kang; Golubkov, Vladislav S; Krajewski, Stan; Strongin, Alex Y

    2008-06-01

    Invasion-promoting MT1-MMP is directly linked to tumorigenesis and metastasis. Our studies led us to identify those genes, the expression of which is universally linked to MT1-MMP in multiple tumor types. Genome-wide expression profiling of MT1-MMP-overexpressing versus MT1-MMP-silenced cancer cells and a further data mining analysis of the preexisting expression database of 190 human tumors of 14 cancer types led us to identify 11 genes, the expression of which correlated firmly and universally with that of MT1-MMP (P < 0.00001). These genes included regulators of energy metabolism (NNT), trafficking and membrane fusion (SLCO2A1 and ANXA7), signaling and transcription (NR3C1, JAG1, PI3K delta, and CK2 alpha), chromatin rearrangement (SMARCA1), cell division (STK38/NDR1), apoptosis (DAPK1), and mRNA splicing (SNRPB2). Our subsequent extensive analysis of cultured cells, tumor xenografts, and cancer patient biopsies supported our data mining. Our results suggest that transcriptional reprogramming of the specific downstream genes, which themselves are associated with tumorigenesis, represents a distinctive "molecular signature" of the proteolytically active MT1-MMP. We suggest that the transactivation activity of MT1-MMP contributes to the promigratory cell phenotype, which is induced by this tumorigenic proteinase. The activated downstream gene network then begins functioning in unison with MT1-MMP to rework the signaling, transport, cell division, energy metabolism, and other critical cell functions and to commit the cell to migration, invasion, and, consequently, tumorigenesis.

  13. Conserved signature indels and signature proteins as novel tools for understanding microbial phylogeny and systematics: identification of molecular signatures that are specific for the phytopathogenic genera Dickeya, Pectobacterium and Brenneria.

    PubMed

    Naushad, Hafiz Sohail; Lee, Brian; Gupta, Radhey S

    2014-02-01

    Genome sequences are enabling applications of different approaches to more clearly understand microbial phylogeny and systematics. Two of these approaches involve identification of conserved signature indels (CSIs) and conserved signature proteins (CSPs) that are specific for different lineages. These molecular markers provide novel and more definitive means for demarcation of prokaryotic taxa and for identification of species from these groups. Genome sequences are also enabling determination of phylogenetic relationships among species based upon sequences for multiple proteins. In this work, we have used all of these approaches for studying the phytopathogenic bacteria belonging to the genera Dickeya, Pectobacterium and Brenneria. Members of these genera, which cause numerous diseases in important food crops and ornamental plants, are presently distinguished mainly on the basis of their branching in phylogenetic trees. No biochemical or molecular characteristic is known that is uniquely shared by species from these genera. Hence, detailed studies using the above approaches were carried out on proteins from the genomes of these bacteria to identify molecular markers that are specific for them. In phylogenetic trees based upon concatenated sequences for 23 conserved proteins, members of the genera Dickeya, Pectobacterium and Brenneria formed a strongly supported clade within the other Enterobacteriales. Comparative analysis of protein sequences from the Dickeya, Pectobacterium and Brenneria genomes has identified 10 CSIs and five CSPs that are either uniquely or largely found in all genome-sequenced species from these genera, but not present in any other bacteria in the database. In addition, our analyses have identified 10 CSIs and 17 CSPs that are specifically present in either all or most sequenced Dickeya species/strains, and six CSIs and 19 CSPs that are uniquely found in the sequenced Pectobacterium genomes. Finally, our analysis also identified three CSIs

  14. Closely spaced multiple mutations as potential signatures of transient hypermutability in human genes.

    PubMed

    Chen, Jian-Min; Férec, Claude; Cooper, David N

    2009-10-01

    Data from diverse organisms suggests that transient hypermutability is a general mutational mechanism with the potential to generate multiple synchronous mutations, a phenomenon probably best exemplified by closely spaced multiple mutations (CSMMs). Here we have attempted to extend the concept of transient hypermutability from somatic cells to the germline, using human inherited disease-causing multiple mutations as a model system. Employing stringent criteria for data inclusion, we have retrospectively identified numerous potential examples of pathogenic CSMMs that exhibit marked similarities to the CSMMs reported in other systems. These examples include (1) eight multiple mutations, each comprising three or more components within a sequence tract of <100 bp; (2) three possible instances of "mutation showers"; and (3) numerous highly informative "homocoordinate" mutations. Using the proportion of CpG substitution as a crude indicator of the relative likelihood of transient hypermutability, we present evidence to suggest that CSMMs comprising at least one pair of mutations separated by < or =100 bp may constitute signatures of transient hypermutability in human genes. Although this analysis extends the generality of the concept of transient hypermutability and provides new insights into what may be considered a novel mechanism of mutagenesis underlying human inherited disease, it has raised serious concerns regarding current practices in mutation screening.

  15. Nuclear factor, erythroid 2-like 2-associated molecular signature predicts lung cancer survival.

    PubMed

    Qian, Zhongqing; Zhou, Tong; Gurguis, Christopher I; Xu, Xiaoyan; Wen, Qing; Lv, Jingzhu; Fang, Fang; Hecker, Louise; Cress, Anne E; Natarajan, Viswanathan; Jacobson, Jeffrey R; Zhang, Donna D; Garcia, Joe G N; Wang, Ting

    2015-11-24

    Nuclear factor, erythroid 2-like 2 (NFE2L2), a transcription factor also known as NF-E2-related factor 2 (Nrf2), is a key cytoprotective gene that regulates critical antioxidant and stress-responsive genes. Nrf2 has been demonstrated to be a promising therapeutic target and useful biomarker in malignant disease. We hypothesized that NFE2L2-mediated gene expression would reflect cancer severity and progression. We conducted a meta-analysis of microarray data for 240 NFE2L2-mediated genes that were enriched in tumor tissues. We then developed a risk scoring system based on NFE2L2 gene expression profiling and designated 50 tumor-associated genes as the NFE2L2-associated molecular signature (NAMS). We tested the relationship between this gene expression signature and both recurrence-free survival and overall survival in lung cancer patients. We find that NAMS predicts clinical outcome in the training cohort and in 12 out of 20 validation cohorts. Cox proportional hazard regressions indicate that NAMS is a robust prognostic gene signature, independent of other clinical and pathological factors including patient age, gender, smoking, gene alteration, MYC level, and cancer stage. NAMS is an excellent predictor of recurrence-free survival and overall survival in human lung cancer. This gene signature represents a promising prognostic biomarker in human lung cancer.

  16. Nuclear factor, erythroid 2-like 2-associated molecular signature predicts lung cancer survival

    PubMed Central

    Qian, Zhongqing; Zhou, Tong; Gurguis, Christopher I.; Xu, Xiaoyan; Wen, Qing; Lv, Jingzhu; Fang, Fang; Hecker, Louise; Cress, Anne E.; Natarajan, Viswanathan; Jacobson, Jeffrey R.; Zhang, Donna D.; Garcia, Joe G. N.; Wang, Ting

    2015-01-01

    Nuclear factor, erythroid 2-like 2 (NFE2L2), a transcription factor also known as NF-E2-related factor 2 (Nrf2), is a key cytoprotective gene that regulates critical antioxidant and stress-responsive genes. Nrf2 has been demonstrated to be a promising therapeutic target and useful biomarker in malignant disease. We hypothesized that NFE2L2-mediated gene expression would reflect cancer severity and progression. We conducted a meta-analysis of microarray data for 240 NFE2L2-mediated genes that were enriched in tumor tissues. We then developed a risk scoring system based on NFE2L2 gene expression profiling and designated 50 tumor-associated genes as the NFE2L2-associated molecular signature (NAMS). We tested the relationship between this gene expression signature and both recurrence-free survival and overall survival in lung cancer patients. We find that NAMS predicts clinical outcome in the training cohort and in 12 out of 20 validation cohorts. Cox proportional hazard regressions indicate that NAMS is a robust prognostic gene signature, independent of other clinical and pathological factors including patient age, gender, smoking, gene alteration, MYC level, and cancer stage. NAMS is an excellent predictor of recurrence-free survival and overall survival in human lung cancer. This gene signature represents a promising prognostic biomarker in human lung cancer. PMID:26596768

  17. Intraindividual genome expression analysis reveals a specific molecular signature of psoriasis and eczema.

    PubMed

    Quaranta, Maria; Knapp, Bettina; Garzorz, Natalie; Mattii, Martina; Pullabhatla, Venu; Pennino, Davide; Andres, Christian; Traidl-Hoffmann, Claudia; Cavani, Andrea; Theis, Fabian J; Ring, Johannes; Schmidt-Weber, Carsten B; Eyerich, Stefanie; Eyerich, Kilian

    2014-07-09

    Previous attempts to gain insight into the pathogenesis of psoriasis and eczema by comparing their molecular signatures were hampered by the high interindividual variability of those complex diseases. In patients affected by both psoriasis and nonatopic or atopic eczema simultaneously (n = 24), an intraindividual comparison of the molecular signatures of psoriasis and eczema identified genes and signaling pathways regulated in common and exclusive for each disease across all patients. Psoriasis-specific genes were important regulators of glucose and lipid metabolism, epidermal differentiation, as well as immune mediators of T helper 17 (TH17) responses, interleukin-10 (IL-10) family cytokines, and IL-36. Genes in eczema related to epidermal barrier, reduced innate immunity, increased IL-6, and a TH2 signature. Within eczema subtypes, a mutually exclusive regulation of epidermal differentiation genes was observed. Furthermore, only contact eczema was driven by inflammasome activation, apoptosis, and cellular adhesion. On the basis of this comprehensive picture of the pathogenesis of psoriasis and eczema, a disease classifier consisting of NOS2 and CCL27 was created. In an independent cohort of eczema (n = 28) and psoriasis patients (n = 25), respectively, this classifier diagnosed all patients correctly and also identified initially misdiagnosed or clinically undifferentiated patients.

  18. Optical signatures of molecular dissymmetry: Combining theory with experiments to address stereochemical puzzles

    PubMed Central

    Mukhopadhyay, Parag; Wipf, Peter; Beratan, David N.

    2009-01-01

    Conspectus Modern chemistry emerged from the quest to describe the three-dimensional structure of molecules: van’t Hoff’s tetravalent carbon placed symmetry and dissymmetry at the heart of chemistry. In this Account, we explore how modern theory, synthesis, and spectroscopy can be used in concert to elucidate the symmetry and dissymmetry of molecules and their assemblies. Chiroptical spectroscopy—including optical rotatory dispersion (ORD), electronic circular dichroism (ECD), vibrational circular dichroism (VCD), and Raman optical activity (ROA)—measures the response of dissymmetric structures to electromagnetic radiation. This response can in turn reveal the arrangement of atoms in space, but deciphering the molecular information encoded in chiroptical spectra requires an effective theoretical approach. Although important correlations between ECD and molecular stereochemistry have existed for some time, a battery of accurate new theoretical methods that link a much wider range of chiroptical spectroscopies to structure have emerged over the last decade. The promise of this field is considerable: theory and spectroscopy can assist in assigning the relative and absolute configurations of complex products, in revealing the structure of non-covalent aggregates, in defining metrics for molecular diversity based upon polarization response, and in designing chirally imprinted nanomaterials. The physical organic chemistry of chirality is fascinating in its own right: defining atomic and group contributions to optical rotation (OR) is now possible. Although the common expectation is that chiroptical response is determined solely by a chiral solute’s electronic structure in a given environment, chiral imprinting effects on the surrounding medium and molecular assembly can, in fact, dominate the chiroptical signatures. The theoretical interpretation of chiroptical markers is challenging because the optical properties are subtle, which results from the strong

  19. Optical signatures of molecular dissymmetry: combining theory with experiments to address stereochemical puzzles.

    PubMed

    Mukhopadhyay, Parag; Wipf, Peter; Beratan, David N

    2009-06-16

    Modern chemistry emerged from the quest to describe the three-dimensional structure of molecules: van't Hoff's tetravalent carbon placed symmetry and dissymmetry at the heart of chemistry. In this Account, we explore how modern theory, synthesis, and spectroscopy can be used in concert to elucidate the symmetry and dissymmetry of molecules and their assemblies. Chiroptical spectroscopy, including optical rotatory dispersion (ORD), electronic circular dichroism (ECD), vibrational circular dichroism (VCD), and Raman optical activity (ROA), measures the response of dissymmetric structures to electromagnetic radiation. This response can in turn reveal the arrangement of atoms in space, but deciphering the molecular information encoded in chiroptical spectra requires an effective theoretical approach. Although important correlations between ECD and molecular stereochemistry have existed for some time, a battery of accurate new theoretical methods that link a much wider range of chiroptical spectroscopies to structure have emerged over the past decade. The promise of this field is considerable: theory and spectroscopy can assist in assigning the relative and absolute configurations of complex products, revealing the structure of noncovalent aggregates, defining metrics for molecular diversity based on polarization response, and designing chirally imprinted nanomaterials. The physical organic chemistry of chirality is fascinating in its own right: defining atomic and group contributions to optical rotation (OR) is now possible. Although the common expectation is that chiroptical response is determined solely by a chiral solute's electronic structure in a given environment, chiral imprinting effects on the surrounding medium and molecular assembly can, in fact, dominate the chiroptical signatures. The theoretical interpretation of chiroptical markers is challenging because the optical properties are subtle, resulting from the strong electric dipole and the weaker electric

  20. Molecular signatures of transgenerational response to ocean acidification in a species of reef fish

    NASA Astrophysics Data System (ADS)

    Schunter, Celia; Welch, Megan J.; Ryu, Taewoo; Zhang, Huoming; Berumen, Michael L.; Nilsson, Göran E.; Munday, Philip L.; Ravasi, Timothy

    2016-11-01

    The impact of ocean acidification on marine ecosystems will depend on species capacity to adapt. Recent studies show that the behaviour of reef fishes is impaired at projected CO 2 levels; however, individual variation exists that might promote adaptation. Here, we show a clear signature of parental sensitivity to high CO 2 in the brain molecular phenotype of juvenile spiny damselfish, Acanthochromis polyacanthus, primarily driven by circadian rhythm genes. Offspring of CO 2-tolerant and CO 2-sensitive parents were reared at near-future CO 2 (754 μatm) or present-day control levels (414 μatm). By integrating 33 brain transcriptomes and proteomes with a de novo assembled genome we investigate the molecular responses of the fish brain to increased CO 2 and the expression of parental tolerance to high CO 2 in the offspring molecular phenotype. Exposure to high CO 2 resulted in differential regulation of 173 and 62 genes and 109 and 68 proteins in the tolerant and sensitive groups, respectively. Importantly, the majority of differences between offspring of tolerant and sensitive parents occurred in high CO 2 conditions. This transgenerational molecular signature suggests that individual variation in CO 2 sensitivity could facilitate adaptation of fish populations to ocean acidification.

  1. Metabolic Signatures Uncover Distinct Targets in Molecular Subsets of Diffuse Large B-Cell Lymphoma

    PubMed Central

    Caro, Pilar; Kishan, Amar U.; Norberg, Erik; Stanley, Illana; Chapuy, Bjoern; Ficarro, Scott B.; Polak, Klaudia; Tondera, Daniel; Gounarides, John; Yin, Hong; Zhou, Feng; Green, Michael R.; Chen, Linfeng; Monti, Stefano; Marto, Jarrod A.; Shipp, Margaret A.; Danial, Nika N.

    2012-01-01

    SUMMARY Molecular signatures have identified several subsets of Diffuse Large B-Cell Lymphoma (DLBCL) and rational targets within the B-cell receptor (BCR) signaling axis. The OxPhos-DLBCL subset, which harbors the signature of genes involved in mitochondrial metabolism, is insensitive to inhibition of BCR survival signaling, but is functionally undefined. We show that compared with BCR-DLBCLs, OxPhos-DLBCLs display enhanced mitochondrial energy transduction, greater incorporation of nutrient-derived carbons into the TCA cycle and increased glutathione levels. Importantly, perturbation of the fatty acid oxidation program and glutathione synthesis proved selectively toxic to this tumor subset. Our analysis provides evidence for distinct metabolic fingerprints and associated survival mechanisms in DLBCL and may have therapeutic implications. PMID:23079663

  2. Hormone-induced protection against mammary tumorigenesis is conserved in multiple rat strains and identifies a core gene expression signature induced by pregnancy.

    PubMed

    Blakely, Collin M; Stoddard, Alexander J; Belka, George K; Dugan, Katherine D; Notarfrancesco, Kathleen L; Moody, Susan E; D'Cruz, Celina M; Chodosh, Lewis A

    2006-06-15

    Women who have their first child early in life have a substantially lower lifetime risk of breast cancer. The mechanism for this is unknown. Similar to humans, rats exhibit parity-induced protection against mammary tumorigenesis. To explore the basis for this phenomenon, we identified persistent pregnancy-induced changes in mammary gene expression that are tightly associated with protection against tumorigenesis in multiple inbred rat strains. Four inbred rat strains that exhibit marked differences in their intrinsic susceptibilities to carcinogen-induced mammary tumorigenesis were each shown to display significant protection against methylnitrosourea-induced mammary tumorigenesis following treatment with pregnancy levels of estradiol and progesterone. Microarray expression profiling of parous and nulliparous mammary tissue from these four strains yielded a common 70-gene signature. Examination of the genes constituting this signature implicated alterations in transforming growth factor-beta signaling, the extracellular matrix, amphiregulin expression, and the growth hormone/insulin-like growth factor I axis in pregnancy-induced alterations in breast cancer risk. Notably, related molecular changes have been associated with decreased mammographic density, which itself is strongly associated with decreased breast cancer risk. Our findings show that hormone-induced protection against mammary tumorigenesis is widely conserved among divergent rat strains and define a gene expression signature that is tightly correlated with reduced mammary tumor susceptibility as a consequence of a normal developmental event. Given the conservation of this signature, these pathways may contribute to pregnancy-induced protection against breast cancer.

  3. Molecular signatures that are distinctive characteristics of the vertebrates and chordates and supporting a grouping of vertebrates with the tunicates.

    PubMed

    Gupta, Radhey S

    2016-01-01

    Members of the phylum Chordata and the subphylum Vertebrata are presently distinguished solely on the basis of morphological characteristics. The relationship of the vertebrates to the two non-vertebrate chordate subphyla is also a subject of debate. Analyses of protein sequences have identified multiple conserved signature indels (CSIs) that are specific for Chordata or for Vertebrata. Five CSIs in 4 important proteins are specific for the Vertebrata, whereas two other CSIs are uniquely found in all sequenced chordate species including Ciona intestinalis and Oikapleura dioica (Tunicates) as well as Branchiostoma floridae (Cephalochordates). The shared presence of these molecular signatures by all vertebrates/chordate species, but in no other animal taxa, strongly indicates that the genetic changes represented by the identified CSIs diagnose monophyletic groups. Two other discovered CSIs are uniquely shared by different vertebrate species and by either one (Ciona intestinalis) or both tunicate (Ciona and Oikapleura) species, but they are not found in Branchiostoma or other animal species. Specific presence of these CSIs in different vertebrates and either one or both tunicate species provides strong independent evidence that the vertebrate species are more closely related to the urochordates (tunicates) than to the cephalochordates.

  4. Computing Molecular Signatures as Optima of a Bi-Objective Function: Method and Application to Prediction in Oncogenomics

    PubMed Central

    Gardeux, Vincent; Chelouah, Rachid; Wanderley, Maria F Barbosa; Siarry, Patrick; Braga, Antônio P; Reyal, Fabien; Rouzier, Roman; Pusztai, Lajos; Natowicz, René

    2015-01-01

    BACKGROUND Filter feature selection methods compute molecular signatures by selecting subsets of genes in the ranking of a valuation function. The motivations of the valuation functions choice are almost always clearly stated, but those for selecting the genes according to their ranking are hardly ever explicit. METHOD We addressed the computation of molecular signatures by searching the optima of a bi-objective function whose solution space was the set of all possible molecular signatures, ie, the set of subsets of genes. The two objectives were the size of the signature–to be minimized–and the interclass distance induced by the signature–to be maximized–. RESULTS We showed that: 1) the convex combination of the two objectives had exactly n optimal non empty signatures where n was the number of genes, 2) the n optimal signatures were nested, and 3) the optimal signature of size k was the subset of k top ranked genes that contributed the most to the interclass distance. We applied our feature selection method on five public datasets in oncology, and assessed the prediction performances of the optimal signatures as input to the diagonal linear discriminant analysis (DLDA) classifier. They were at the same level or better than the best-reported ones. The predictions were robust, and the signatures were almost always significantly smaller. We studied in more details the performances of our predictive modeling on two breast cancer datasets to predict the response to a preoperative chemotherapy: the performances were higher than the previously reported ones, the signatures were three times smaller (11 versus 30 gene signatures), and the genes member of the signature were known to be involved in the response to chemotherapy. CONCLUSIONS Defining molecular signatures as the optima of a bi-objective function that combined the signature size and the interclass distance was well founded and efficient for prediction in oncogenomics. The complexity of the computation

  5. A common molecular signature in ASD gene expression: following Root 66 to autism.

    PubMed

    Diaz-Beltran, L; Esteban, F J; Wall, D P

    2016-01-05

    Several gene expression experiments on autism spectrum disorders have been conducted using both blood and brain tissue. Individually, these studies have advanced our understanding of the molecular systems involved in the molecular pathology of autism and have formed the bases of ongoing work to build autism biomarkers. In this study, we conducted an integrated systems biology analysis of 9 independent gene expression experiments covering 657 autism, 9 mental retardation and developmental delay and 566 control samples to determine if a common signature exists and to test whether regulatory patterns in the brain relevant to autism can also be detected in blood. We constructed a matrix of differentially expressed genes from these experiments and used a Jaccard coefficient to create a gene-based phylogeny, validated by bootstrap. As expected, experiments and tissue types clustered together with high statistical confidence. However, we discovered a statistically significant subgrouping of 3 blood and 2 brain data sets from 3 different experiments rooted by a highly correlated regulatory pattern of 66 genes. This Root 66 appeared to be non-random and of potential etiologic relevance to autism, given their enriched roles in neurological processes key for normal brain growth and function, learning and memory, neurodegeneration, social behavior and cognition. Our results suggest that there is a detectable autism signature in the blood that may be a molecular echo of autism-related dysregulation in the brain.

  6. Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment

    PubMed Central

    Kim, E-S; Elbeltagy, A R; Aboul-Naga, A M; Rischkowsky, B; Sayre, B; Mwacharo, J M; Rothschild, M F

    2016-01-01

    Goats and sheep are versatile domesticates that have been integrated into diverse environments and production systems. Natural and artificial selection have shaped the variation in the two species, but natural selection has played the major role among indigenous flocks. To investigate signals of natural selection, we analyzed genotype data generated using the caprine and ovine 50K SNP BeadChips from Barki goats and sheep that are indigenous to a hot arid environment in Egypt's Coastal Zone of the Western Desert. We identify several candidate regions under selection that spanned 119 genes. A majority of the genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. In particular, selection signatures spanning several genes that directly or indirectly influenced traits for adaptation to hot arid environments, such as thermo-tolerance (melanogenesis) (FGF2, GNAI3, PLCB1), body size and development (BMP2, BMP4, GJA3, GJB2), energy and digestive metabolism (MYH, TRHDE, ALDH1A3), and nervous and autoimmune response (GRIA1, IL2, IL7, IL21, IL1R1) were identified. We also identified eight common candidate genes under selection in the two species and a shared selection signature that spanned a conserved syntenic segment to bovine chromosome 12 on caprine and ovine chromosomes 12 and 10, respectively, providing, most likely, the evidence for selection in a common environment in two different but closely related species. Our study highlights the importance of indigenous livestock as model organisms for investigating selection sweeps and genome-wide association mapping. PMID:26555032

  7. A gene expression inflammatory signature specifically predicts multiple myeloma evolution and patients survival

    PubMed Central

    Botta, C; Di Martino, M T; Ciliberto, D; Cucè, M; Correale, P; Rossi, M; Tagliaferri, P; Tassone, P

    2016-01-01

    Multiple myeloma (MM) is closely dependent on cross-talk between malignant plasma cells and cellular components of the inflammatory/immunosuppressive bone marrow milieu, which promotes disease progression, drug resistance, neo-angiogenesis, bone destruction and immune-impairment. We investigated the relevance of inflammatory genes in predicting disease evolution and patient survival. A bioinformatics study by Ingenuity Pathway Analysis on gene expression profiling dataset of monoclonal gammopathy of undetermined significance, smoldering and symptomatic-MM, identified inflammatory and cytokine/chemokine pathways as the most progressively affected during disease evolution. We then selected 20 candidate genes involved in B-cell inflammation and we investigated their role in predicting clinical outcome, through univariate and multivariate analyses (log-rank test, logistic regression and Cox-regression model). We defined an 8-genes signature (IL8, IL10, IL17A, CCL3, CCL5, VEGFA, EBI3 and NOS2) identifying each condition (MGUS/smoldering/symptomatic-MM) with 84% accuracy. Moreover, six genes (IFNG, IL2, LTA, CCL2, VEGFA, CCL3) were found independently correlated with patients' survival. Patients whose MM cells expressed high levels of Th1 cytokines (IFNG/LTA/IL2/CCL2) and low levels of CCL3 and VEGFA, experienced the longest survival. On these six genes, we built a prognostic risk score that was validated in three additional independent datasets. In this study, we provide proof-of-concept that inflammation has a critical role in MM patient progression and survival. The inflammatory-gene prognostic signature validated in different datasets clearly indicates novel opportunities for personalized anti-MM treatment. PMID:27983725

  8. Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment.

    PubMed

    Kim, E-S; Elbeltagy, A R; Aboul-Naga, A M; Rischkowsky, B; Sayre, B; Mwacharo, J M; Rothschild, M F

    2016-03-01

    Goats and sheep are versatile domesticates that have been integrated into diverse environments and production systems. Natural and artificial selection have shaped the variation in the two species, but natural selection has played the major role among indigenous flocks. To investigate signals of natural selection, we analyzed genotype data generated using the caprine and ovine 50K SNP BeadChips from Barki goats and sheep that are indigenous to a hot arid environment in Egypt's Coastal Zone of the Western Desert. We identify several candidate regions under selection that spanned 119 genes. A majority of the genes were involved in multiple signaling and signal transduction pathways in a wide variety of cellular and biochemical processes. In particular, selection signatures spanning several genes that directly or indirectly influenced traits for adaptation to hot arid environments, such as thermo-tolerance (melanogenesis) (FGF2, GNAI3, PLCB1), body size and development (BMP2, BMP4, GJA3, GJB2), energy and digestive metabolism (MYH, TRHDE, ALDH1A3), and nervous and autoimmune response (GRIA1, IL2, IL7, IL21, IL1R1) were identified. We also identified eight common candidate genes under selection in the two species and a shared selection signature that spanned a conserved syntenic segment to bovine chromosome 12 on caprine and ovine chromosomes 12 and 10, respectively, providing, most likely, the evidence for selection in a common environment in two different but closely related species. Our study highlights the importance of indigenous livestock as model organisms for investigating selection sweeps and genome-wide association mapping.

  9. Molecular signatures for the main phyla of photosynthetic bacteria and their subgroups.

    PubMed

    Gupta, Radhey S

    2010-06-01

    The bacterial groups corresponding to different photosynthetic prokaryotes are presently identified mainly on the basis of their branching in phylogenetic trees. The availability of genome sequences is enabling identification of many molecular signatures that are specific for different groups of photosynthetic bacteria. Our recent work has identified large numbers of signatures consisting of conserved inserts or deletions (indels) in widely distributed proteins, as well as whole proteins that are specific for various sequenced species/strains from Cyanobacteria, Chlorobi, and Proteobacteria phyla. Based upon these signatures, it is now possible to identify/distinguish bacteria from these phyla of photosynthetic bacteria as well as their major subclades in clear molecular terms. The use of these signatures in conjunction with phylogenomic analyses, summarized here, is leading to a holistic picture concerning the branching order and evolutionary relationships among the above groups of photosynthetic bacteria. Although detailed studies in this regard have not yet been carried on Chloroflexi and Heliobacteriaceae, we have identified some conserved indels that are specific for these groups. Some of the conserved indels for the photosynthetic bacteria are present in photosynthesis-related proteins. These include a 4 aa insert in the pyruvate flavodoxin/ferridoxin oxidoreductase that is specific for the genus Chloroflexus, a 2 aa insert in magnesium chelatase that is uniquely shared by all Cyanobacteria except the deepest branching Clade A (Gloebacterales), a 6 aa insert in an A-type flavoprotein that is specific for various marine unicellular Cyanobacteria, a 2 aa insert in heme oxygenase that is specific for various Prochlorococcus strains/isolates, and 1 aa deletion in the protein protochlorophyllide oxidoreductase that is commonly shared by various Prochlorococcus strains except the deepest branching isolates MIT 9303 and MIT 9313. The identified CSIs are located in

  10. Molecular signatures of biogeochemical transformations in dissolved organic matter from ten World Rivers

    NASA Astrophysics Data System (ADS)

    Riedel, Thomas; Zark, Maren; Vähätalo, Anssi; Niggemann, Jutta; Spencer, Robert; Hernes, Peter; Dittmar, Thorsten

    2016-09-01

    Rivers carry large amounts of dissolved organic matter (DOM) to the oceans thereby connecting terrestrial and marine element cycles. Photo-degradation in conjunction with microbial turnover is considered a major pathway by which terrigenous DOM is decomposed. To reveal globally relevant patterns behind this process, we performed photo-degradation experiments and year-long bio-assays on DOM from ten of the largest world rivers that collectively account for more than one-third of the fresh water discharge to the global ocean. We furthermore tested the hypothesis that the terrigenous component in deep ocean DOM may be far higher than biomarker studies suggest, because of the selective photochemical destruction of characteristic biomolecules from vascular plants. DOM was molecularly characterized by a combination of non-targeted ultrahigh-resolution mass spectrometry and quantitative molecular tracer analyses. We show that the reactivity of DOM is globally related to broad catchment properties. Basins that are dominated by forest and grassland export more photo-degradable DOM than other rivers. Chromophoric compounds are mainly vascular plant-derived polyphenols, and partially carry a pyrogenic signature from vegetation fires. These forest and grassland dominated rivers lost up to 50% of dissolved organic carbon (DOC) during irradiation, and up to 85% of DOC was lost in total if subsequently bio-incubated for one year. Basins covered by cropland, on the other hand, export DOM with a higher proportion of photo-resistant and bio-available DOM which is enriched in nitrogen. In these rivers, 30% or less of DOC was photodegraded. Consistent with previous studies, we found that riverine DOM resembled marine DOM in its broad molecular composition after extensive degradation, mainly due to almost complete removal of aromatics. More detailed molecular fingerprinting analysis (based on the relative abundance of >4000 DOM molecular formulae), however, revealed clear differences

  11. Identification of Single- and Multiple-Class Specific Signature Genes from Gene Expression Profiles by Group Marker Index

    PubMed Central

    Tsai, Yu-Shuen; Aguan, Kripamoy; Pal, Nikhil R.; Chung, I-Fang

    2011-01-01

    Informative genes from microarray data can be used to construct prediction model and investigate biological mechanisms. Differentially expressed genes, the main targets of most gene selection methods, can be classified as single- and multiple-class specific signature genes. Here, we present a novel gene selection algorithm based on a Group Marker Index (GMI), which is intuitive, of low-computational complexity, and efficient in identification of both types of genes. Most gene selection methods identify only single-class specific signature genes and cannot identify multiple-class specific signature genes easily. Our algorithm can detect de novo certain conditions of multiple-class specificity of a gene and makes use of a novel non-parametric indicator to assess the discrimination ability between classes. Our method is effective even when the sample size is small as well as when the class sizes are significantly different. To compare the effectiveness and robustness we formulate an intuitive template-based method and use four well-known datasets. We demonstrate that our algorithm outperforms the template-based method in difficult cases with unbalanced distribution. Moreover, the multiple-class specific genes are good biomarkers and play important roles in biological pathways. Our literature survey supports that the proposed method identifies unique multiple-class specific marker genes (not reported earlier to be related to cancer) in the Central Nervous System data. It also discovers unique biomarkers indicating the intrinsic difference between subtypes of lung cancer. We also associate the pathway information with the multiple-class specific signature genes and cross-reference to published studies. We find that the identified genes participate in the pathways directly involved in cancer development in leukemia data. Our method gives a promising way to find genes that can involve in pathways of multiple diseases and hence opens up the possibility of using an existing

  12. The molecular signature of AML mesenchymal stromal cells reveals candidate genes related to the leukemogenic process.

    PubMed

    Binato, Renata; de Almeida Oliveira, Nathalia Correa; Du Rocher, Barbara; Abdelhay, Eliana

    2015-12-01

    Acute myeloid leukemia (AML) is a heterogeneous disease characterized by myeloid precursor proliferation in the bone marrow, apoptosis reduction and differentiation arrest. Although there are several studies in this field, events related to disease initiation and progression remain unknown. The malignant transformation of hematopoietic stem cells (HSC) is thought to generate leukemic stem cells, and this transformation could be related to changes in mesenchymal stromal cell (hMSC) signaling. Thus, the aim of this work was to analyze the gene expression profile of hMSC from AML patients (hMSC-AML) compared to healthy donors hMSCs (hMSC-HD). The results showed a common molecular signature for all hMSC-AML. Other assays were performed with a large number of patients and the results confirmed a molecular signature that is capable of distinguishing hMSC-AML from hMSC-HD. Moreover, CCL2 and BMP4 genes encode secreted proteins that could affect HSCs. To verify whether these proteins are differentially expressed in AML patients, ELISA was performed with plasma samples. CCL2 and BMP4 proteins are differentially expressed in AML patients, indicating changes in hMSC-AML signaling. Altogether, hMSCs-AML signaling alterations could be an important factor in the leukemic transformation process.

  13. Gene Expression Profiling Identifies IRF4-Associated Molecular Signatures in Hematological Malignancies

    PubMed Central

    Wang, Ling; Yao, Zhi Q.; Moorman, Jonathan P.; Xu, Yanji; Ning, Shunbin

    2014-01-01

    The lymphocyte-specific transcription factor Interferon (IFN) Regulatory Factor 4 (IRF4) is implicated in certain types of lymphoid and myeloid malignancies. However, the molecular mechanisms underlying its interactions with these malignancies are largely unknown. In this study, we have first profiled molecular signatures associated with IRF4 expression in associated cancers, by analyzing existing gene expression profiling datasets. Our results show that IRF4 is overexpressed in melanoma, in addition to previously reported contexts including leukemia, myeloma, and lymphoma, and that IRF4 is associated with a unique gene expression pattern in each context. A pool of important genes involved in B-cell development, oncogenesis, cell cycle regulation, and cell death including BATF, LIMD1, CFLAR, PIM2, and CCND2 are common signatures associated with IRF4 in non-Hodgkin B cell lymphomas. We confirmed the correlation of IRF4 with LIMD1 and CFLAR in a panel of cell lines derived from lymphomas. Moreover, we profiled the IRF4 transcriptome in the context of EBV latent infection, and confirmed several genes including IFI27, IFI44, GBP1, and ARHGAP18, as well as CFLAR as novel targets for IRF4. These results provide valuable information for understanding the IRF4 regulatory network, and improve our knowledge of the unique roles of IRF4 in different hematological malignancies. PMID:25207815

  14. AGE AND MASS SEGREGATION OF MULTIPLE STELLAR POPULATIONS IN GALACTIC NUCLEI AND THEIR OBSERVATIONAL SIGNATURES

    SciTech Connect

    Perets, Hagai B.; Mastrobuono-Battisti, Alessandra

    2014-04-01

    Nuclear stellar clusters (NSCs) are known to exist around massive black holes in galactic nuclei. They are thought to have formed through in situ star formation following gas inflow to the nucleus of the galaxy and/or through the infall of multiple stellar clusters. Here we study the latter, and explore the composite structure of the NSC and its relation to the various stellar populations originating from its progenitor infalling clusters. We use N-body simulations of cluster infalls and show that this scenario may produce observational signatures in the form of age segregation: the distribution of the stellar properties (e.g., stellar age and/or metallicity) in the NSCs reflects the infall history of the different clusters. The stellar populations of clusters, infalling at different times (dynamical ages), are differentially segregated in the NSC and are not fully mixed even after a few gigayears of evolution. Moreover, the radial properties of stellar populations in the progenitor cluster are mapped to their radial distribution in the final NSC, potentially leading to efficient mass segregation in NSCs, even those where relaxation times are longer than a Hubble time. Finally, the overall structures of the stellar populations present non-spherical configurations and show significant cluster to cluster population differences.

  15. Connectivity mapping using a combined gene signature from multiple colorectal cancer datasets identified candidate drugs including existing chemotherapies

    PubMed Central

    2015-01-01

    Background While the discovery of new drugs is a complex, lengthy and costly process, identifying new uses for existing drugs is a cost-effective approach to therapeutic discovery. Connectivity mapping integrates gene expression profiling with advanced algorithms to connect genes, diseases and small molecule compounds and has been applied in a large number of studies to identify potential drugs, particularly to facilitate drug repurposing. Colorectal cancer (CRC) is a commonly diagnosed cancer with high mortality rates, presenting a worldwide health problem. With the advancement of high throughput omics technologies, a number of large scale gene expression profiling studies have been conducted on CRCs, providing multiple datasets in gene expression data repositories. In this work, we systematically apply gene expression connectivity mapping to multiple CRC datasets to identify candidate therapeutics to this disease. Results We developed a robust method to compile a combined gene signature for colorectal cancer across multiple datasets. Connectivity mapping analysis with this signature of 148 genes identified 10 candidate compounds, including irinotecan and etoposide, which are chemotherapy drugs currently used to treat CRCs. These results indicate that we have discovered high quality connections between the CRC disease state and the candidate compounds, and that the gene signature we created may be used as a potential therapeutic target in treating the disease. The method we proposed is highly effective in generating quality gene signature through multiple datasets; the publication of the combined CRC gene signature and the list of candidate compounds from this work will benefit both cancer and systems biology research communities for further development and investigations. PMID:26356760

  16. Specific molecular signatures of non-tumor liver tissue may predict a risk of hepatocarcinogenesis

    PubMed Central

    Utsunomiya, Tohru; Shimada, Mitsuo; Morine, Yuji; Tajima, Atsushi; Imoto, Issei

    2014-01-01

    Hepatocellular carcinoma (HCC) is one of the most common human cancers and a major cause of cancer-related death worldwide. The bleak outcomes of HCC patients even after curative treatment have been, at least partially, attributed to its multicentric origin. Therefore, it is necessary to examine not only tumor tissue but also non-tumor liver tissue to investigate the molecular mechanisms operating during hepatocarcinogenesis based on the concept of “field cancerization”. Several studies previously investigated the association of molecular alterations in non-tumor liver tissue with clinical features and prognosis in HCC patients on a genome-wide scale. In particular, specific alterations of DNA methylation profiles have been confirmed in non-tumor liver tissue. This review focuses on the possible clinical value of array-based comprehensive analyses of molecular alterations, especially aberrant DNA methylation, in non-tumor liver tissue to clarify the risk of hepatocarcinogenesis. Carcinogenetic risk estimation based on specific methylation signatures may be advantageous for close follow-up of patients who are at high risk of HCC development. Furthermore, epigenetic therapies for patients with chronic liver diseases may be helpful to reduce the risk of HCC development because epigenetic alterations are potentially reversible, and thus provide promising molecular targets for therapeutic intervention. PMID:24766251

  17. Phylogenetic framework and molecular signatures for the main clades of the phylum Actinobacteria.

    PubMed

    Gao, Beile; Gupta, Radhey S

    2012-03-01

    The phylum Actinobacteria harbors many important human pathogens and also provides one of the richest sources of natural products, including numerous antibiotics and other compounds of biotechnological interest. Thus, a reliable phylogeny of this large phylum and the means to accurately identify its different constituent groups are of much interest. Detailed phylogenetic and comparative analyses of >150 actinobacterial genomes reported here form the basis for achieving these objectives. In phylogenetic trees based upon 35 conserved proteins, most of the main groups of Actinobacteria as well as a number of their superageneric clades are resolved. We also describe large numbers of molecular markers consisting of conserved signature indels in protein sequences and whole proteins that are specific for either all Actinobacteria or their different clades (viz., orders, families, genera, and subgenera) at various taxonomic levels. These signatures independently support the existence of different phylogenetic clades, and based upon them, it is now possible to delimit the phylum Actinobacteria (excluding Coriobacteriia) and most of its major groups in clear molecular terms. The species distribution patterns of these markers also provide important information regarding the interrelationships among different main orders of Actinobacteria. The identified molecular markers, in addition to enabling the development of a stable and reliable phylogenetic framework for this phylum, also provide novel and powerful means for the identification of different groups of Actinobacteria in diverse environments. Genetic and biochemical studies on these Actinobacteria-specific markers should lead to the discovery of novel biochemical and/or other properties that are unique to different groups of Actinobacteria.

  18. Phylogenetic Framework and Molecular Signatures for the Main Clades of the Phylum Actinobacteria

    PubMed Central

    Gao, Beile

    2012-01-01

    Summary: The phylum Actinobacteria harbors many important human pathogens and also provides one of the richest sources of natural products, including numerous antibiotics and other compounds of biotechnological interest. Thus, a reliable phylogeny of this large phylum and the means to accurately identify its different constituent groups are of much interest. Detailed phylogenetic and comparative analyses of >150 actinobacterial genomes reported here form the basis for achieving these objectives. In phylogenetic trees based upon 35 conserved proteins, most of the main groups of Actinobacteria as well as a number of their superageneric clades are resolved. We also describe large numbers of molecular markers consisting of conserved signature indels in protein sequences and whole proteins that are specific for either all Actinobacteria or their different clades (viz., orders, families, genera, and subgenera) at various taxonomic levels. These signatures independently support the existence of different phylogenetic clades, and based upon them, it is now possible to delimit the phylum Actinobacteria (excluding Coriobacteriia) and most of its major groups in clear molecular terms. The species distribution patterns of these markers also provide important information regarding the interrelationships among different main orders of Actinobacteria. The identified molecular markers, in addition to enabling the development of a stable and reliable phylogenetic framework for this phylum, also provide novel and powerful means for the identification of different groups of Actinobacteria in diverse environments. Genetic and biochemical studies on these Actinobacteria-specific markers should lead to the discovery of novel biochemical and/or other properties that are unique to different groups of Actinobacteria. PMID:22390973

  19. Molecular signature of differential virulence in natural isolates of Erwinia amylovora.

    PubMed

    Wang, Dongping; Korban, Schuyler S; Zhao, Youfu

    2010-02-01

    ABSTRACT Erwinia amylovora, the causal agent of fire blight, is considered to be a genetically homogeneous species based on physiological, biochemical, phylogenetic, and genetic analysis. However, E. amylovora strains exhibiting differential virulence are isolated from nature. The exopolysaccharide amylovoran and type III secretion system (T3SS) are two major yet separate virulence factors in E. amylovora. The objective of this study was to investigate whether there is a correlation between E. amylovora virulence and levels of virulence gene expression. Four wild-type strains (Ea1189, Ea273, Ea110, and CFBP1430), widely used in studies of E. amylovora pathogenesis, have been analyzed and compared. E. amylovora strains Ea273 and Ea110 elicited higher severity of disease symptoms than those of Ea1189 and CFBP1430 on apple cv. Golden Delicious and G16 apple root stock plants but not on susceptible Gala plants. In addition, Ea273 and Ea110 elicited severe hypersensitive responses within shorter periods of time at lower inoculum concentrations than those of Ea1189 and CFBP1430 on tobacco plants. Further molecular analyses have revealed that amylovoran production and expression of both amylovoran (amsG) and T3SS (dspE and hrpL) genes were significantly higher in Ea273 and Ea110 than those in Ea1189 and CFBP1430. Other phenotypes such as swarming motility in these four strains also differed significantly. These results indicate that E. amylovora strains of different origin can be divided into subgroups based on molecular signatures of virulence gene expression. Therefore, these molecular signatures may be used to differentiate E. amylovora strains, which may have taxonomical and evolutionary implications.

  20. biosigner: A New Method for the Discovery of Significant Molecular Signatures from Omics Data.

    PubMed

    Rinaudo, Philippe; Boudah, Samia; Junot, Christophe; Thévenot, Etienne A

    2016-01-01

    identify robust molecular signatures from large omics datasets in the process of developing new diagnostics.

  1. biosigner: A New Method for the Discovery of Significant Molecular Signatures from Omics Data

    PubMed Central

    Rinaudo, Philippe; Boudah, Samia; Junot, Christophe; Thévenot, Etienne A.

    2016-01-01

    identify robust molecular signatures from large omics datasets in the process of developing new diagnostics. PMID:27446929

  2. Comparative Systems Analyses Reveal Molecular Signatures of Clinically tested Vaccine Adjuvants

    NASA Astrophysics Data System (ADS)

    Olafsdottir, Thorunn A.; Lindqvist, Madelene; Nookaew, Intawat; Andersen, Peter; Maertzdorf, Jeroen; Persson, Josefine; Christensen, Dennis; Zhang, Yuan; Anderson, Jenna; Khoomrung, Sakda; Sen, Partho; Agger, Else Marie; Coler, Rhea; Carter, Darrick; Meinke, Andreas; Rappuoli, Rino; Kaufmann, Stefan H. E.; Reed, Steven G.; Harandi, Ali M.

    2016-12-01

    A better understanding of the mechanisms of action of human adjuvants could inform a rational development of next generation vaccines for human use. Here, we exploited a genome wide transcriptomics analysis combined with a systems biology approach to determine the molecular signatures induced by four clinically tested vaccine adjuvants, namely CAF01, IC31, GLA-SE and Alum in mice. We report signature molecules, pathways, gene modules and networks, which are shared by or otherwise exclusive to these clinical-grade adjuvants in whole blood and draining lymph nodes of mice. Intriguingly, co-expression analysis revealed blood gene modules highly enriched for molecules with documented roles in T follicular helper (TFH) and germinal center (GC) responses. We could show that all adjuvants enhanced, although with different magnitude and kinetics, TFH and GC B cell responses in draining lymph nodes. These results represent, to our knowledge, the first comparative systems analysis of clinically tested vaccine adjuvants that may provide new insights into the mechanisms of action of human adjuvants.

  3. Comparative Systems Analyses Reveal Molecular Signatures of Clinically tested Vaccine Adjuvants

    PubMed Central

    Olafsdottir, Thorunn A.; Lindqvist, Madelene; Nookaew, Intawat; Andersen, Peter; Maertzdorf, Jeroen; Persson, Josefine; Christensen, Dennis; Zhang, Yuan; Anderson, Jenna; Khoomrung, Sakda; Sen, Partho; Agger, Else Marie; Coler, Rhea; Carter, Darrick; Meinke, Andreas; Rappuoli, Rino; Kaufmann, Stefan H. E.; Reed, Steven G.; Harandi, Ali M.

    2016-01-01

    A better understanding of the mechanisms of action of human adjuvants could inform a rational development of next generation vaccines for human use. Here, we exploited a genome wide transcriptomics analysis combined with a systems biology approach to determine the molecular signatures induced by four clinically tested vaccine adjuvants, namely CAF01, IC31, GLA-SE and Alum in mice. We report signature molecules, pathways, gene modules and networks, which are shared by or otherwise exclusive to these clinical-grade adjuvants in whole blood and draining lymph nodes of mice. Intriguingly, co-expression analysis revealed blood gene modules highly enriched for molecules with documented roles in T follicular helper (TFH) and germinal center (GC) responses. We could show that all adjuvants enhanced, although with different magnitude and kinetics, TFH and GC B cell responses in draining lymph nodes. These results represent, to our knowledge, the first comparative systems analysis of clinically tested vaccine adjuvants that may provide new insights into the mechanisms of action of human adjuvants. PMID:27958370

  4. Molecular signatures associated with ZIKV exposure in human cortical neural progenitors

    PubMed Central

    Zhang, Feiran; Hammack, Christy; Ogden, Sarah C.; Cheng, Yichen; Lee, Emily M.; Wen, Zhexing; Qian, Xuyu; Nguyen, Ha Nam; Li, Yujing; Yao, Bing; Xu, Miao; Xu, Tianlei; Chen, Li; Wang, Zhiqin; Feng, Hao; Huang, Wei-Kai; Yoon, Ki-jun; Shan, Chao; Huang, Luoxiu; Qin, Zhaohui; Christian, Kimberly M.; Shi, Pei-Yong; Xu, Mingjiang; Xia, Menghang; Zheng, Wei; Wu, Hao; Song, Hongjun; Tang, Hengli; Ming, Guo-Li; Jin, Peng

    2016-01-01

    Zika virus (ZIKV) infection causes microcephaly and has been linked to other brain abnormalities. How ZIKV impairs brain development and function is unclear. Here we systematically profiled transcriptomes of human neural progenitor cells exposed to Asian ZIKVC, African ZIKVM, and dengue virus (DENV). In contrast to the robust global transcriptome changes induced by DENV, ZIKV has a more selective and larger impact on expression of genes involved in DNA replication and repair. While overall expression profiles are similar, ZIKVC, but not ZIKVM, induces upregulation of viral response genes and TP53. P53 inhibitors can block the apoptosis induced by both ZIKVC and ZIKVM in hNPCs, with higher potency against ZIKVC-induced apoptosis. Our analyses reveal virus- and strain-specific molecular signatures associated with ZIKV infection. These datasets will help to investigate ZIKV-host interactions and identify neurovirulence determinants of ZIKV. PMID:27580721

  5. Searching for chemical signatures of multiple stellar populations in the old, massive open cluster NGC 6791

    SciTech Connect

    Bragaglia, Angela; Carretta, Eugenio; Sneden, Christopher; Gratton, Raffaele G.; Lucatello, Sara; Bernath, Peter F.; Brooke, James S. A.; Ram, Ram S. E-mail: eugenio.carretta@oabo.inaf.it E-mail: raffaele.gratton@oapd.inaf.it E-mail: pbernath@odu.edu E-mail: rr662@york.ac.uk

    2014-11-20

    Galactic open and globular clusters (OCs, GCs) appear to inhabit separate regions of the age-mass plane. However, the transition between them is not easily defined because there is some overlap between high-mass, old OCs and low-mass, young GCs. We are exploring the possibility of a clear-cut separation between OCs and GCs using an abundance feature that has been found so far only in GCs: (anti)correlations between light elements. Among the coupled abundance trends, the Na-O anticorrelation is the most widely studied. These anticorrelations are the signature of self-enrichment, i.e., of a formation mechanism that implies multiple generations of stars. Here we concentrate on the old, massive, metal-rich OC NGC 6791. We analyzed archival Keck/HIRES spectra of 15 NGC 6791 main-sequence turnoff and evolved stars, concentrating on the derivation of C, N, O, and Na abundances. We also used WIYN/Hydra spectra of 21 evolved stars (one is in common). Given the spectral complexity of the very metal-rich NGC 6791 stars, we employed spectrum synthesis to measure most of the abundances. We confirmed the cluster super-solar metallicity and abundances of Ca and Ni that have been derived in past studies. More importantly, we did not detect any significant star-to-star abundance dispersion in C, N, O, and Na. Based on the absence of a clear Na-O anticorrelation, NGC 6791 can still be considered a true OC, hosting a single generation of stars and not a low-mass GC.

  6. Baseline Gene Expression Signatures in Monocytes from Multiple Sclerosis Patients Treated with Interferon-beta

    PubMed Central

    Bustamante, Marta F.; Nurtdinov, Ramil N.; Río, Jordi; Montalban, Xavier; Comabella, Manuel

    2013-01-01

    Background A relatively large proportion of relapsing-remitting multiple sclerosis (RRMS) patients do not respond to interferon-beta (IFNb) treatment. In previous studies with peripheral blood mononuclear cells (PBMC), we identified a subgroup of IFNb non-responders that was characterized by a baseline over-expression of type I IFN inducible genes. Additional mechanistic experiments carried out in IFNb non-responders suggested a selective alteration of the type I IFN signaling pathway in the population of blood monocytes. Here, we aimed (i) to investigate whether the type I IFN signaling pathway is up-regulated in isolated monocytes from IFNb non-responders at baseline; and (ii) to search for additional biological pathways in this cell population that may be implicated in the response to IFNb treatment. Methods Twenty RRMS patients classified according to their clinical response to IFNb treatment and 10 healthy controls were included in the study. Monocytes were purified from PBMC obtained before treatment by cell sorting and the gene expression profiling was determined with oligonucleotide microarrays. Results and discussion Purified monocytes from IFNb non-responders were characterized by an over-expression of type I IFN responsive genes, which confirms the type I IFN signature in monocytes suggested from previous studies. Other relevant signaling pathways that were up-regulated in IFNb non-responders were related with the mitochondrial function and processes such as protein synthesis and antigen presentation, and together with the type I IFN signaling pathway, may also be playing roles in the response to IFNb. PMID:23637780

  7. Molecular signatures distinguish human central memory from effector memory CD8 T cell subsets.

    PubMed

    Willinger, Tim; Freeman, Tom; Hasegawa, Hitoshi; McMichael, Andrew J; Callan, Margaret F C

    2005-11-01

    Memory T cells are heterogeneous in terms of their phenotype and functional properties. We investigated the molecular profiles of human CD8 naive central memory (T(CM)), effector memory (T(EM)), and effector memory RA (T(EMRA)) T cells using gene expression microarrays and phospho-protein-specific intracellular flow cytometry. We demonstrate that T(CM) have a gene expression and cytokine signaling signature that lies between that of naive and T(EM) or T(EMRA) cells, whereas T(EM) and T(EMRA) are closely related. Our data define the molecular basis for the different functional properties of central and effector memory subsets. We show that T(EM) and T(EMRA) cells strongly express genes with known importance in CD8 T cell effector function. In contrast, T(CM) are characterized by high basal and cytokine-induced STAT5 phosphorylation, reflecting their capacity for self-renewal. Altogether, our results distinguish T(CM) and T(EM)/T(EMRA) at the molecular level and are consistent with the concept that T(CM) represent memory stem cells.

  8. Molecular signatures of age-associated chronic degeneration of shoulder muscles.

    PubMed

    Raz, Yotam; Henseler, Jan Ferdinand; Kolk, Arjen; Tatum, Zuotian; Groosjohan, Niels Kuipers; Verwey, Nisha E; Arindrarto, Wibowo; Kielbasa, Szymon M; Nagels, Jochem; 't Hoen, Peter A C; Nelissen, Rob G H H; Raz, Vered

    2016-02-23

    Chronic muscle diseases are highly prevalent in the elderly causing severe mobility limitations, pain and frailty. The intrinsic molecular mechanisms are poorly understood due to multifactorial causes, slow progression with age and variations between individuals. Understanding the underlying molecular mechanisms could lead to new treatment options which are currently limited. Shoulder complaints are highly common in the elderly, and therefore, muscles of the shoulder's rotator cuff could be considered as a model for chronic age-associated muscle degeneration. Diseased shoulder muscles were characterized by muscle atrophy and fatty infiltration compared with unaffected shoulder muscles. We confirmed fatty infiltration using histochemical analysis. Additionally, fibrosis and loss of contractile myosin expression were found in diseased muscles. Most cellular features, including proliferation rate, apoptosis and cell senescence, remained unchanged and genome-wide molecular signatures were predominantly similar between diseased and intact muscles. However, we found down-regulation of a small subset of muscle function genes, and up-regulation of extracellular region genes. Myogenesis was defected in muscle cell culture from diseased muscles but was restored by elevating MyoD levels. We suggest that impaired muscle functionality in a specific environment of thickened extra-cellular matrix is crucial for the development of chronic age-associated muscle degeneration.

  9. Molecular signatures of age-associated chronic degeneration of shoulder muscles

    PubMed Central

    Raz, Yotam; Henseler, Jan Ferdinand; Kolk, Arjen; Tatum, Zuotian; Groosjohan, Niels Kuipers; Verwey, Nisha E.; Arindrarto, Wibowo; Kielbasa, Szymon M.; Nagels, Jochem; Hoen, Peter A. C. 't; Nelissen, Rob G. H. H.; Raz, Vered

    2016-01-01

    Chronic muscle diseases are highly prevalent in the elderly causing severe mobility limitations, pain and frailty. The intrinsic molecular mechanisms are poorly understood due to multifactorial causes, slow progression with age and variations between individuals. Understanding the underlying molecular mechanisms could lead to new treatment options which are currently limited. Shoulder complaints are highly common in the elderly, and therefore, muscles of the shoulder's rotator cuff could be considered as a model for chronic age-associated muscle degeneration. Diseased shoulder muscles were characterized by muscle atrophy and fatty infiltration compared with unaffected shoulder muscles. We confirmed fatty infiltration using histochemical analysis. Additionally, fibrosis and loss of contractile myosin expression were found in diseased muscles. Most cellular features, including proliferation rate, apoptosis and cell senescence, remained unchanged and genome-wide molecular signatures were predominantly similar between diseased and intact muscles. However, we found down-regulation of a small subset of muscle function genes, and up-regulation of extracellular region genes. Myogenesis was defected in muscle cell culture from diseased muscles but was restored by elevating MyoD levels. We suggest that impaired muscle functionality in a specific environment of thickened extra-cellular matrix is crucial for the development of chronic age-associated muscle degeneration. PMID:26885755

  10. Molecular signature of amniotic fluid derived stem cells in the fetal sheep model of myelomeningocele.

    PubMed

    Ceccarelli, Gabriele; Pozzo, Enrico; Scorletti, Federico; Benedetti, Laura; Cusella, Gabriella; Ronzoni, Flavio Lorenzo; Sahakyan, Vardine; Zambaiti, Elisa; Mimmi, Maria Chiara; Calcaterra, Valeria; Deprest, Jan; Sampaolesi, Maurilio; Pelizzo, Gloria

    2015-09-01

    Abnormal cord development results in spinal cord damage responsible for myelomeningocele (MMC). Amniotic fluid-derived stem cells (AFSCs) have emerged as a potential candidate for applications in regenerative medicine. However, their differentiation potential is largely unknown as well as the molecular signaling orchestrating the accurate spinal cord development. Fetal lambs underwent surgical creation of neural tube defect and its subsequent repair. AFSCs were isolated, cultured and characterized at the 12th (induction of MMC), 16th (repair of malformation), and 20th week of gestation (delivery). After performing open hysterectomy, AF collections on fetuses with sham procedures at the same time points as the MMC creation group have been used as controls. Cytological analyses with the colony forming unit assay, XTT and alkaline-phosphatase staining, qRT-PCR gene expression analyses (normalized with aged match controls) and NMR metabolomics profiling were performed. Here we show for the first time the metabolomics and molecular signature variation in AFSCs isolated in the sheep model of MMC, which may be used as diagnostic tools for the in utero identification of the neural tube damage. Intriguingly, PAX3 gene involved in the murine model for spina bifida is modulated in AFSCs reaching the peak of expression at 16 weeks of gestation, 4 weeks after the intervention. Our data strongly suggest that AFSCs reorganize their differentiation commitment in order to generate PAX3-expressing progenitors to counteract the MMC induced in the sheep model. The gene expression signature of AFSCs highlights the plasticity of these cells reflecting possible alterations of embryonic development.

  11. Osmoadaptative Strategy and Its Molecular Signature in Obligately Halophilic Heterotrophic Protists

    PubMed Central

    Harding, Tommy; Brown, Matthew W.; Simpson, Alastair G.B.; Roger, Andrew J.

    2016-01-01

    Halophilic microbes living in hypersaline environments must counteract the detrimental effects of low water activity and salt interference. Some halophilic prokaryotes equilibrate their intracellular osmotic strength with the extracellular milieu by importing inorganic solutes, mainly potassium. These “salt-in” organisms characteristically have proteins that are highly enriched with acidic and hydrophilic residues. In contrast, “salt-out” halophiles accumulate large amounts of organic solutes like amino acids, sugars and polyols, and lack a strong signature of halophilicity in the amino acid composition of cytoplasmic proteins. Studies to date have examined halophilic prokaryotes, yeasts, or algae, thus virtually nothing is known about the molecular adaptations of the other eukaryotic microbes, that is, heterotrophic protists (protozoa), that also thrive in hypersaline habitats. We conducted transcriptomic investigations to unravel the molecular adaptations of two obligately halophilic protists, Halocafeteria seosinensis and Pharyngomonas kirbyi. Their predicted cytoplasmic proteomes showed increased hydrophilicity compared with marine protists. Furthermore, analysis of reconstructed ancestral sequences suggested that, relative to mesophiles, proteins in halophilic protists have undergone fewer substitutions from hydrophilic to hydrophobic residues since divergence from their closest relatives. These results suggest that these halophilic protists have a higher intracellular salt content than marine protists. However, absence of the acidic signature of salt-in microbes suggests that Haloc. seosinensis and P. kirbyi utilize organic osmolytes to maintain osmotic equilibrium. We detected increased expression of enzymes involved in synthesis and transport of organic osmolytes, namely hydroxyectoine and myo-inositol, at maximal salt concentration for growth in Haloc. seosinensis, suggesting possible candidates for these inferred organic osmolytes. PMID:27412608

  12. Molecular Signatures of Psychosocial Stress and Cognition Are Modulated by Chronic Lithium Treatment.

    PubMed

    Brzózka, Magdalena M; Havemann-Reinecke, Ursula; Wichert, Sven P; Falkai, Peter; Rossner, Moritz J

    2016-07-01

    Chronic psychosocial stress is an important environmental risk factor of psychiatric diseases such as schizophrenia. Social defeat in rodents has been shown to be associated with maladaptive cellular and behavioral consequences including cognitive impairments. Although gene expression changes upon psychosocial stress have been described, a comprehensive transcriptome profiling study at the global level in precisely defined hippocampal subregions which are associated with learning has been lacking. In this study, we exposed adult C57Bl/6N mice for 3 weeks to "resident-intruder" paradigm and combined laser capture microdissection with microarray analyses to identify transcriptomic signatures of chronic psychosocial stress in dentate gyrus and CA3 subregion of the dorsal hippocampus. At the individual transcript level, we detected subregion specific stress responses whereas gene set enrichment analyses (GSEA) identified several common pathways upregulated upon chronic psychosocial stress related to proteasomal function and energy supply. Behavioral profiling revealed stress-associated impairments most prominent in fear memory formation which was prevented by chronic lithium treatment. Thus, we again microdissected the CA3 region and performed global transcriptome analysis to search for molecular signatures altered by lithium treatment in stressed animals. By combining GSEA with unsupervised clustering, we detected pathways that are regulated by stress and lithium in the CA3 region of the hippocampus including proteasomal components, oxidative phosphorylation, and anti-oxidative mechanisms. Our study thus provides insight into hidden molecular phenotypes of chronic psychosocial stress and lithium treatment and proves a beneficial role for lithium treatment as an agent attenuating negative effects of psychosocial stress on cognition.

  13. Molecular Signatures of the Evolving Immune Response in Mice following a Bordetella pertussis Infection

    PubMed Central

    Raeven, René H. M.; Brummelman, Jolanda; Pennings, Jeroen L. A.; Nijst, Olaf E. M.; Kuipers, Betsy; Blok, Laura E. R.; Helm, Kina; van Riet, Elly; Jiskoot, Wim; van Els, Cecile A. C. M.; Han, Wanda G. H.; Kersten, Gideon F. A.; Metz, Bernard

    2014-01-01

    Worldwide resurgence of pertussis necessitates the need for improvement of pertussis vaccines and vaccination strategies. Since natural infections induce a longer-lasting immunity than vaccinations, detailed knowledge of the immune responses following natural infection can provide important clues for such improvement. The purpose was to elucidate the kinetics of the protective immune response evolving after experimental Bordetella pertussis (B. pertussis) infection in mice. Data were collected from (i) individual analyses, i.e. microarray, flow cytometry, multiplex immunoassays, and bacterial clearance; (ii) twelve time points during the infection; and (iii) different tissues involved in the immune responses, i.e. lungs, spleen and blood. Combined data revealed detailed insight in molecular and cellular sequence of events connecting different phases (innate, bridging and adaptive) of the immune response following the infection. We detected a prolonged acute phase response, broad pathogen recognition, and early gene signatures of subsequent T-cell recruitment in the lungs. Activation of particular transcription factors and specific cell markers provided insight into the time course of the transition from innate towards adaptive immune responses, which resulted in a broad spectrum of systemic antibody subclasses and splenic Th1/Th17 memory cells against B. pertussis. In addition, signatures preceding the local generation of Th1 and Th17 cells as well as IgA in the lungs, considered key elements in protection against B. pertussis, were established. In conclusion, molecular and cellular immunological processes in response to live B. pertussis infection were unraveled, which may provide guidance in selecting new vaccine candidates that should evoke local and prolonged protective immune responses. PMID:25137043

  14. Molecular signatures of the evolving immune response in mice following a Bordetella pertussis infection.

    PubMed

    Raeven, René H M; Brummelman, Jolanda; Pennings, Jeroen L A; Nijst, Olaf E M; Kuipers, Betsy; Blok, Laura E R; Helm, Kina; van Riet, Elly; Jiskoot, Wim; van Els, Cecile A C M; Han, Wanda G H; Kersten, Gideon F A; Metz, Bernard

    2014-01-01

    Worldwide resurgence of pertussis necessitates the need for improvement of pertussis vaccines and vaccination strategies. Since natural infections induce a longer-lasting immunity than vaccinations, detailed knowledge of the immune responses following natural infection can provide important clues for such improvement. The purpose was to elucidate the kinetics of the protective immune response evolving after experimental Bordetella pertussis (B. pertussis) infection in mice. Data were collected from (i) individual analyses, i.e. microarray, flow cytometry, multiplex immunoassays, and bacterial clearance; (ii) twelve time points during the infection; and (iii) different tissues involved in the immune responses, i.e. lungs, spleen and blood. Combined data revealed detailed insight in molecular and cellular sequence of events connecting different phases (innate, bridging and adaptive) of the immune response following the infection. We detected a prolonged acute phase response, broad pathogen recognition, and early gene signatures of subsequent T-cell recruitment in the lungs. Activation of particular transcription factors and specific cell markers provided insight into the time course of the transition from innate towards adaptive immune responses, which resulted in a broad spectrum of systemic antibody subclasses and splenic Th1/Th17 memory cells against B. pertussis. In addition, signatures preceding the local generation of Th1 and Th17 cells as well as IgA in the lungs, considered key elements in protection against B. pertussis, were established. In conclusion, molecular and cellular immunological processes in response to live B. pertussis infection were unraveled, which may provide guidance in selecting new vaccine candidates that should evoke local and prolonged protective immune responses.

  15. Interim Report on Multiple Sequence Alignments and TaqMan Signature Mapping to Phylogenetic Trees

    SciTech Connect

    Gardner, S; Jaing, C

    2012-03-27

    The goal of this project is to develop forensic genotyping assays for select agent viruses, addressing a significant capability gap for the viral bioforensics and law enforcement community. We used a multipronged approach combining bioinformatics analysis, PCR-enriched samples, microarrays and TaqMan assays to develop high resolution and cost effective genotyping methods for strain level forensic discrimination of viruses. We have leveraged substantial experience and efficiency gained through year 1 on software development, SNP discovery, TaqMan signature design and phylogenetic signature mapping to scale up the development of forensics signatures in year 2. In this report, we have summarized the Taqman signature development for South American hemorrhagic fever viruses, tick-borne encephalitis viruses and henipaviruses, Old World Arenaviruses, filoviruses, Crimean-Congo hemorrhagic fever virus, Rift Valley fever virus and Japanese encephalitis virus.

  16. A multiple redundant genetic switch locks in the transcriptional signature of T regulatory cells

    PubMed Central

    Fu, Wenxian; Ergun, Ayla; Lu, Ting; Hill, Jonathan A.; Haxhinasto, Sokol; Fassett, Marlys S.; Gazit, Roi; Adoro, Stanley; Glimcher, Laurie; Chan, Susan; Kastner, Philippe; Rossi, Derrick; Collins, James J.; Mathis, Diane; Benoist, Christophe

    2013-01-01

    The transcription factor FoxP3 partakes dominantly in the specification and function of FoxP3+CD4+ T regulatory cells (Tregs), but is neither strictly necessary nor sufficient to determine the characteristic Treg signature. Computational network inference and experimental testing assessed the contribution of other transcription factors (TF). Enforced expression of Helios or Xbp1 elicited specific signatures, but Eos, Irf4, Satb1, Lef1 and Gata1 elicited exactly the same outcome, synergizing with FoxP3 to activate most of the Treg signature, including key TFs, and enhancing FoxP3 occupancy at its genomic targets. Conversely, the Treg signature was robust to inactivation of any single cofactor. A redundant genetic switch thus locks-in the Treg phenotype, a model which accounts for several aspects of Treg physiology, differentiation and stability. PMID:22961053

  17. Lock-in by molecular multiplication

    NASA Astrophysics Data System (ADS)

    Braun, Dieter; Libchaber, Albert

    2003-12-01

    A lock-in amplifier is physically realized at the level of fluorescent dye molecules. It is based on the general property that the emission of a fluorescent dye is the product of quantum efficiency and illumination intensity. For each pixel of a microscopic image, we measure in amplitude and phase an environment property of the dye, such as conformation, membrane voltage, or temperature. This lock-in implementation is highly parallel and reaches the ultimate photon shot noise limit. Using fast temperature oscillations, we apply it to measure the opening/closing kinetics of a molecular beacon (DNA hairpin) at 5 μs resolution.

  18. Phylogenomic Analyses and Comparative Studies on Genomes of the Bifidobacteriales: Identification of Molecular Signatures Specific for the Order Bifidobacteriales and Its Different Subclades.

    PubMed

    Zhang, Grace; Gao, Beile; Adeolu, Mobolaji; Khadka, Bijendra; Gupta, Radhey S

    2016-01-01

    The order Bifidobacteriales comprises a diverse variety of species found in the gastrointestinal tract of humans and other animals, some of which are opportunistic pathogens, whereas a number of others exhibit health-promoting effects. However, currently very few biochemical or molecular characteristics are known which are specific for the order Bifidobacteriales, or specific clades within this order, which distinguish them from other bacteria. This study reports the results of detailed comparative genomic and phylogenetic studies on 62 genome-sequenced species/strains from the order Bifidobacteriales. In a robust phylogenetic tree for the Bifidobacteriales constructed based on 614 core proteins, a number of well-resolved clades were observed including a clade separating the Scarodvia-related genera (Scardovia clade) from the genera Bifidobacterium and Gardnerella, as well as a number of previously reported clusters of Bifidobacterium spp. In parallel, our comparative analyses of protein sequences from the Bifidobacteriales genomes have identified numerous molecular markers that are specific for this group of bacteria. Of these markers, 32 conserved signature indels (CSIs) in widely distributed proteins and 10 signature proteins are distinctive characteristics of all sequenced Bifidobacteriales species and provide novel and highly specific means for distinguishing these bacteria. In addition, multiple other molecular signatures are specific for the following clades of Bifidobacteriales: (i) 5 CSIs specific for a clade comprising of the Scardovia-related genera; (ii) 3 CSIs and 2 CSPs specific for a clade consisting of the Bifidobacterium and Gardnerella spp.; (iii) multiple other signatures demarcating a number of clusters of the B. asteroides-and B. longum- related species. The described molecular markers provide novel and reliable means for distinguishing the Bifidobacteriales and a number of their clades in molecular terms and for the classification of these

  19. Phylogenomic Analyses and Comparative Studies on Genomes of the Bifidobacteriales: Identification of Molecular Signatures Specific for the Order Bifidobacteriales and Its Different Subclades

    PubMed Central

    Zhang, Grace; Gao, Beile; Adeolu, Mobolaji; Khadka, Bijendra; Gupta, Radhey S.

    2016-01-01

    The order Bifidobacteriales comprises a diverse variety of species found in the gastrointestinal tract of humans and other animals, some of which are opportunistic pathogens, whereas a number of others exhibit health-promoting effects. However, currently very few biochemical or molecular characteristics are known which are specific for the order Bifidobacteriales, or specific clades within this order, which distinguish them from other bacteria. This study reports the results of detailed comparative genomic and phylogenetic studies on 62 genome-sequenced species/strains from the order Bifidobacteriales. In a robust phylogenetic tree for the Bifidobacteriales constructed based on 614 core proteins, a number of well-resolved clades were observed including a clade separating the Scarodvia-related genera (Scardovia clade) from the genera Bifidobacterium and Gardnerella, as well as a number of previously reported clusters of Bifidobacterium spp. In parallel, our comparative analyses of protein sequences from the Bifidobacteriales genomes have identified numerous molecular markers that are specific for this group of bacteria. Of these markers, 32 conserved signature indels (CSIs) in widely distributed proteins and 10 signature proteins are distinctive characteristics of all sequenced Bifidobacteriales species and provide novel and highly specific means for distinguishing these bacteria. In addition, multiple other molecular signatures are specific for the following clades of Bifidobacteriales: (i) 5 CSIs specific for a clade comprising of the Scardovia-related genera; (ii) 3 CSIs and 2 CSPs specific for a clade consisting of the Bifidobacterium and Gardnerella spp.; (iii) multiple other signatures demarcating a number of clusters of the B. asteroides-and B. longum- related species. The described molecular markers provide novel and reliable means for distinguishing the Bifidobacteriales and a number of their clades in molecular terms and for the classification of these

  20. Histology-driven data mining of lipid signatures from multiple imaging mass spectrometry analyses: application to human colorectal cancer liver metastasis biopsies.

    PubMed

    Thomas, Aurélien; Patterson, Nathan Heath; Marcinkiewicz, Martin M; Lazaris, Anthoula; Metrakos, Peter; Chaurand, Pierre

    2013-03-05

    Imaging mass spectrometry (IMS) represents an innovative tool in the cancer research pipeline, which is increasingly being used in clinical and pharmaceutical applications. The unique properties of the technique, especially the amount of data generated, make the handling of data from multiple IMS acquisitions challenging. This work presents a histology-driven IMS approach aiming to identify discriminant lipid signatures from the simultaneous mining of IMS data sets from multiple samples. The feasibility of the developed workflow is evaluated on a set of three human colorectal cancer liver metastasis (CRCLM) tissue sections. Lipid IMS on tissue sections was performed using MALDI-TOF/TOF MS in both negative and positive ionization modes after 1,5-diaminonaphthalene matrix deposition by sublimation. The combination of both positive and negative acquisition results was performed during data mining to simplify the process and interrogate a larger lipidome into a single analysis. To reduce the complexity of the IMS data sets, a sub data set was generated by randomly selecting a fixed number of spectra from a histologically defined region of interest, resulting in a 10-fold data reduction. Principal component analysis confirmed that the molecular selectivity of the regions of interest is maintained after data reduction. Partial least-squares and heat map analyses demonstrated a selective signature of the CRCLM, revealing lipids that are significantly up- and down-regulated in the tumor region. This comprehensive approach is thus of interest for defining disease signatures directly from IMS data sets by the use of combinatory data mining, opening novel routes of investigation for addressing the demands of the clinical setting.

  1. Phylogenomics and molecular signatures for species from the plant pathogen-containing order xanthomonadales.

    PubMed

    Naushad, Hafiz Sohail; Gupta, Radhey S

    2013-01-01

    The species from the order Xanthomonadales, which harbors many important plant pathogens and some human pathogens, are currently distinguished primarily on the basis of their branching in the 16S rRNA tree. No molecular or biochemical characteristic is known that is specific for these bacteria. Phylogenetic and comparative analyses were conducted on 26 sequenced Xanthomonadales genomes to delineate their branching order and to identify molecular signatures consisting of conserved signature indels (CSIs) in protein sequences that are specific for these bacteria. In a phylogenetic tree based upon sequences for 28 proteins, Xanthomonadales species formed a strongly supported clade with Rhodanobacter sp. 2APBS1 as its deepest branch. Comparative analyses of protein sequences have identified 13 CSIs in widely distributed proteins such as GlnRS, TypA, MscL, LysRS, LipA, Tgt, LpxA, TolQ, ParE, PolA and TyrB that are unique to all species/strains from this order, but not found in any other bacteria. Fifteen additional CSIs in proteins (viz. CoxD, DnaE, PolA, SucA, AsnB, RecA, PyrG, LigA, MutS and TrmD) are uniquely shared by different Xanthomonadales except Rhodanobacter and in a few cases by Pseudoxanthomonas species, providing further support for the deep branching of these two genera. Five other CSIs are commonly shared by Xanthomonadales and 1-3 species from the orders Chromatiales, Methylococcales and Cardiobacteriales suggesting that these deep branching orders of Gammaproteobacteria might be specifically related. Lastly, 7 CSIs in ValRS, CarB, PyrE, GlyS, RnhB, MinD and X001065 are commonly shared by Xanthomonadales and a limited number of Beta- or Gamma-proteobacteria. Our analysis indicates that these CSIs have likely originated independently and they are not due to lateral gene transfers. The Xanthomonadales-specific CSIs reported here provide novel molecular markers for the identification of these important plant and human pathogens and also as potential targets

  2. Phylogenomics and Molecular Signatures for Species from the Plant Pathogen-Containing Order Xanthomonadales

    PubMed Central

    Naushad, Hafiz Sohail; Gupta, Radhey S.

    2013-01-01

    The species from the order Xanthomonadales, which harbors many important plant pathogens and some human pathogens, are currently distinguished primarily on the basis of their branching in the 16S rRNA tree. No molecular or biochemical characteristic is known that is specific for these bacteria. Phylogenetic and comparative analyses were conducted on 26 sequenced Xanthomonadales genomes to delineate their branching order and to identify molecular signatures consisting of conserved signature indels (CSIs) in protein sequences that are specific for these bacteria. In a phylogenetic tree based upon sequences for 28 proteins, Xanthomonadales species formed a strongly supported clade with Rhodanobacter sp. 2APBS1 as its deepest branch. Comparative analyses of protein sequences have identified 13 CSIs in widely distributed proteins such as GlnRS, TypA, MscL, LysRS, LipA, Tgt, LpxA, TolQ, ParE, PolA and TyrB that are unique to all species/strains from this order, but not found in any other bacteria. Fifteen additional CSIs in proteins (viz. CoxD, DnaE, PolA, SucA, AsnB, RecA, PyrG, LigA, MutS and TrmD) are uniquely shared by different Xanthomonadales except Rhodanobacter and in a few cases by Pseudoxanthomonas species, providing further support for the deep branching of these two genera. Five other CSIs are commonly shared by Xanthomonadales and 1–3 species from the orders Chromatiales, Methylococcales and Cardiobacteriales suggesting that these deep branching orders of Gammaproteobacteria might be specifically related. Lastly, 7 CSIs in ValRS, CarB, PyrE, GlyS, RnhB, MinD and X001065 are commonly shared by Xanthomonadales and a limited number of Beta- or Gamma-proteobacteria. Our analysis indicates that these CSIs have likely originated independently and they are not due to lateral gene transfers. The Xanthomonadales-specific CSIs reported here provide novel molecular markers for the identification of these important plant and human pathogens and also as potential

  3. Molecular signature of pancreatic adenocarcinoma: an insight from genotype to phenotype and challenges for targeted therapy

    PubMed Central

    Sahin, Ibrahim H; Iacobuzio-Donahue, Christine A; O’Reilly, Eileen M

    2016-01-01

    Introduction Pancreatic adenocarcinoma remains one of the most clinically challenging cancers despite an in-depth characterization of the molecular underpinnings and biology of this disease. Recent whole-genome-wide studies have elucidated the diverse and complex genetic alterations which generate a unique oncogenic signature for an individual pancreatic cancer patient and which may explain diverse disease behavior in a clinical setting. Areas covered In this review article, we discuss the key oncogenic pathways of pancreatic cancer including RAS-MAPK, PI3KCA and TGF-β signaling, as well as the impact of these pathways on the disease behavior and their potential targetability. The role of tumor suppressors particularly BRCA1 and BRCA2 genes and their role in pancreatic cancer treatment are elaborated upon. We further review recent genomic studies and their impact on future pancreatic cancer treatment. Expert opinion Targeted therapies inhibiting pro-survival pathways have limited impact on pancreatic cancer outcomes. Activation of pro-apoptotic pathways along with suppression of cancer-stem-related pathways may reverse treatment resistance in pancreatic cancer. While targeted therapy or a ‘precision medicine’ approach in pancreatic adenocarcinoma remains an elusive challenge for the majority of patients, there is a real sense of optimism that the strides made in understanding the molecular underpinnings of this disease will translate into improved outcomes. PMID:26439702

  4. Nuclear signature effect on spatial distribution of molecular harmonic in the presence of spatial inhomogeneous field

    NASA Astrophysics Data System (ADS)

    Feng, Liqiang; Li, Wenliang

    2017-01-01

    Spatial distribution of the molecular harmonic spectra from \\text{H}\\text{2}+ in the presence of inhomogeneous field has been theoretically investigated. It shows that (i) the harmonic intensities from the negative-H nucleus play the dominating role in harmonic emission spectra. (ii) Through the investigations of the nuclear signature effect on the spatial distribution of the molecular harmonic spectra, the differences of the harmonic intensities between the negative-H nucleus and the positive-H nucleus can be enhanced and reduced with the introduction of the higher vibrational state and the heavy nucleus (i.e. \\text{D}2+ ), respectively. The time-frequency analyses of the harmonic spectra, the time-dependent wave function and the electron localization have been shown to explain the harmonic spatial distribution and the electron motion. (iii) Due to the plasmon-resonance-enhancement near the metallic nanostructure, the harmonic cutoff can be remarkably enhanced as the spatial position of the inhomogeneous field moving away from the gap center. The ionization probabilities have been shown to explain the harmonic cutoff extension.

  5. Multiple Sclerosis: Molecular Mechanisms and Therapeutic Opportunities

    PubMed Central

    Miljković, Djordje; Spasojević, Ivan

    2013-01-01

    Abstract The pathophysiology of multiple sclerosis (MS) involves several components: redox, inflammatory/autoimmune, vascular, and neurodegenerative. All of them are supported by the intertwined lines of evidence, and none of them should be written off. However, the exact mechanisms of MS initiation, its development, and progression are still elusive, despite the impressive pace by which the data on MS are accumulating. In this review, we will try to integrate the current facts and concepts, focusing on the role of redox changes and various reactive species in MS. Knowing the schedule of initial changes in pathogenic factors and the key turning points, as well as understanding the redox processes involved in MS pathogenesis is the way to enable MS prevention, early treatment, and the development of therapies that target specific pathophysiological components of the heterogeneous mechanisms of MS, which could alleviate the symptoms and hopefully stop MS. Pertinent to this, we will outline (i) redox processes involved in MS initiation; (ii) the role of reactive species in inflammation; (iii) prooxidative changes responsible for neurodegeneration; and (iv) the potential of antioxidative therapy. Antioxid. Redox Signal. 19, 2286–2334. PMID:23473637

  6. Low variance RNAs identify Parkinson’s disease molecular signature in blood

    PubMed Central

    Chikina, Maria D.; Gerald, Christophe P.; Li, Xianting; Ge, Yongchao; Pincas, Hanna; Nair, Venugopalan D.; Wong, Aaron K.; Krishnan, Arjun; Troyanskaya, Olga G.; Raymond, Deborah; Saunders-Pullman, Rachel; Bressman, Susan B.; Yue, Zhenyu; Sealfon, Stuart C.

    2015-01-01

    Background The diagnosis of Parkinson’s disease (PD) is usually not established until advanced neurodegeneration leads to clinically detectable symptoms. Previous blood PD transcriptome studies show low concordance, possibly due to the use of microarray technology, which has high measurement variation. The Leucine-rich repeat kinase 2 (LRRK2) G2019S mutation predisposes to PD. Using preclinical and clinical studies, we sought to develop a novel statistically motivated transcriptomic-based approach to identify a molecular signature in the blood of Ashkenazi Jewish PD patients including LRRK2 mutation carriers. Methods Using a digital gene expression platform to quantify 175 mRNA markers with low coefficients of variation (CV), we first compared whole blood transcript levels in mouse models 1) over-expressing wild-type (WT) LRRK2, 2) overexpressing G2019S LRRK2, 3) lacking LRRK2 (knockout), 4) and in WT controls. We then studied an Ashkenazi Jewish cohort of 34 symptomatic PD patients (both WT LRRK2 and G2019S LRRK2) and 32 asymptomatic controls. Results The expression profiles distinguished the 4 mouse groups with different genetic background. In patients, we detected significant differences in blood transcript levels both between individuals differing in LRRK2 genotype and between PD patients and controls. Discriminatory PD markers included genes associated with innate and adaptive immunity and inflammatory disease. Notably, gene expression patterns in L-DOPA-treated PD patients were significantly closer to those of healthy controls in a dose-dependent manner. Conclusions We identify whole blood mRNA signatures correlating with LRRK2 genotype and with PD disease state. This approach may provide insight into pathogenesis and a route to early disease detection. PMID:25786808

  7. Integrated, multi-cohort analysis identifies conserved transcriptional signatures across multiple respiratory viruses

    PubMed Central

    Andres-Terre, Marta; McGuire, Helen M; Pouliot, Yannick; Bongen, Erika; Sweeney, Timothy E.; Tato, Cristina M; Khatri, Purvesh

    2015-01-01

    Respiratory viral infections are a significant burden to healthcare worldwide. Many whole genome expression profiles have identified different respiratory viral infection signatures, but these have not translated to clinical practice. Here, we performed two integrated, multi-cohort analyses of publicly available transcriptional data of viral infections. First, we identified a common host signature across different respiratory viral infections that could distinguish (a) individuals with viral infections from healthy controls and from those with bacterial infections, and (b) symptomatic from asymptomatic subjects prior to symptom onset in challenge studies. Second, we identified an influenza-specific host response signature that (a) could distinguish influenza-infected samples from those with bacterial and other respiratory viral infections, (b) was a diagnostic and prognostic marker in influenza-pneumonia patients and influenza challenge studies, and (c) was predictive of response to influenza vaccine. Our results have applications in the diagnosis, prognosis, and identification of drug targets in viral infections. PMID:26682989

  8. Whole-genome resequencing uncovers molecular signatures of natural and sexual selection in wild bighorn sheep.

    PubMed

    Kardos, Marty; Luikart, Gordon; Bunch, Rowan; Dewey, Sarah; Edwards, William; McWilliam, Sean; Stephenson, John; Allendorf, Fred W; Hogg, John T; Kijas, James

    2015-11-01

    The identification of genes influencing fitness is central to our understanding of the genetic basis of adaptation and how it shapes phenotypic variation in wild populations. Here, we used whole-genome resequencing of wild Rocky Mountain bighorn sheep (Ovis canadensis) to >50-fold coverage to identify 2.8 million single nucleotide polymorphisms (SNPs) and genomic regions bearing signatures of directional selection (i.e. selective sweeps). A comparison of SNP diversity between the X chromosome and the autosomes indicated that bighorn males had a dramatically reduced long-term effective population size compared to females. This probably reflects a long history of intense sexual selection mediated by male-male competition for mates. Selective sweep scans based on heterozygosity and nucleotide diversity revealed evidence for a selective sweep shared across multiple populations at RXFP2, a gene that strongly affects horn size in domestic ungulates. The massive horns carried by bighorn rams appear to have evolved in part via strong positive selection at RXFP2. We identified evidence for selection within individual populations at genes affecting early body growth and cellular response to hypoxia; however, these must be interpreted more cautiously as genetic drift is strong within local populations and may have caused false positives. These results represent a rare example of strong genomic signatures of selection identified at genes with known function in wild populations of a nonmodel species. Our results also showcase the value of reference genome assemblies from agricultural or model species for studies of the genomic basis of adaptation in closely related wild taxa.

  9. Competence for Chemical Reprogramming of Sexual Fate Correlates with an Intersexual Molecular Signature in Caenorhabditis elegans

    PubMed Central

    Sorokin, Elena P.; Gasch, Audrey P.; Kimble, Judith

    2014-01-01

    In multicellular organisms, genetic programs guide cells to adopt cell fates as tissues are formed during development, maintained in adults, and repaired after injury. Here we explore how a small molecule in the environment can switch a genetic program from one fate to another. Wild-type Caenorhabditis elegans XX adult hermaphrodites make oocytes continuously, but certain mutant XX adults make sperm instead in an otherwise hermaphrodite soma. Thus, puf-8; lip-1 XX adults make only sperm, but they can be switched from sperm to oocyte production by treatment with a small-molecule MEK inhibitor. To ask whether this chemical reprogramming is common, we tested six XX sperm-only mutants, but found only one other capable of cell fate switching, fbf-1; lip-1. Therefore, reprogramming competence relies on genotype, with only certain mutants capable of responding to the MEK inhibitor with a cell fate change. To gain insight into the molecular basis of competence for chemical reprogramming, we compared polyadenylated transcriptomes of competent and noncompetent XX sperm-only mutants in the absence of the MEK inhibitor and hence in the absence of cell fate reprogramming. Despite their cellular production of sperm, competent mutants were enriched for oogenic messenger RNAs relative to mutants lacking competence for chemical reprogramming. In addition, competent mutants expressed the oocyte-specific protein RME-2, whereas those lacking competence did not. Therefore, mutants competent for reprogramming possess an intersexual molecular profile at both RNA and protein levels. We suggest that this intersexual molecular signature is diagnostic of an intermediate network state that poises the germline tissue for changing its cellular fate in response to environmental cues. PMID:25146970

  10. Competence for chemical reprogramming of sexual fate correlates with an intersexual molecular signature in Caenorhabditis elegans.

    PubMed

    Sorokin, Elena P; Gasch, Audrey P; Kimble, Judith

    2014-10-01

    In multicellular organisms, genetic programs guide cells to adopt cell fates as tissues are formed during development, maintained in adults, and repaired after injury. Here we explore how a small molecule in the environment can switch a genetic program from one fate to another. Wild-type Caenorhabditis elegans XX adult hermaphrodites make oocytes continuously, but certain mutant XX adults make sperm instead in an otherwise hermaphrodite soma. Thus, puf-8; lip-1 XX adults make only sperm, but they can be switched from sperm to oocyte production by treatment with a small-molecule MEK inhibitor. To ask whether this chemical reprogramming is common, we tested six XX sperm-only mutants, but found only one other capable of cell fate switching, fbf-1; lip-1. Therefore, reprogramming competence relies on genotype, with only certain mutants capable of responding to the MEK inhibitor with a cell fate change. To gain insight into the molecular basis of competence for chemical reprogramming, we compared polyadenylated transcriptomes of competent and noncompetent XX sperm-only mutants in the absence of the MEK inhibitor and hence in the absence of cell fate reprogramming. Despite their cellular production of sperm, competent mutants were enriched for oogenic messenger RNAs relative to mutants lacking competence for chemical reprogramming. In addition, competent mutants expressed the oocyte-specific protein RME-2, whereas those lacking competence did not. Therefore, mutants competent for reprogramming possess an intersexual molecular profile at both RNA and protein levels. We suggest that this intersexual molecular signature is diagnostic of an intermediate network state that poises the germline tissue for changing its cellular fate in response to environmental cues.

  11. In vivo epigenomic profiling of germ cells reveals germ cell molecular signatures.

    PubMed

    Ng, Jia-Hui; Kumar, Vibhor; Muratani, Masafumi; Kraus, Petra; Yeo, Jia-Chi; Yaw, Lai-Ping; Xue, Kun; Lufkin, Thomas; Prabhakar, Shyam; Ng, Huck-Hui

    2013-02-11

    The limited number of in vivo germ cells poses an impediment to genome-wide studies. Here, we applied a small-scale chromatin immunoprecipitation sequencing (ChIP-seq) method on purified mouse fetal germ cells to generate genome-wide maps of four histone modifications (H3K4me3, H3K27me3, H3K27ac, and H2BK20ac). Comparison of active chromatin state between somatic, embryonic stem, and germ cells revealed promoters and enhancers needed for stem cell maintenance and germ cell development. We found the nuclear receptor Nr5a2 motif to be enriched at a subset of germ cell cis-regulatory regions, and our results implicate Nr5a2 in germ cell biology. Interestingly, in germ cells, the H3K27me3 histone modification occurs more frequently at regions that are enriched for retrotransposons and MHC genes, indicating that these loci are specifically silenced in germ cells. Together, our study provides genome-wide histone modification maps of in vivo germ cells and reveals the molecular chromatin signatures of germ cells.

  12. Structural signatures of DRD4 mutants revealed using molecular dynamics simulations: Implications for drug targeting.

    PubMed

    Jatana, Nidhi; Thukral, Lipi; Latha, N

    2016-01-01

    Human Dopamine Receptor D4 (DRD4) orchestrates several neurological functions and represents a target for many psychological disorders. Here, we examined two rare variants in DRD4; V194G and R237L, which elicit functional alterations leading to disruption of ligand binding and G protein coupling, respectively. Using atomistic molecular dynamics (MD) simulations, we provide in-depth analysis to reveal structural signatures of wild and mutant complexes with their bound agonist and antagonist ligands. We constructed intra-protein network graphs to discriminate the global conformational changes induced by mutations. The simulations also allowed us to elucidate the local side-chain dynamical variations in ligand-bound mutant receptors. The data suggest that the mutation in transmembrane V (V194G) drastically disrupts the organization of ligand binding site and causes disorder in the native helical arrangement. Interestingly, the R237L mutation leads to significant rewiring of side-chain contacts in the intracellular loop 3 (site of mutation) and also affects the distant transmembrane topology. Additionally, these mutations lead to compact ICL3 region compared to the wild type, indicating that the receptor would be inaccessible for G protein coupling. Our findings thus reveal unreported structural determinants of the mutated DRD4 receptor and provide a robust framework for design of effective novel drugs.

  13. Determination of the molecular signature of fossil conifers by experimental palaeochemotaxonomy - Part 1: The Araucariaceae family

    NASA Astrophysics Data System (ADS)

    Lu, Y.; Hautevelle, Y.; Michels, R.

    2013-03-01

    Twelve species of the conifer family Araucariaceae, including Araucaria (6 species), Agathis (3 species) and Wollemia (1 species) genera, were submitted to artificial maturation by confined pyrolysis. The aim of these experiments is to transform the biomolecules synthesized by these species into their homologous geomolecules in laboratory conditions. Determination of the diagenetic molecular signatures of Araucariaceae through experimentation on extant representatives allows us to complete our knowledge in botanical palaeochemotaxonomy. Such knowledge is relevant to palaeoenvironmental, environmental and archaeology purposes. All artificially diagenetic species of Araucariaceae are firstly characterized by a predominance of saturated tetracyclic diterpenoids including ent-beyerane, phyllocladanes and ent-kauranes. Moreover, Araucaria genus shows a high relative abundance of bicyclic sesquiterpenoids, particularly the cadalane-type compounds accompanied by those of eudesmane and bisabolane types as well as chamazulene and pentamethyl-dihydroindenes. Diterpenoids are of labdane, isopimarane and abietane types (essentially derived from abietanoic acids) as well as isohexyl alkylaromatic hydrocarbons. Compared to the tetracyclic diterpenoids, these compounds show a relatively lower abundance, reaching trace levels in the case of saturated abietanes. Distributions of sesquiterpenoids and diterpenoids of Agathis show some similarities to that of Araucaria, with the exception of one species, in which the tetracyclic compounds are absent and the abietane type (essentially derived from abietanoic acids) predominant. High similarities between the Wollemia and Araucaria genera are observed. Both are characterized by some high relative abundance of tetracyclic compounds with no predominance of other specific diterpenoids.

  14. Molecular signatures to define spermatogenic cells in common marmoset (Callithrix jacchus).

    PubMed

    Lin, Zachary Yu-Ching; Imamura, Masanori; Sano, Chiaki; Nakajima, Ryusuke; Suzuki, Tomoko; Yamadera, Rie; Takehara, Yuji; Okano, Hirotaka James; Sasaki, Erika; Okano, Hideyuki

    2012-05-01

    Germ cell development is a fundamental process required to produce offspring. The developmental program of spermatogenesis has been assumed to be similar among mammals. However, recent studies have revealed differences in the molecular properties of primate germ cells compared with the well-characterized mouse germ cells. This may prevent simple application of rodent insights into higher primates. Therefore, thorough investigation of primate germ cells is necessary, as this may lead to the development of more appropriate animal models. The aim of this study is to define molecular signatures of spermatogenic cells in the common marmoset, Callithrix jacchus. Interestingly, NANOG, PRDM1, DPPA3 (STELLA), IFITM3, and ZP1 transcripts, but no POU5F1 (OCT4), were detected in adult marmoset testis. Conversely, mouse testis expressed Pou5f1 but not Nanog, Prdm1, Dppa3, Ifitm3, and Zp1. Other previously described mouse germ cell markers were conserved in marmoset and mouse testes. Intriguingly, marmoset spermatogenic cells underwent dynamic protein expression in a developmental stage-specific manner; DDX4 (VASA) protein was present in gonocytes, diminished in spermatogonial cells, and reexpressed in spermatocytes. To investigate epigenetic differences between adult marmoset and mice, DNA methylation analyses identified unique epigenetic profiles to marmoset and mice. Marmoset NANOG and POU5F1 promoters in spermatogenic cells exhibited a methylation status opposite to that in mice, while the DDX4 and LEFTY1 loci, as well as imprinted genes, displayed an evolutionarily conserved methylation pattern. Marmosets have great advantages as models for human reproductive biology and are also valuable as experimental nonhuman primates; thus, the current study provides an important platform for primate reproductive biology, including possible applications to humans.

  15. Effect of heparin on the biological properties and molecular signature of human mesenchymal stem cells.

    PubMed

    Ling, Ling; Camilleri, Emily T; Helledie, Torben; Samsonraj, Rebekah M; Titmarsh, Drew M; Chua, Ren Jie; Dreesen, Oliver; Dombrowski, Christian; Rider, David A; Galindo, Mario; Lee, Ian; Hong, Wanjin; Hui, James H; Nurcombe, Victor; van Wijnen, Andre J; Cool, Simon M

    2016-01-15

    Chronic use of heparin as an anti-coagulant for the treatment of thrombosis or embolism invokes many adverse systemic events including thrombocytopenia, vascular reactions and osteoporosis. Here, we addressed whether adverse effects might also be directed to mesenchymal stem cells that reside in the bone marrow compartment. Harvested human bone marrow-derived mesenchymal stem cells (hMSCs) were exposed to varying doses of heparin and their responses profiled. At low doses (<200 ng/ml), serial passaging with heparin exerted a variable effect on hMSC proliferation and multipotentiality across multiple donors, while at higher doses (≥ 100 μg/ml), heparin supplementation inhibited cell growth and increased both senescence and cell size. Gene expression profiling using cDNA arrays and RNA-seq analysis revealed pleiotropic effects of low-dose heparin on signaling pathways essential to hMSC growth and differentiation (including the TGFβ/BMP superfamily, FGFs, and Wnts). Cells serially passaged in low-dose heparin possess a donor-dependent gene signature that reflects their altered phenotype. Our data indicate that heparin supplementation during the culturing of hMSCs can alter their biological properties, even at low doses. This warrants caution in the application of heparin as a culture supplement for the ex vivo expansion of hMSCs. It also highlights the need for careful evaluation of the bone marrow compartment in patients receiving chronic heparin treatment.

  16. Effect of heparin on the biological properties and molecular signature of human mesenchymal stem cells

    PubMed Central

    Ling, Ling; Camilleri, Emily T.; Helledie, Torben; Samsonraj, Rebekah M.; Titmarsh, Drew M.; Chua, Ren Jie; Dreesen, Oliver; Dombrowski, Christian; Rider, David A.; Galindo, Mario; Lee, Ian; Hong, Wanjin; Hui, James H.; Nurcombe, Victor; van Wijnen, Andre J.; Cool, Simon M.

    2017-01-01

    Chronic use of heparin as an anti-coagulant for the treatment of thrombosis or embolism invokes many adverse systemic events including thrombocytopenia, vascular reactions and osteoporosis. Here, we addressed whether adverse effects might also be directed to mesenchymal stem cells that reside in the bone marrow compartment. Harvested human bone marrow-derived mesenchymal stem cells (hMSCs) were exposed to varying doses of heparin and their responses profiled. At low doses (<200 ng/ml), serial passaging with heparin exerted a variable effect on hMSC proliferation and multipotentiality across multiple donors, while at higher doses (≥100 µg/ml), heparin supplementation inhibited cell growth and increased both senescence and cell size. Gene expression profiling using cDNA arrays and RNA-seq analysis revealed pleiotropic effects of low-dose heparin on signaling pathways essential to hMSC growth and differentiation (including the TGFβ/BMP superfamily, FGFs, and Wnts). Cells serially passaged in low-dose heparin possess a donor-dependent gene signature that reflects their altered phenotype. Our data indicate that heparin supplementation during the culturing of hMSCs can alter their biological properties, even at low doses. This warrants caution in the application of heparin as a culture supplement for the ex vivo expansion of hMSCs. It also highlights the need for careful evaluation of the bone marrow compartment in patients receiving chronic heparin treatment. PMID:26484394

  17. Genome Diversity and Divergence in Drosophila mauritiana: Multiple Signatures of Faster X Evolution

    PubMed Central

    Garrigan, Daniel; Kingan, Sarah B.; Geneva, Anthony J.; Vedanayagam, Jeffrey P.; Presgraves, Daven C.

    2014-01-01

    Drosophila mauritiana is an Indian Ocean island endemic species that diverged from its two sister species, Drosophila simulans and Drosophila sechellia, approximately 240,000 years ago. Multiple forms of incomplete reproductive isolation have evolved among these species, including sexual, gametic, ecological, and intrinsic postzygotic barriers, with crosses among all three species conforming to Haldane’s rule: F1 hybrid males are sterile and F1 hybrid females are fertile. Extensive genetic resources and the fertility of hybrid females have made D. mauritiana, in particular, an important model for speciation genetics. Analyses between D. mauritiana and both of its siblings have shown that the X chromosome makes a disproportionate contribution to hybrid male sterility. But why the X plays a special role in the evolution of hybrid sterility in these, and other, species remains an unsolved problem. To complement functional genetic analyses, we have investigated the population genomics of D. mauritiana, giving special attention to differences between the X and the autosomes. We present a de novo genome assembly of D. mauritiana annotated with RNAseq data and a whole-genome analysis of polymorphism and divergence from ten individuals. Our analyses show that, relative to the autosomes, the X chromosome has reduced nucleotide diversity but elevated nucleotide divergence; an excess of recurrent adaptive evolution at its protein-coding genes; an excess of recent, strong selective sweeps; and a large excess of satellite DNA. Interestingly, one of two centimorgan-scale selective sweeps on the D. mauritiana X chromosome spans a region containing two sex-ratio meiotic drive elements and a high concentration of satellite DNA. Furthermore, genes with roles in reproduction and chromosome biology are enriched among genes that have histories of recurrent adaptive protein evolution. Together, these genome-wide analyses suggest that genetic conflict and frequent positive natural

  18. Molecular signatures for the phylum Synergistetes and some of its subclades.

    PubMed

    Bhandari, Vaibhav; Gupta, Radhey S

    2012-11-01

    Species belonging to the phylum Synergistetes are poorly characterized. Though the known species display Gram-negative characteristics and the ability to ferment amino acids, no single characteristic is known which can define this group. For eight Synergistetes species, complete genome sequences or draft genomes have become available. We have used these genomes to construct detailed phylogenetic trees for the Synergistetes species and carried out comprehensive analysis to identify molecular markers consisting of conserved signature indels (CSIs) in protein sequences that are specific for either all Synergistetes or some of their sub-groups. We report here identification of 32 CSIs in widely distributed proteins such as RpoB, RpoC, UvrD, GyrA, PolA, PolC, MraW, NadD, PyrE, RpsA, RpsH, FtsA, RadA, etc., including a large >300 aa insert within the RpoC protein, that are present in various Synergistetes species, but except for isolated bacteria, these CSIs are not found in the protein homologues from any other organisms. These CSIs provide novel molecular markers that distinguish the species of the phylum Synergistetes from all other bacteria. The large numbers of other CSIs discovered in this work provide valuable information that supports and consolidates evolutionary relationships amongst the sequenced Synergistetes species. Of these CSIs, seven are specifically present in Jonquetella, Pyramidobacter and Dethiosulfovibrio species indicating a cladal relationship among them, which is also strongly supported by phylogenetic trees. A further 15 CSIs that are only present in Jonquetella and Pyramidobacter indicate a close association between these two species. Additionally, a previously described phylogenetic relationship between the Aminomonas and Thermanaerovibrio species was also supported by 9 CSIs. The strong relationships indicated by the indel analysis provide incentives for the grouping of species from these clades into higher taxonomic groups such as families

  19. Phylogeny and molecular signatures for the phylum Thermotogae and its subgroups.

    PubMed

    Gupta, Radhey S; Bhandari, Vaibhav

    2011-06-01

    Thermotogae species are currently identified mainly on the basis of their unique toga and distinct branching in the rRNA and other phylogenetic trees. No biochemical or molecular markers are known that clearly distinguish the species from this phylum from all other bacteria. The taxonomic/evolutionary relationships within this phylum, which consists of a single family, are also unclear. We report detailed phylogenetic analyses on Thermotogae species based on concatenated sequences for many ribosomal as well as other conserved proteins that identify a number of distinct clades within this phylum. Additionally, comprehensive analyses of protein sequences from Thermotogae genomes have identified >60 Conserved Signature Indels (CSI) that are specific for the Thermotogae phylum or its different subgroups. Eighteen CSIs in important proteins such as PolI, RecA, TrpRS and ribosomal proteins L4, L7/L12, S8, S9, etc. are uniquely present in various Thermotogae species and provide molecular markers for the phylum. Many CSIs were specific for a number of Thermotogae subgroups. Twelve of these CSIs were specific for a clade consisting of various Thermotoga species except Tt. lettingae, which was separated from other Thermotoga species by a long branch in phylogenetic trees; Fourteen CSIs were specific for a clade consisting of the Fervidobacterium and Thermosipho genera and eight additional CSIs were specific for the genus Thermosipho. In addition, the existence of a clade consisting of the deep branching species Petrotoga mobilis, Kosmotoga olearia and Thermotogales bacterium mesG1 was supported by seven CSIs. The deep branching of this clade was also supported by a number of CSIs that were present in various Thermotogae species, but absent in this clade and all other bacteria. Most of these clades were strongly supported by phylogenetic analyses based on two datasets of protein sequences and they identify potential higher taxonomic grouping (viz. families) within this phylum

  20. Tissue-Specific Molecular Biomarker Signatures of Type 2 Diabetes: An Integrative Analysis of Transcriptomics and Protein-Protein Interaction Data.

    PubMed

    Calimlioglu, Beste; Karagoz, Kubra; Sevimoglu, Tuba; Kilic, Elif; Gov, Esra; Arga, Kazim Yalcin

    2015-09-01

    Type 2 diabetes mellitus is a major global public health burden. A complex metabolic disease, type 2 diabetes affects multiple different tissues, demanding a "systems medicine" approach to biomarker and novel diagnostic discovery, not to mention data integration across omics-es. In the present study, transcriptomics data from different tissues including beta-cells, pancreatic islets, arterial tissue, peripheral blood mononuclear cells, liver, and skeletal muscle of 228 samples were integrated with protein-protein interaction data and genome scale metabolic models to unravel the molecular and tissue-specific biomarker signatures of type 2 diabetes mellitus. Classifying differentially expressed genes, reconstruction and topological analysis of active protein-protein interaction subnetworks indicated that genomic reprogramming depends on the type of tissue, whereas there are common signatures at different levels. Among all tissue and cell types, Mannosidase Alpha Class 1A Member 2 was the common signature at genome level, and activation-ppara reaction, which stimulates a nuclear receptor protein, was found out as the mutual reporter at metabolic level. Moreover, miR-335 and miR-16-5p came into prominence in regulation of transcription at different tissues. On the other hand, distinct signatures were observed for different tissues at the metabolome level. Various coenzyme-A derivatives were significantly enriched metabolites in pancreatic islets, whereas skeletal muscle was enriched for cholesterol, malate, L-carnitine, and several amino acids. Results have showed utmost importance concerning relations between T2D and cancer, blood coagulation, neurodegenerative diseases, and specific metabolic and signaling pathways.

  1. Using Multiple Sulfur Isotope Signatures to Delineate Terrane Boundaries and Investigate Crustal Formation Mechanisms during the Paleoproterozoic

    NASA Astrophysics Data System (ADS)

    LaFlamme, C.; Fiorentini, M. L.; Johnson, S.; Occhipinti, S.; Wing, B. A.; Jeon, H.

    2015-12-01

    Proterozoic cratonic margins are structurally and magmatically complex areas of the Earth's crust, having undergone one or more orogenic cycles. Syn- to late-orogenic plutonic suites have a profound effect on the stabilization of cratonic margins by enabling the development of a refractory and buoyant subcontinental mantle and/or lower crust from which they were derived. In addition, these intrusive bodies act as isotopic tracers to the underlying lithospheric keel and its intricate and often obscured architecture. In situ multiple sulfur isotope systematics are a robust and powerful tool for fingerprinting spatially and temporally anomalous signatures found in the crust. When combined, δ34S and Δ33S have the potential to link source environment and age of a sulfur-bearing mineral. Here, we investigate the multiple sulfur isotopic signatures of two syn- to late-orogenic supersuites that form a large component of the Paleoproterozoic Capricorn Orogen of Western Australia: the ca. 1820-1775 Ma Moorarie Supersuite and the ca. 1680-1620 Ma Durlacher Supersuite. Results from secondary ion mass spectrometry demonstrate that the magmatic pyrite from the Moorarie Supersuite yields two differing signatures with δ34S and Δ33S equal to: 1) 3.1-4.8; ~0.00, and 2) 5.1-8.4; 0.1-0.24. This dichotomy is spatially associated with unexposed seismic blocks defined by Johnson et al., (2013).Multiple sulfur isotope systematics also lend insight into the poorly understood formation mechanisms and sources of syn- to late-orogenic plutonic suites. The Durlacher Supersuite does not preserve sample-to-sample variation (δ34S=5.0-8.3; Δ33S=0.0), indicating that it crystallized from a widespread and homogeneous source. This is in direct contrast to the systematic δ34S and Δ33S variation preserved in the Moorarie Supersuite, a feature that we attribute to smaller batch melting of localized and isotopically separate blocks. Lastly, the Durlacher Supersuite contains anomalous within

  2. Molecular Signatures Reveal Circadian Clocks May Orchestrate the Homeorhetic Response to Lactation

    PubMed Central

    Casey, Theresa; Patel, Osman; Dykema, Karl; Dover, Heather; Furge, Kyle; Plaut, Karen

    2009-01-01

    Genes associated with lactation evolved more slowly than other genes in the mammalian genome. Higher conservation of milk and mammary genes suggest that species variation in milk composition is due in part to the environment and that we must look deeper into the genome for regulation of lactation. At the onset of lactation, metabolic changes are coordinated among multiple tissues through the endocrine system to accommodate the increased demand for nutrients and energy while allowing the animal to remain in homeostasis. This process is known as homeorhesis. Homeorhetic adaptation to lactation has been extensively described; however how these adaptations are orchestrated among multiple tissues remains elusive. To develop a clearer picture of how gene expression is coordinated across multiple tissues during the pregnancy to lactation transition, total RNA was isolated from mammary, liver and adipose tissues collected from rat dams (n = 5) on day 20 of pregnancy and day 1 of lactation, and gene expression was measured using Affymetrix GeneChips. Two types of gene expression analysis were performed. Genes that were differentially expressed between days within a tissue were identified with linear regression, and univariate regression was used to identify genes commonly up-regulated and down-regulated across all tissues. Gene set enrichment analysis showed genes commonly up regulated among the three tissues enriched gene ontologies primary metabolic processes, macromolecular complex assembly and negative regulation of apoptosis ontologies. Genes enriched in transcription regulator activity showed the common up regulation of 2 core molecular clock genes, ARNTL and CLOCK. Commonly down regulated genes enriched Rhythmic process and included: NR1D1, DBP, BHLHB2, OPN4, and HTR7, which regulate intracellular circadian rhythms. Changes in mammary, liver and adipose transcriptomes at the onset of lactation illustrate the complexity of homeorhetic adaptations and suggest that

  3. Determination of the molecular signature of fossil conifers by experimental palaeochemotaxonomy - Part 1: The Araucariaceae family

    NASA Astrophysics Data System (ADS)

    Lu, Y.; Hautevelle, Y.; Michels, R.

    2012-08-01

    Several extant species of the Araucariaceae family (one of the families of conifers) were invested for the experimental artificial maturation by confined pyrolysis, in order to realize the transformation of biomolecules to geomolecules in laboratory conditions. The experimental study of diagenetized molecular signatures of the Araucariaceae species (common, inter- and infra-generic characteristics) allow to complete our knowledge in botanical palaeochemotaxonomy. Such knowledge is relevant to the reconstitution of palaeoflora and palaeoclimatic reconstruction, archaeology and environmental studies. In this work, major carbon skeleton types of Araucariaceae are detected in the organic solvent extracts of fresh and pyrolyzed plants using gas chromatography-mass spectrometry. The results show that all species of Araucariaceae are firstly characterized by a predominance of saturated tetracyclic diterpenoids. Moreover, the Araucaria genus shows a high relative abundance of bicyclic sesquiterpenoids, particularly compounds of the cadalane-type compounds accompanied by those of eudesmane-type, bisabolane-type as well as chamazulene, pentamethyl-dihydroindenes. Diterpenoids are of the labdane-type, isopimarane, abietane-type (essentially derived from abietanoic acids) as well as isohexyl alkylaromatic hydrocarbons. Compared to the tetracyclic diterpenoids, these compounds show a relatively lower abundance, reaching trace levels in the case of saturated abietanes. Distribution of sesqui- and diterpenoids of Agathis shows some similarities to that of Araucaria, with the exception of one species, in which the tetracyclic compounds are absent and the abietane-type (essentially derived from abietanoic acids) predominant. High similarities between the Wollemia and Araucaria genera are observed. Both are characterized by some high relative abundance of tetracyclic compounds with no predominance of other specific diterpenoids.

  4. The proteome signature of the inflammatory breast cancer plasma membrane identifies novel molecular markers of disease

    PubMed Central

    Suárez-Arroyo, Ivette J; Feliz-Mosquea, Yismeilin R; Pérez-Laspiur, Juliana; Arju, Rezina; Giashuddin, Shah; Maldonado-Martínez, Gerónimo; Cubano, Luis A; Schneider, Robert J; Martínez-Montemayor, Michelle M

    2016-01-01

    Inflammatory Breast Cancer (IBC) is the most lethal form of breast cancer with a 35% 5-year survival rate. The accurate and early diagnosis of IBC and the development of targeted therapy against this deadly disease remain a great medical challenge. Plasma membrane proteins (PMPs) such as E-cadherin and EGFR, play an important role in the progression of IBC. Because the critical role of PMPs in the oncogenic processes they are the perfect candidates as molecular markers and targets for cancer therapies. In the present study, Stable Isotope Labeling with Amino Acids in Cell Culture (SILAC) followed by mass spectrometry analysis was used to compare the relative expression levels of membrane proteins (MP) between non-cancerous mammary epithelial and IBC cells, MCF-10A and SUM-149, respectively. Six of the identified PMPs were validated by immunoblotting using the membrane fractions of non-IBC and IBC cell lines, compared with MCF-10A cells. Immunohistochemical analysis using IBC, invasive ductal carcinoma or normal mammary tissue samples was carried out to complete the validation method in nine of the PMPs. We identified and quantified 278 MPs, 76% of which classified as PMPs with 1.3-fold or higher change. We identified for the first time the overexpression of the novel plasminogen receptor, PLGRKT in IBC and of the carrier protein, SCAMP3. Furthermore, we describe the positive relationship between L1CAM expression and metastasis in IBC patients and the role of SCAMP3 as a tumor-related protein. Overall, the membrane proteomic signature of IBC reflects a global change in cellular organization and suggests additional strategies for cancer progression. Together, this study provides insight into the specialized IBC plasma membrane proteome with the potential to identify a number of novel therapeutic targets for IBC. PMID:27648361

  5. Aqueous Cation-Amide Binding: Free Energies and IR Spectral Signatures by Ab Initio Molecular Dynamics

    SciTech Connect

    Pluharova, Eva; Baer, Marcel D.; Mundy, Christopher J.; Schmidt, Burkhard; Jungwirth, Pavel

    2014-07-03

    Understanding specific ion effects on proteins remains a considerable challenge. N-methylacetamide serves as a useful proxy for the protein backbone that can be well characterized both experimentally and theoretically. The spectroscopic signatures in the amide I band reflecting the strength of the interaction of alkali cations and alkali earth dications with the carbonyl group remain difficult to assign and controversial to interpret. Herein, we directly compute the IR shifts corresponding to the binding of either sodium or calcium to aqueous N-methylacetamide using ab initio molecular dynamics simulations. We show that the two cations interact with aqueous N-methylacetamide with different affinities and in different geometries. Since sodium exhibits a weak interaction with the carbonyl group, the resulting amide I band is similar to an unperturbed carbonyl group undergoing aqueous solvation. In contrast, the stronger calcium binding results in a clear IR shift with respect to N-methylacetamide in pure water. Support from the Czech Ministry of Education (grant LH12001) is gratefully acknowledged. EP thanks the International Max-Planck Research School for support and the Alternative Sponsored Fellowship program at Pacific Northwest National Laboratory (PNNL). PJ acknowledges the Praemium Academie award from the Academy of Sciences. Calculations of the free energy profiles were made possible through generous allocation of computer time from the North-German Supercomputing Alliance (HLRN). Calculations of vibrational spectra were performed in part using the computational resources in the National Energy Research Supercomputing Center (NERSC) at Lawrence Berkeley National Laboratory. This work was supported by National Science Foundation grant CHE-0431312. CJM is supported by the U.S. Department of Energy`s (DOE) Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences and Biosciences. PNNL is operated for the Department of Energy by Battelle. MDB is

  6. Infrared (1-12 Micrometers) Atomic and Molecular Emission Signatures from Energetic Materials using Laser Induced Breakdown Spectroscopy

    DTIC Science & Technology

    2013-01-01

    chlorate and nitrate compounds including KClO3, NaClO3, KNO3, and NaNO3 to produce intense plasma at the target surface. IR LIBS studies on...molecular LIBS signatures from chlorate and nitrate compounds were observed at ~10 um and ~7.3 um, respectively. The observed molecular emissions showed... chlorate and nitrate compounds including KClO3, NaClO3, KNO3, and NaNO3 to produce intense plasma at the target surface. IR LIBS studies on

  7. Study of correlations in molecular motion by multiple quantum NMR

    SciTech Connect

    Tang, J.H.

    1981-11-01

    Nuclear magnetic resonance is a very useful tool for characterizing molecular configurations through the measurement of transition frequencies and dipolar couplings. The measurement of spectral lineshapes, spin-lattice relaxation times, and transverse relaxation times also provide us with valuable information about correlations in molecular motion. The new technique of multiple quantum nuclear magnetic resonance has numerous advantages over the conventional single quantum NMR techniques in obtaining information about static and dynamic interactions of coupled spin systems. In the first two chapters, the theoretical background of spin Hamiltonians and the density matrix formalism of multiple quantum NMR is discussed. The creation and detection of multiple quantum coherence by multiple pulse sequence are discussed. Prototype multiple quantum spectra of oriented benzene are presented. Redfield relaxation theory and the application of multiple quantum NMR to the study of correlations in fluctuations are presented. A specific example of an oriented methyl group relaxed by paramagnetic impurities is studied in detail. The study of possible correlated motion between two coupled methyl groups by multiple quantum NMR is presented. For a six spin system it is shown that the four-quantum spectrum is sensitive to two-body correlations, and serves a ready test of correlated motion. The study of the spin-lattice dynamics of orienting or tunneling methyl groups (CH/sub 3/ and CD/sub 3/) at low temperatures is presented. The anisotropic spin-lattice relaxation of deuterated hexamethylbenzene, caused by the sixfold reorientation of the molecules, is investigated, and the NMR spectrometers and other experimental details are discussed.

  8. Attentional Signatures of Perception: Multiple Object Tracking Reveals the Automaticity of Contour Interpolation

    ERIC Educational Resources Information Center

    Keane, Brian P.; Mettler, Everett; Tsoi, Vicky; Kellman, Philip J.

    2011-01-01

    Multiple object tracking (MOT) is an attentional task wherein observers attempt to track multiple targets among moving distractors. Contour interpolation is a perceptual process that fills-in nonvisible edges on the basis of how surrounding edges (inducers) are spatiotemporally related. In five experiments, we explored the automaticity of…

  9. Application of cascaded frequency multiplication to molecular spectroscopy

    NASA Astrophysics Data System (ADS)

    Drouin, Brian J.; Maiwald, Frank W.; Pearson, John C.

    2005-09-01

    Laboratory molecular spectroscopy provides the basis for interpretation of atmospheric, planetary, and astrophysical data gathered by remote sensing. Laboratory studies of atomic and molecular signatures across the electromagnetic spectrum provide high-precision, quantitative data used to interpret the observed environment from remote measurements. Historically, the region of the spectrum above 500 GHz has been relatively unexplored due to atmospheric absorption and technical difficulties generating and detecting radiation. Laboratory spectroscopy at these frequencies has traditionally involved measurement of one or two absorption features and relied on fitting of models to the limited data. We report a new spectrometer built around a computer-controlled commercial synthesizer and millimeter-wave module driving a series of amplifiers followed by a series of wide-bandwidth frequency doublers and triplers. The spectrometer provides the ability to rapidly measure large pieces of frequency space with higher resolution, accuracy, and sensitivity than with Fourier transform infrared techniques. The approach is simple, modular, and requires no custom-built electronics or high voltage and facilitates the use of infrared data analysis techniques on complex submillimeter spectra.

  10. Multiple time step integrators in ab initio molecular dynamics

    SciTech Connect

    Luehr, Nathan; Martínez, Todd J.; Markland, Thomas E.

    2014-02-28

    Multiple time-scale algorithms exploit the natural separation of time-scales in chemical systems to greatly accelerate the efficiency of molecular dynamics simulations. Although the utility of these methods in systems where the interactions are described by empirical potentials is now well established, their application to ab initio molecular dynamics calculations has been limited by difficulties associated with splitting the ab initio potential into fast and slowly varying components. Here we present two schemes that enable efficient time-scale separation in ab initio calculations: one based on fragment decomposition and the other on range separation of the Coulomb operator in the electronic Hamiltonian. We demonstrate for both water clusters and a solvated hydroxide ion that multiple time-scale molecular dynamics allows for outer time steps of 2.5 fs, which are as large as those obtained when such schemes are applied to empirical potentials, while still allowing for bonds to be broken and reformed throughout the dynamics. This permits computational speedups of up to 4.4x, compared to standard Born-Oppenheimer ab initio molecular dynamics with a 0.5 fs time step, while maintaining the same energy conservation and accuracy.

  11. Identification of Interplanetary Coronal Mass Ejections at Ulysses Using Multiple Solar Wind Signatures

    NASA Astrophysics Data System (ADS)

    Richardson, I. G.

    2014-10-01

    Previous studies have discussed the identification of interplanetary coronal mass ejections (ICMEs) near the Earth based on various solar wind signatures. In particular, methods have been developed of identifying regions of anomalously low solar wind proton temperatures ( T p) and plasma compositional anomalies relative to the composition of the ambient solar wind that are frequently indicative of ICMEs. In this study, similar methods are applied to observations from the Ulysses spacecraft that was launched in 1990 and placed in a heliocentric orbit over the poles of the Sun. Some 279 probable ICMEs are identified during the spacecraft mission, which ended in 2009. The identifications complement those found independently in other studies of the Ulysses data, but a number of additional events are identified. The properties of the ICMEs detected at Ulysses and those observed near the Earth and in the inner heliosphere are compared.

  12. Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies.

    PubMed

    Patalano, Solenn; Vlasova, Anna; Wyatt, Chris; Ewels, Philip; Camara, Francisco; Ferreira, Pedro G; Asher, Claire L; Jurkowski, Tomasz P; Segonds-Pichon, Anne; Bachman, Martin; González-Navarrete, Irene; Minoche, André E; Krueger, Felix; Lowy, Ernesto; Marcet-Houben, Marina; Rodriguez-Ales, Jose Luis; Nascimento, Fabio S; Balasubramanian, Shankar; Gabaldon, Toni; Tarver, James E; Andrews, Simon; Himmelbauer, Heinz; Hughes, William O H; Guigó, Roderic; Reik, Wolf; Sumner, Seirian

    2015-11-10

    Phenotypic plasticity is important in adaptation and shapes the evolution of organisms. However, we understand little about what aspects of the genome are important in facilitating plasticity. Eusocial insect societies produce plastic phenotypes from the same genome, as reproductives (queens) and nonreproductives (workers). The greatest plasticity is found in the simple eusocial insect societies in which individuals retain the ability to switch between reproductive and nonreproductive phenotypes as adults. We lack comprehensive data on the molecular basis of plastic phenotypes. Here, we sequenced genomes, microRNAs (miRNAs), and multiple transcriptomes and methylomes from individual brains in a wasp (Polistes canadensis) and an ant (Dinoponera quadriceps) that live in simple eusocial societies. In both species, we found few differences between phenotypes at the transcriptional level, with little functional specialization, and no evidence that phenotype-specific gene expression is driven by DNA methylation or miRNAs. Instead, phenotypic differentiation was defined more subtly by nonrandom transcriptional network organization, with roles in these networks for both conserved and taxon-restricted genes. The general lack of highly methylated regions or methylome patterning in both species may be an important mechanism for achieving plasticity among phenotypes during adulthood. These findings define previously unidentified hypotheses on the genomic processes that facilitate plasticity and suggest that the molecular hallmarks of social behavior are likely to differ with the level of social complexity.

  13. Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies

    PubMed Central

    Patalano, Solenn; Vlasova, Anna; Wyatt, Chris; Ewels, Philip; Camara, Francisco; Ferreira, Pedro G.; Asher, Claire L.; Jurkowski, Tomasz P.; Segonds-Pichon, Anne; Bachman, Martin; González-Navarrete, Irene; Minoche, André E.; Krueger, Felix; Lowy, Ernesto; Marcet-Houben, Marina; Rodriguez-Ales, Jose Luis; Nascimento, Fabio S.; Balasubramanian, Shankar; Gabaldon, Toni; Tarver, James E.; Andrews, Simon; Himmelbauer, Heinz; Hughes, William O. H.; Guigó, Roderic; Reik, Wolf; Sumner, Seirian

    2015-01-01

    Phenotypic plasticity is important in adaptation and shapes the evolution of organisms. However, we understand little about what aspects of the genome are important in facilitating plasticity. Eusocial insect societies produce plastic phenotypes from the same genome, as reproductives (queens) and nonreproductives (workers). The greatest plasticity is found in the simple eusocial insect societies in which individuals retain the ability to switch between reproductive and nonreproductive phenotypes as adults. We lack comprehensive data on the molecular basis of plastic phenotypes. Here, we sequenced genomes, microRNAs (miRNAs), and multiple transcriptomes and methylomes from individual brains in a wasp (Polistes canadensis) and an ant (Dinoponera quadriceps) that live in simple eusocial societies. In both species, we found few differences between phenotypes at the transcriptional level, with little functional specialization, and no evidence that phenotype-specific gene expression is driven by DNA methylation or miRNAs. Instead, phenotypic differentiation was defined more subtly by nonrandom transcriptional network organization, with roles in these networks for both conserved and taxon-restricted genes. The general lack of highly methylated regions or methylome patterning in both species may be an important mechanism for achieving plasticity among phenotypes during adulthood. These findings define previously unidentified hypotheses on the genomic processes that facilitate plasticity and suggest that the molecular hallmarks of social behavior are likely to differ with the level of social complexity. PMID:26483466

  14. Quantitative Proteomic Profiling the Molecular Signatures of Annexin A5 in Lung Squamous Carcinoma Cells

    PubMed Central

    Zhang, Liyuan; Gong, Linlin; Qi, Xiaoyu; Li, Huizhen; Wang, Faming; Chi, Xinming; Jiang, Yulin; Shao, Shujuan

    2016-01-01

    Lung cancer remains the leading cancer killer around the world. It’s crucial to identify newer mechanism-based targets to effectively manage lung cancer. Annexin A5 (ANXA5) is a protein kinase C inhibitory protein and calcium dependent phospholipid-binding protein, which may act as an endogenous regulator of various pathophysiological processes. However, its molecular mechanism in lung cancer remains poorly understood. This study was designed to determine the mechanism of ANXA5 in lung cancer with a hope to obtain useful information to provide a new therapeutic target. We used a stable isotope dimethyl labeling based quantitative proteomic method to identify differentially expressed proteins in NSCLC cell lines after ANXA5 transfection. Out of 314 proteins, we identified 26 and 44 proteins that were down- and up-regulated upon ANXA5 modulation, respectively. The IPA analysis revealed that glycolysis and gluconeogenesis were the predominant pathways modulated by ANXA5. Multiple central nodes, namely HSPA5, FN1, PDIA6, ENO1, ALDOA, JUP and KRT6A appeared to occupy regulatory nodes in the protein-protein networks upon ANXA5 modulation. Taken together, ANXA5 appears to have pleotropic effects, as it modulates multiple key signaling pathways, supporting the potential usefulness of ANXA5 as a potential target in lung cancer. This study might provide a new insight into the mechanism of ANXA5 in lung cancer. PMID:27684953

  15. Xmrk, Kras and Myc Transgenic Zebrafish Liver Cancer Models Share Molecular Signatures with Subsets of Human Hepatocellular Carcinoma

    PubMed Central

    Zheng, Weiling; Li, Zhen; Nguyen, Anh Tuan; Li, Caixia; Emelyanov, Alexander; Gong, Zhiyuan

    2014-01-01

    Previously three oncogene transgenic zebrafish lines with inducible expression of xmrk, kras or Myc in the liver have been generated and these transgenic lines develop oncogene-addicted liver tumors upon chemical induction. In the current study, comparative transcriptomic approaches were used to examine the correlation of the three induced transgenic liver cancers with human liver cancers. RNA profiles from the three zebrafish tumors indicated relatively small overlaps of significantly deregulated genes and biological pathways. Nevertheless, the three transgenic tumor signatures all showed significant correlation with advanced or very advanced human hepatocellular carcinoma (HCC). Interestingly, molecular signature from each oncogene-induced zebrafish liver tumor correlated with only a small subset of human HCC samples (24–29%) and there were conserved up-regulated pathways between the zebrafish and correlated human HCC subgroup. The three zebrafish liver cancer models together represented nearly half (47.2%) of human HCCs while some human HCCs showed significant correlation with more than one signature defined from the three oncogene-addicted zebrafish tumors. In contrast, commonly deregulated genes (21 up and 16 down) in the three zebrafish tumor models generally showed accordant deregulation in the majority of human HCCs, suggesting that these genes might be more consistently deregulated in a broad range of human HCCs with different molecular mechanisms and thus serve as common diagnosis markers and therapeutic targets. Thus, these transgenic zebrafish models with well-defined oncogene-induced tumors are valuable tools for molecular classification of human HCCs and for understanding of molecular drivers in hepatocarcinogenesis in each human HCC subgroup. PMID:24633177

  16. The Dual Wavelength Ratio knee: a signature of multiple scattering in airborne Ku-Ka observations

    NASA Astrophysics Data System (ADS)

    Battaglia, Alessandro; Tanelli, Simone; Heymsfield, Gerald; Tian, Lin

    2014-05-01

    Deep convective systems observed by the HIWRAP radar during the 2011 MC3E field campaign in Oklahoma provide the first evidence of multiple scattering effects simultaneously at Ku and Ka band. One feature is novel and noteworthy: often, in correspondence to shafts with strong convection and when moving from the top of the cloud downward, the dual wavelength ratio (DWR) first increases as usual in Ku-/Ka-band observations, but then it reaches a maximum and after that point it steadily decreases all the way to the surface, forming what will be hereinafter referred to as a knee. This DWR knee cannot be reproduced by single-scattering theory under almost any plausible cloud microphysical profile, on the other hand it is explained straightforwardly with the help of multiple scattering theory when simulations involving hail-bearing convective cores with large horizontal extents are performed. The DWR reduction in the lower troposphere (i.e., DWR increasing with altitude) is interpreted as the result of multiple scattering pulse stretching caused by the highly-diffusive hail layer positioned high up in the atmosphere, with Ka multiple scattering typically exceeding that occurring in the Ku channel. Since the effects of multiple scattering increase with increasing footprint size, if multiple scattering effects are present in the aircraft measurements, they are likely to be more pronounced in the space-borne dual-frequency Ku - Ka radar observations, envisaged for the NASA-JAXA Global Precipitation (GPM) Measurement Mission, whose launch is expected in February 2014. Our notional study supports the idea that DWR knees will be observed by the GPM radar when overflying high-density ice shafts embedded in large convective systems and suggests that their explanation must not be sought in differential attenuation or differential Mie but via multiple scattering effects.

  17. Understanding star formation in molecular clouds. II. Signatures of gravitational collapse of IRDCs

    NASA Astrophysics Data System (ADS)

    Schneider, N.; Csengeri, T.; Klessen, R. S.; Tremblin, P.; Ossenkopf, V.; Peretto, N.; Simon, R.; Bontemps, S.; Federrath, C.

    2015-06-01

    We analyse column density and temperature maps derived from Herschel dust continuum observations of a sample of prominent, massive infrared dark clouds (IRDCs) i.e. G11.11-0.12, G18.82-0.28, G28.37+0.07, and G28.53-0.25. We disentangle the velocity structure of the clouds using 13CO 1→0 and 12CO 3→2 data, showing that these IRDCs are the densest regions in massive giant molecular clouds (GMCs) and not isolated features. The probability distribution function (PDF) of column densities for all clouds have a power-law distribution over all (high) column densities, regardless of the evolutionary stage of the cloud: G11.11-0.12, G18.82-0.28, and G28.37+0.07 contain (proto)-stars, while G28.53-0.25 shows no signs of star formation. This is in contrast to the purely log-normal PDFs reported for near and/or mid-IR extinction maps. We only find a log-normal distribution for lower column densities, if we perform PDFs of the column density maps of the whole GMC in which the IRDCs are embedded. By comparing the PDF slope and the radial column density profile of three of our clouds, we attribute the power law to the effect of large-scale gravitational collapse and to local free-fall collapse of pre- and protostellar cores for the highest column densities. A significant impact on the cloud properties from radiative feedback is unlikely because the clouds are mostly devoid of star formation. Independent from the PDF analysis, we find infall signatures in the spectral profiles of 12CO for G28.37+0.07 and G11.11-0.12, supporting the scenario of gravitational collapse. Our results are in line with earlier interpretations that see massive IRDCs as the densest regions within GMCs, which may be the progenitors of massive stars or clusters. At least some of the IRDCs are probably the same features as ridges (high column density regions with N> 1023 cm-2 over small areas), which were defined for nearby IR-bright GMCs. Because IRDCs are only confined to the densest (gravity dominated

  18. Monitoring a Nuclear Factor-κB Signature of Drug Resistance in Multiple Myeloma*

    PubMed Central

    Xiang, Yun; Remily-Wood, Elizabeth R.; Oliveira, Vasco; Yarde, Danielle; He, Lili; Cheng, Jin Q.; Mathews, Linda; Boucher, Kelly; Cubitt, Christopher; Perez, Lia; Gauthier, Ted J.; Eschrich, Steven A.; Shain, Kenneth H.; Dalton, William S.; Hazlehurst, Lori; Koomen, John M.

    2011-01-01

    The emergence of acquired drug resistance results from multiple compensatory mechanisms acting to prevent cell death. Simultaneous monitoring of proteins involved in drug resistance is a major challenge for both elucidation of the underlying biology and development of candidate biomarkers for assessment of personalized cancer therapy. Here, we have utilized an integrated analytical platform based on SDS-PAGE protein fractionation prior to liquid chromatography coupled to multiple reaction monitoring mass spectrometry, a versatile and powerful tool for targeted quantification of proteins in complex matrices, to evaluate a well-characterized model system of melphalan resistance in multiple myeloma (MM). Quantitative assays were developed to measure protein expression related to signaling events and biological processes relevant to melphalan resistance in multiple myeloma, specifically: nuclear factor-κB subunits, members of the Bcl-2 family of apoptosis-regulating proteins, and Fanconi Anemia DNA repair components. SDS-PAGE protein fractionation prior to liquid chromatography coupled to multiple reaction monitoring methods were developed for quantification of these selected target proteins in amounts of material compatible with direct translation to clinical specimens (i.e. less than 50,000 cells). As proof of principle, both relative and absolute quantification were performed on cell line models of MM to compare protein expression before and after drug treatment in naïve cells and in drug resistant cells; these liquid chromatography-multiple reaction monitoring results are compared with existing literature and Western blots. The initial stage of a systems biology platform for examining drug resistance in MM has been implemented in cell line models and has been translated to MM cells isolated from a patient. The ultimate application of this platform could assist in clinical decision-making for individualized patient treatment. Although these specific assays have

  19. Signatures of complex magnetic topologies from multiple reconnection sites induced by Kelvin-Helmholtz instability

    NASA Astrophysics Data System (ADS)

    Vernisse, Y.; Lavraud, B.; Eriksson, S.; Gershman, D. J.; Dorelli, J.; Pollock, C.; Giles, B.; Aunai, N.; Avanov, L.; Burch, J.; Chandler, M.; Coffey, V.; Dargent, J.; Ergun, R. E.; Farrugia, C. J.; Génot, V.; Graham, D. B.; Hasegawa, H.; Jacquey, C.; Kacem, I.; Khotyaintsev, Y.; Li, W.; Magnes, W.; Marchaudon, A.; Moore, T.; Paterson, W.; Penou, E.; Phan, T. D.; Retino, A.; Russell, C. T.; Saito, Y.; Sauvaud, J.-A.; Torbert, R.; Wilder, F. D.; Yokota, S.

    2016-10-01

    The Magnetospheric Multiscale mission has demonstrated the frequent presence of reconnection exhausts at thin current sheets within Kelvin-Helmholtz (KH) waves at the flank magnetopause. Motivated by these recent observations, we performed a statistical analysis of the boundary layers on the magnetosheath side of all KH current sheets on 8 September 2015. We show 86% consistency between the exhaust flows and particle leakage in the magnetosheath boundary layers but further highlight the very frequent presence of additional boundary layer signatures that do not come from the locally observed reconnection exhausts. These additional electron and ion boundary layers, of various durations and at various positions with respect to the leading and trailing boundaries of the KH waves, signal connections to reconnection sites at other locations. Based on the directionality and extent of these layers, we provide an interpretation whereby complex magnetic topologies can arise within KH waves from the combination of reconnection in the equatorial plane and at midlatitudes in the Southern and Northern Hemispheres, where additional reconnection sites are expected to be triggered by the three-dimensional field lines interweaving induced by the KH waves at the flanks (owing to differential flow and magnetic field shear with latitude). The present event demonstrates that the three-dimensional development of KH waves can induce plasma entry (through reconnection at both midlatitude and equatorial regions) already sunward of the terminator where the instability remains in its linear stage.

  20. Dissecting the molecular signatures of apical cell-type shoot meristems from two ancient land plant lineages.

    PubMed

    Frank, Margaret H; Edwards, Molly B; Schultz, Eric R; McKain, Michael R; Fei, Zhangjun; Sørensen, Iben; Rose, Jocelyn K C; Scanlon, Michael J

    2015-08-01

    Shoot apical meristem (SAM) structure varies markedly within the land plants. The SAMs of many seedless vascular plants contain a conspicuous inverted, pyramidal cell called the apical cell (AC), which is unidentified in angiosperms. In this study, we use transcriptomic sequencing with precise laser microdissections of meristem subdomains to define the molecular signatures of anatomically distinct zones from the AC-type SAMs of a lycophyte (Selaginella moellendorffii) and a monilophyte (Equisetum arvense). The two model species for this study represent vascular plant lineages that diverged > 400 million yr ago. Our data comprise comprehensive molecular signatures for the distinct subdomains within AC-type SAMs, an anatomical anomaly whose functional significance has been debated in the botanical literature for over two centuries. Moreover, our data provide molecular support for distinct gene expression programs between the AC-type SAMs of Selaginella and Equisetum, as compared with the SAM transcriptome of the angiosperm maize. The results are discussed in light of the functional significance and evolutionary success of the AC-type SAM within the embryophytes.

  1. Efficient Molecular Dynamics Simulations of Multiple Radical Center Systems Based on the Fragment Molecular Orbital Method

    SciTech Connect

    Nakata, Hiroya; Schmidt, Michael W; Fedorov, Dmitri G; Kitaura, Kazuo; Nakamura, Shinichiro; Gordon, Mark S

    2014-10-16

    The fully analytic energy gradient has been developed and implemented for the restricted open-shell Hartree–Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF energy gradient is compared with the corresponding numerical gradient, illustrating the accuracy of the analytic gradient. The ROHF analytic gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen. These molecular dynamics simulations provide some insight about how triplet oxygen molecules interact with each other. Timings reveal that the method can calculate the energy gradient for a system containing 4000 atoms in only 6 h. Therefore, it is concluded that the FMO-ROHF method will be useful for investigating systems with multiple open shells.

  2. Efficient molecular dynamics simulations of multiple radical center systems based on the fragment molecular orbital method.

    PubMed

    Nakata, Hiroya; Schmidt, Michael W; Fedorov, Dmitri G; Kitaura, Kazuo; Nakamura, Shinichiro; Gordon, Mark S

    2014-10-16

    The fully analytic energy gradient has been developed and implemented for the restricted open-shell Hartree-Fock (ROHF) method based on the fragment molecular orbital (FMO) theory for systems that have multiple open-shell molecules. The accuracy of the analytic ROHF energy gradient is compared with the corresponding numerical gradient, illustrating the accuracy of the analytic gradient. The ROHF analytic gradient is used to perform molecular dynamics simulations of an unusual open-shell system, liquid oxygen, and mixtures of oxygen and nitrogen. These molecular dynamics simulations provide some insight about how triplet oxygen molecules interact with each other. Timings reveal that the method can calculate the energy gradient for a system containing 4000 atoms in only 6 h. Therefore, it is concluded that the FMO-ROHF method will be useful for investigating systems with multiple open shells.

  3. Gene Expression Deconvolution for Uncovering Molecular Signatures in Response to Therapy in Juvenile Idiopathic Arthritis

    PubMed Central

    Rosenberg, Alan M.; Yeung, Rae S. M.; Morris, Quaid

    2016-01-01

    Gene expression-based signatures help identify pathways relevant to diseases and treatments, but are challenging to construct when there is a diversity of disease mechanisms and treatments in patients with complex diseases. To overcome this challenge, we present a new application of an in silico gene expression deconvolution method, ISOpure-S1, and apply it to identify a common gene expression signature corresponding to response to treatment in 33 juvenile idiopathic arthritis (JIA) patients. Using pre- and post-treatment gene expression profiles only, we found a gene expression signature that significantly correlated with a reduction in the number of joints with active arthritis, a measure of clinical outcome (Spearman rho = 0.44, p = 0.040, Bonferroni correction). This signature may be associated with a decrease in T-cells, monocytes, neutrophils and platelets. The products of most differentially expressed genes include known biomarkers for JIA such as major histocompatibility complexes and interleukins, as well as novel biomarkers including α-defensins. This method is readily applicable to expression datasets of other complex diseases to uncover shared mechanistic patterns in heterogeneous samples. PMID:27244050

  4. Derivation of molecular signatures for breast cancer recurrence prediction using a two-way validation approach

    PubMed Central

    Sun, Yijun; Urquidi, Virginia

    2010-01-01

    Previous studies have demonstrated the potential value of gene expression signatures in assessing the risk of post-surgical breast cancer recurrence, however, many of these predictive models have been derived using simple computational algorithms and validated internally or using one-way validation on a single dataset. We have recently developed a new feature selection algorithm that overcomes some limitations inherent to high-dimensional data analysis. In this study, we applied this algorithm to two publicly available gene expression datasets obtained from over 400 patients with breast cancer to investigate whether we could derive more accurate prognostic signatures and reveal common predictive factors across independent datasets. We compared the performance of three advanced computational algorithms using a robust two-way validation method, where one dataset was used for training and to establish a prediction model that was then blindly tested on the other dataset. The experiment was then repeated in the reverse direction. Analyses identified prognostic signatures that while comprised of only 10–13 genes, significantly outperformed previously reported signatures for breast cancer evaluation. The cross-validation approach revealed CEGP1 and PRAME as major candidates for breast cancer biomarker development. PMID:19291396

  5. Singlet oxygen signatures are detected independent of light or chloroplasts in response to multiple stresses.

    PubMed

    Mor, Avishai; Koh, Eugene; Weiner, Lev; Rosenwasser, Shilo; Sibony-Benyamini, Hadas; Fluhr, Robert

    2014-05-01

    The production of singlet oxygen is typically associated with inefficient dissipation of photosynthetic energy or can arise from light reactions as a result of accumulation of chlorophyll precursors as observed in fluorescent (flu)-like mutants. Such photodynamic production of singlet oxygen is thought to be involved in stress signaling and programmed cell death. Here we show that transcriptomes of multiple stresses, whether from light or dark treatments, were correlated with the transcriptome of the flu mutant. A core gene set of 118 genes, common to singlet oxygen, biotic and abiotic stresses was defined and confirmed to be activated photodynamically by the photosensitizer Rose Bengal. In addition, induction of the core gene set by abiotic and biotic selected stresses was shown to occur in the dark and in nonphotosynthetic tissue. Furthermore, when subjected to various biotic and abiotic stresses in the dark, the singlet oxygen-specific probe Singlet Oxygen Sensor Green detected rapid production of singlet oxygen in the Arabidopsis (Arabidopsis thaliana) root. Subcellular localization of Singlet Oxygen Sensor Green fluorescence showed its accumulation in mitochondria, peroxisomes, and the nucleus, suggesting several compartments as the possible origins or targets for singlet oxygen. Collectively, the results show that singlet oxygen can be produced by multiple stress pathways and can emanate from compartments other than the chloroplast in a light-independent manner. The results imply that the role of singlet oxygen in plant stress regulation and response is more ubiquitous than previously thought.

  6. Distinct T cell signatures define subsets of patients with multiple sclerosis

    PubMed Central

    Johnson, Mark C.; Pierson, Emily R.; Spieker, Andrew J.; Nielsen, A. Scott; Posso, Sylvia; Kita, Mariko; Buckner, Jane H.

    2016-01-01

    Objective: We investigated T cell responses to myelin proteins in the blood of healthy controls and 2 groups of patients with relapsing-remitting multiple sclerosis (RRMS) who exhibited lesions either predominantly in the brain or predominantly in the spinal cord in order to assess whether distinct neuroinflammatory patterns were associated with different myelin protein–specific T cell effector function profiles and whether these profiles differed from healthy controls. Methods: Peripheral blood mononuclear cells were obtained from patients with brain-predominant RRMS, patients with spinal cord–predominant RRMS, and age-matched healthy controls and analyzed by enzyme-linked immunosorbent spot assays to quantify interferon gamma–secreting (Th1) and interleukin 17–secreting (Th17) cells responding directly ex vivo to myelin basic protein (MBP) and myelin oligodendrocyte glycoprotein (MOG). Results: Although MBP and MOG elicited different responses, patients with multiple sclerosis (MS) who had spinal cord–predominant lesions exhibited significantly higher Th17:Th1 ratios in response to both MBP and MOG compared to patients with brain-predominant MS. Incorporating the cytokine responses to both antigens into logistic regression models showed that these cytokine responses were able to provide good discrimination between patients with distinct neuroinflammatory patterns. Conclusions: Our findings suggest that the localization of lesions within the brain vs the spinal cord in patients with MS is associated with different effector T cell responses to myelin proteins. Further investigation of the relationship between T cell effector function, antigen specificities, and lesion sites may reveal features of pathogenic pathways that are distinct to patients with different neuroinflammatory patterns. PMID:27606354

  7. Multiple-time-scale motion in molecularly linked nanoparticle arrays.

    PubMed

    George, Christopher; Szleifer, Igal; Ratner, Mark

    2013-01-22

    We explore the transport of electrons between electrodes that encase a two-dimensional array of metallic quantum dots linked by molecular bridges (such as α,ω alkaline dithiols). Because the molecules can move at finite temperatures, the entire transport structure comprising the quantum dots and the molecules is in dynamical motion while the charge is being transported. There are then several physical processes (physical excursions of molecules and quantum dots, electronic migration, ordinary vibrations), all of which influence electronic transport. Each can occur on a different time scale. It is therefore not appropriate to use standard approaches to this sort of electron transfer problem. Instead, we present a treatment in which three different theoretical approaches-kinetic Monte Carlo, classical molecular dynamics, and quantum transport-are all employed. In certain limits, some of the dynamical effects are unimportant. But in general, the transport seems to follow a sort of dynamic bond percolation picture, an approach originally introduced as formal models and later applied to polymer electrolytes. Different rate-determining steps occur in different limits. This approach offers a powerful scheme for dealing with multiple time scale transport problems, as will exist in many situations with several pathways through molecular arrays or even individual molecules that are dynamically disordered.

  8. Molecular Signatures for the PVC Clade (Planctomycetes, Verrucomicrobia, Chlamydiae, and Lentisphaerae) of Bacteria Provide Insights into Their Evolutionary Relationships.

    PubMed

    Gupta, Radhey S; Bhandari, Vaibhav; Naushad, Hafiz Sohail

    2012-01-01

    The PVC superphylum is an amalgamation of species from the phyla Planctomycetes, Verrucomicrobia, and Chlamydiae, along with the Lentisphaerae, Poribacteria, and two other candidate divisions. The diverse species of this superphylum lack any significant marker that differentiates them from other bacteria. Recently, genome sequences for 37 species covering all of the main PVC groups of bacteria have become available. We have used these sequences to construct a phylogenetic tree based upon concatenated sequences for 16 proteins and identify molecular signatures in protein sequences that are specific for the species from these phyla or those providing molecular links among them. Of the useful molecular markers identified in the present work, six conserved signature indels (CSIs) in the proteins Cyt c oxidase, UvrD helicase, urease, and a helicase-domain containing protein are specific for the species from the Verrucomicrobia phylum; three other CSIs in an ABC transporter protein, cobyrinic acid ac-diamide synthase, and SpoVG protein are specific for the Planctomycetes species. Additionally, a 3 aa insert in the RpoB protein is uniquely present in all sequenced Chlamydiae, Verrucomicrobia, and Lentisphaerae species, providing evidence for the shared ancestry of the species from these three phyla. Lastly, we have also identified a conserved protein of unknown function that is exclusively found in all sequenced species from the phyla Chlamydiae, Verrucomicrobia, Lentisphaerae, and Planctomycetes suggesting a specific linkage among them. The absence of this protein in Poribacteria, which branches separately from other members of the PVC clade, indicates that it is not specifically related to the PVC clade of bacteria. The molecular markers described here in addition to clarifying the evolutionary relationships among the PVC clade of bacteria also provide novel tools for their identification and for genetic and biochemical studies on these organisms.

  9. Molecular Signatures for the PVC Clade (Planctomycetes, Verrucomicrobia, Chlamydiae, and Lentisphaerae) of Bacteria Provide Insights into Their Evolutionary Relationships

    PubMed Central

    Gupta, Radhey S.; Bhandari, Vaibhav; Naushad, Hafiz Sohail

    2012-01-01

    The PVC superphylum is an amalgamation of species from the phyla Planctomycetes, Verrucomicrobia, and Chlamydiae, along with the Lentisphaerae, Poribacteria, and two other candidate divisions. The diverse species of this superphylum lack any significant marker that differentiates them from other bacteria. Recently, genome sequences for 37 species covering all of the main PVC groups of bacteria have become available. We have used these sequences to construct a phylogenetic tree based upon concatenated sequences for 16 proteins and identify molecular signatures in protein sequences that are specific for the species from these phyla or those providing molecular links among them. Of the useful molecular markers identified in the present work, six conserved signature indels (CSIs) in the proteins Cyt c oxidase, UvrD helicase, urease, and a helicase-domain containing protein are specific for the species from the Verrucomicrobia phylum; three other CSIs in an ABC transporter protein, cobyrinic acid ac-diamide synthase, and SpoVG protein are specific for the Planctomycetes species. Additionally, a 3 aa insert in the RpoB protein is uniquely present in all sequenced Chlamydiae, Verrucomicrobia, and Lentisphaerae species, providing evidence for the shared ancestry of the species from these three phyla. Lastly, we have also identified a conserved protein of unknown function that is exclusively found in all sequenced species from the phyla Chlamydiae, Verrucomicrobia, Lentisphaerae, and Planctomycetes suggesting a specific linkage among them. The absence of this protein in Poribacteria, which branches separately from other members of the PVC clade, indicates that it is not specifically related to the PVC clade of bacteria. The molecular markers described here in addition to clarifying the evolutionary relationships among the PVC clade of bacteria also provide novel tools for their identification and for genetic and biochemical studies on these organisms. PMID:23060863

  10. Molecular systems pharmacology: isoelectric focusing signature of protein kinase Cδ provides an integrated measure of its modulation in response to ligands.

    PubMed

    Kedei, Noemi; Chen, Jin-Qiu; Herrmann, Michelle A; Telek, Andrea; Goldsmith, Paul K; Petersen, Mark E; Keck, Gary E; Blumberg, Peter M

    2014-06-26

    Protein kinase C (PKC), a validated therapeutic target for cancer chemotherapy, provides a paradigm for assessing structure-activity relations, where ligand binding has multiple consequences for a target. For PKC, ligand binding controls not only PKC activation and multiple phosphorylations but also subcellular localization, affecting subsequent signaling. Using a capillary isoelectric focusing immunoassay system, we could visualize a high resolution isoelectric focusing signature of PKCδ upon stimulation by ligands of the phorbol ester and bryostatin classes. Derivatives that possessed different physicochemical characteristics and induced different patterns of biological response generated different signatures. Consistent with different patterns of PKCδ localization as one factor linked to these different signatures, we found different signatures for activated PKCδ from the nuclear and non-nuclear fractions. We conclude that the capillary isoelectric focusing immunoassay system may provide a window into the integrated consequences of ligand binding and thus afford a powerful platform for compound development.

  11. Molecular Code Division Multiple Access: Gaussian Mixture Modeling

    NASA Astrophysics Data System (ADS)

    Zamiri-Jafarian, Yeganeh

    Communications between nano-devices is an emerging research field in nanotechnology. Molecular Communication (MC), which is a bio-inspired paradigm, is a promising technique for communication in nano-network. In MC, molecules are administered to exchange information among nano-devices. Due to the nature of molecular signals, traditional communication methods can't be directly applied to the MC framework. The objective of this thesis is to present novel diffusion-based MC methods when multi nano-devices communicate with each other in the same environment. A new channel model and detection technique, along with a molecular-based access method, are proposed in here for communication between asynchronous users. In this work, the received molecular signal is modeled as a Gaussian mixture distribution when the MC system undergoes Brownian noise and inter-symbol interference (ISI). This novel approach demonstrates a suitable modeling for diffusion-based MC system. Using the proposed Gaussian mixture model, a simple receiver is designed by minimizing the error probability. To determine an optimum detection threshold, an iterative algorithm is derived which minimizes a linear approximation of the error probability function. Also, a memory-based receiver is proposed to improve the performance of the MC system by considering previously detected symbols in obtaining the threshold value. Numerical evaluations reveal that theoretical analysis of the bit error rate (BER) performance based on the Gaussian mixture model match simulation results very closely. Furthermore, in this thesis, molecular code division multiple access (MCDMA) is proposed to overcome the inter-user interference (IUI) caused by asynchronous users communicating in a shared propagation environment. Based on the selected molecular codes, a chip detection scheme with an adaptable threshold value is developed for the MCDMA system when the proposed Gaussian mixture model is considered. Results indicate that the

  12. No quiet surrender: molecular guardians in multiple sclerosis brain

    PubMed Central

    Steinman, Lawrence

    2015-01-01

    The brain under immunological attack does not surrender quietly. Investigation of brain lesions in multiple sclerosis (MS) reveals a coordinated molecular response involving various proteins and small molecules ranging from heat shock proteins to small lipids, neurotransmitters, and even gases, which provide protection and foster repair. Reduction of inflammation serves as a necessary prerequisite for effective recovery and regeneration. Remarkably, many lesion-resident molecules activate pathways leading to both suppression of inflammation and promotion of repair mechanisms. These guardian molecules and their corresponding physiologic pathways could potentially be exploited to silence inflammation and repair the injured and degenerating brain and spinal cord in both relapsing-remitting and progressive forms of MS and may be beneficial in other neurologic and psychiatric conditions. PMID:25831441

  13. Transcriptome analysis using next generation sequencing reveals molecular signatures of diabetic retinopathy and efficacy of candidate drugs

    PubMed Central

    Rajasimha, Harsha K.; Brooks, Matthew J.; Nellissery, Jacob; Wan, Jun; Qian, Jiang; Kern, Timothy S.; Swaroop, Anand

    2012-01-01

    Purpose To define gene expression changes associated with diabetic retinopathy in a mouse model using next generation sequencing, and to utilize transcriptome signatures to assess molecular pathways by which pharmacological agents inhibit diabetic retinopathy. Methods We applied a high throughput RNA sequencing (RNA-seq) strategy using Illumina GAIIx to characterize the entire retinal transcriptome from nondiabetic and from streptozotocin-treated mice 32 weeks after induction of diabetes. Some of the diabetic mice were treated with inhibitors of receptor for advanced glycation endproducts (RAGE) and p38 mitogen activated protein (MAP) kinase, which have previously been shown to inhibit diabetic retinopathy in rodent models. The transcripts and alternatively spliced variants were determined in all experimental groups. Results Next generation sequencing-based RNA-seq profiles provided comprehensive signatures of transcripts that are altered in early stages of diabetic retinopathy. These transcripts encoded proteins involved in distinct yet physiologically relevant disease-associated pathways such as inflammation, microvasculature formation, apoptosis, glucose metabolism, Wnt signaling, xenobiotic metabolism, and photoreceptor biology. Significant upregulation of crystallin transcripts was observed in diabetic animals, and the diabetes-induced upregulation of these transcripts was inhibited in diabetic animals treated with inhibitors of either RAGE or p38 MAP kinase. These two therapies also showed dissimilar regulation of some subsets of transcripts that included alternatively spliced versions of arrestin, neutral sphingomyelinase activation associated factor (Nsmaf), SH3-domain GRB2-like interacting protein 1 (Sgip1), and axin. Conclusions Diabetes alters many transcripts in the retina, and two therapies that inhibit the vascular pathology similarly inhibit a portion of these changes, pointing to possible molecular mechanisms for their beneficial effects. These

  14. Valproic acid, a molecular lead to multiple regulatory pathways.

    PubMed

    Kostrouchová, M; Kostrouch, Z; Kostrouchová, M

    2007-01-01

    Valproic acid (2-propyl pentanoic acid) is a drug used for the treatment of epilepsy and bipolar disorder. Although very rare, side effects such as spina bifida and other defects of neural tube closure indicate that valproic acid interferes with developmental regulatory pathways. Recently obtained data show that valproic acid affects cell growth, differentiation, apoptosis and immunogenicity of cultured cancer cells and tumours. Focused studies uncovered the potential of valproic acid to interfere with multiple regulatory mechanisms including histone deacetylases, GSK3 alpha and beta, Akt, the ERK pathway, the phosphoinositol pathway, the tricarboxylic acid cycle, GABA, and the OXPHOS system. Valproic acid is emerging as a potential anticancer drug and may also serve as a molecular lead that can help design drugs with more specific and more potent effects on the one side and drugs with wide additive but weaker effects on the other. Valproic acid is thus a powerful molecular tool for better understanding and therapeutic targeting of pathways that regulate the behaviour of cancer cells.

  15. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics.

    PubMed

    Makhov, Dmitry V; Glover, William J; Martinez, Todd J; Shalashilin, Dmitrii V

    2014-08-07

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as "cloning," in analogy to the "spawning" procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, "trains," as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.

  16. Ab initio multiple cloning algorithm for quantum nonadiabatic molecular dynamics

    SciTech Connect

    Makhov, Dmitry V.; Shalashilin, Dmitrii V.; Glover, William J.; Martinez, Todd J.

    2014-08-07

    We present a new algorithm for ab initio quantum nonadiabatic molecular dynamics that combines the best features of ab initio Multiple Spawning (AIMS) and Multiconfigurational Ehrenfest (MCE) methods. In this new method, ab initio multiple cloning (AIMC), the individual trajectory basis functions (TBFs) follow Ehrenfest equations of motion (as in MCE). However, the basis set is expanded (as in AIMS) when these TBFs become sufficiently mixed, preventing prolonged evolution on an averaged potential energy surface. We refer to the expansion of the basis set as “cloning,” in analogy to the “spawning” procedure in AIMS. This synthesis of AIMS and MCE allows us to leverage the benefits of mean-field evolution during periods of strong nonadiabatic coupling while simultaneously avoiding mean-field artifacts in Ehrenfest dynamics. We explore the use of time-displaced basis sets, “trains,” as a means of expanding the basis set for little cost. We also introduce a new bra-ket averaged Taylor expansion (BAT) to approximate the necessary potential energy and nonadiabatic coupling matrix elements. The BAT approximation avoids the necessity of computing electronic structure information at intermediate points between TBFs, as is usually done in saddle-point approximations used in AIMS. The efficiency of AIMC is demonstrated on the nonradiative decay of the first excited state of ethylene. The AIMC method has been implemented within the AIMS-MOLPRO package, which was extended to include Ehrenfest basis functions.

  17. Identification of Multiple Hypoxia Signatures in Neuroblastoma Cell Lines by l1-l2 Regularization and Data Reduction

    PubMed Central

    Fardin, Paolo; Cornero, Andrea; Barla, Annalisa; Mosci, Sofia; Acquaviva, Massimo; Rosasco, Lorenzo; Gambini, Claudio; Verri, Alessandro; Varesio, Luigi

    2010-01-01

    Hypoxia is a condition of low oxygen tension occurring in the tumor and negatively correlated with the progression of the disease. We studied the gene expression profiles of nine neuroblastoma cell lines grown under hypoxic conditions to define gene signatures that characterize hypoxic neuroblastoma. The l1-l2 regularization applied to the entire transcriptome identified a single signature of 11 probesets discriminating the hypoxic state. We demonstrate that new hypoxia signatures, with similar discriminatory power, can be generated by a prior knowledge-based filtering in which a much smaller number of probesets, characterizing hypoxia-related biochemical pathways, are analyzed. l1-l2 regularization identified novel and robust hypoxia signatures within apoptosis, glycolysis, and oxidative phosphorylation Gene Ontology classes. We conclude that the filtering approach overcomes the noisy nature of the microarray data and allows generating robust signatures suitable for biomarker discovery and patients risk assessment in a fraction of computer time. PMID:20652058

  18. Connecting genes, coexpression modules, and molecular signatures to environmental stress phenotypes in plants

    PubMed Central

    Weston, David J; Gunter, Lee E; Rogers, Alistair; Wullschleger, Stan D

    2008-01-01

    Background One of the eminent opportunities afforded by modern genomic technologies is the potential to provide a mechanistic understanding of the processes by which genetic change translates to phenotypic variation and the resultant appearance of distinct physiological traits. Indeed much progress has been made in this area, particularly in biomedicine where functional genomic information can be used to determine the physiological state (e.g., diagnosis) and predict phenotypic outcome (e.g., patient survival). Ecology currently lacks an analogous approach where genomic information can be used to diagnose the presence of a given physiological state (e.g., stress response) and then predict likely phenotypic outcomes (e.g., stress duration and tolerance, fitness). Results Here, we demonstrate that a compendium of genomic signatures can be used to classify the plant abiotic stress phenotype in Arabidopsis according to the architecture of the transcriptome, and then be linked with gene coexpression network analysis to determine the underlying genes governing the phenotypic response. Using this approach, we confirm the existence of known stress responsive pathways and marker genes, report a common abiotic stress responsive transcriptome and relate phenotypic classification to stress duration. Conclusion Linking genomic signatures to gene coexpression analysis provides a unique method of relating an observed plant phenotype to changes in gene expression that underlie that phenotype. Such information is critical to current and future investigations in plant biology and, in particular, to evolutionary ecology, where a mechanistic understanding of adaptive physiological responses to abiotic stress can provide researchers with a tool of great predictive value in understanding species and population level adaptation to climate change. PMID:18248680

  19. Neurodegenerative disease-associated mutants of a human mitochondrial aminoacyl-tRNA synthetase present individual molecular signatures

    PubMed Central

    Sauter, Claude; Lorber, Bernard; Gaudry, Agnès; Karim, Loukmane; Schwenzer, Hagen; Wien, Frank; Roblin, Pierre; Florentz, Catherine; Sissler, Marie

    2015-01-01

    Mutations in human mitochondrial aminoacyl-tRNA synthetases are associated with a variety of neurodegenerative disorders. The effects of these mutations on the structure and function of the enzymes remain to be established. Here, we investigate six mutants of the aspartyl-tRNA synthetase correlated with leukoencephalopathies. Our integrated strategy, combining an ensemble of biochemical and biophysical approaches, reveals that mutants are diversely affected with respect to their solubility in cellular extracts and stability in solution, but not in architecture. Mutations with mild effects on solubility occur in patients as allelic combinations whereas those with strong effects on solubility or on aminoacylation are necessarily associated with a partially functional allele. The fact that all mutations show individual molecular and cellular signatures and affect amino acids only conserved in mammals, points towards an alternative function besides aminoacylation. PMID:26620921

  20. Optical signatures of molecular particles via mass-selected cluster spectroscopy

    NASA Technical Reports Server (NTRS)

    Duncan, Michael A.

    1990-01-01

    A new molecular beam apparatus was developed to study optical absorption in cold (less than 100 K) atomic clusters and complexes produced by their condensation with simple molecular gases. In this instrument, ionized clusters produced in a laser vaporization nozzle source are mass selected and studied with photodissociation spectroscopy at visible and ultraviolet wavelengths. This new approach can be applied to synthesize and characterize numerous particulates and weakly bound complexes expected in planetary atmospheres and in comets.

  1. Multiple biomarkers in molecular oncology. I. Molecular diagnostics applications in cervical cancer detection.

    PubMed

    Malinowski, Douglas P

    2007-03-01

    The screening for cervical carcinoma and its malignant precursors (cervical neoplasia) currently employs morphology-based detection methods (Papanicolaou [Pap] smear) in addition to the detection of high-risk human papillomavirus. The combination of the Pap smear with human papillomavirus testing has achieved significant improvements in sensitivity for the detection of cervical disease. Diagnosis of cervical neoplasia is dependent upon histology assessment of cervical biopsy specimens. Attempts to improve the specificity of cervical disease screening have focused on the investigation of molecular biomarkers for adjunctive use in combination with the Pap smear. Active research into the genomic and proteomic alterations that occur during human papillomavirus-induced neoplastic transformation have begun to characterize some of the basic mechanisms inherent to the disease process of cervical cancer development. This research continues to demonstrate the complexity of multiple genomic and proteomic alterations that accumulate during the tumorigenesis process. Despite this diversity, basic patterns of uncontrolled signal transduction, cell cycle deregulation, activation of DNA replication and altered extracellular matrix interactions are beginning to emerge as common features inherent to cervical cancer development. Some of these gene or protein expression alterations have been investigated as potential biomarkers for screening and diagnostics applications. The contribution of multiple gene alterations in the development of cervical cancer suggests that the application of multiple biomarker panels has the potential to develop clinically useful molecular diagnostics. In this review, the application of biomarkers for the improvement of sensitivity and specificity of the detection of cervical neoplasia within cytology specimens will be discussed.

  2. Phylogenetic analysis and molecular signatures defining a monophyletic clade of heterocystous cyanobacteria and identifying its closest relatives.

    PubMed

    Howard-Azzeh, Mohammad; Shamseer, Larissa; Schellhorn, Herb E; Gupta, Radhey S

    2014-11-01

    Detailed phylogenetic and comparative genomic analyses are reported on 140 genome sequenced cyanobacteria with the main focus on the heterocyst-differentiating cyanobacteria. In a phylogenetic tree for cyanobacteria based upon concatenated sequences for 32 conserved proteins, the available cyanobacteria formed 8-9 strongly supported clades at the highest level, which may correspond to the higher taxonomic clades of this phylum. One of these clades contained all heterocystous cyanobacteria; within this clade, the members exhibiting either true (Nostocales) or false (Stigonematales) branching of filaments were intermixed indicating that the division of the heterocysts-forming cyanobacteria into these two groups is not supported by phylogenetic considerations. However, in both the protein tree as well as in the 16S rRNA gene tree, the akinete-forming heterocystous cyanobacteria formed a distinct clade. Within this clade, the members which differentiate into hormogonia or those which lack this ability were also separated into distinct groups. A novel molecular signature identified in this work that is uniquely shared by the akinete-forming heterocystous cyanobacteria provides further evidence that the members of this group are specifically related and they shared a common ancestor exclusive of the other cyanobacteria. Detailed comparative analyses on protein sequences from the genomes of heterocystous cyanobacteria reported here have also identified eight conserved signature indels (CSIs) in proteins involved in a broad range of functions, and three conserved signature proteins, that are either uniquely or mainly found in all heterocysts-forming cyanobacteria, but generally not found in other cyanobacteria. These molecular markers provide novel means for the identification of heterocystous cyanobacteria, and they provide evidence of their monophyletic origin. Additionally, this work has also identified seven CSIs in other proteins which in addition to the heterocystous

  3. Multiple biomarkers in molecular oncology. II. Molecular diagnostics applications in breast cancer management.

    PubMed

    Malinowski, Douglas P

    2007-05-01

    In recent years, the application of genomic and proteomic technologies to the problem of breast cancer prognosis and the prediction of therapy response have begun to yield encouraging results. Independent studies employing transcriptional profiling of primary breast cancer specimens using DNA microarrays have identified gene expression profiles that correlate with clinical outcome in primary breast biopsy specimens. Recent advances in microarray technology have demonstrated reproducibility, making clinical applications more achievable. In this regard, one such DNA microarray device based upon a 70-gene expression signature was recently cleared by the US FDA for application to breast cancer prognosis. These DNA microarrays often employ at least 70 gene targets for transcriptional profiling and prognostic assessment in breast cancer. The use of PCR-based methods utilizing a small subset of genes has recently demonstrated the ability to predict the clinical outcome in early-stage breast cancer. Furthermore, protein-based immunohistochemistry methods have progressed from using gene clusters and gene expression profiling to smaller subsets of expressed proteins to predict prognosis in early-stage breast cancer. Beyond prognostic applications, DNA microarray-based transcriptional profiling has demonstrated the ability to predict response to chemotherapy in early-stage breast cancer patients. In this review, recent advances in the use of multiple markers for prognosis of disease recurrence in early-stage breast cancer and the prediction of therapy response will be discussed.

  4. Molecular Surveillance Identifies Multiple Transmissions of Typhoid in West Africa

    PubMed Central

    Wong, Vanessa K.; Holt, Kathryn E.; Okoro, Chinyere; Baker, Stephen; Pickard, Derek J.; Marks, Florian; Page, Andrew J.; Olanipekun, Grace; Munir, Huda; Alter, Roxanne; Fey, Paul D.; Feasey, Nicholas A.; Weill, Francois-Xavier; Le Hello, Simon; Hart, Peter J.; Kariuki, Samuel; Breiman, Robert F.; Gordon, Melita A.; Heyderman, Robert S.; Jacobs, Jan; Lunguya, Octavie; Msefula, Chisomo; MacLennan, Calman A.; Keddy, Karen H.; Smith, Anthony M.; Onsare, Robert S.; De Pinna, Elizabeth; Nair, Satheesh; Amos, Ben; Dougan, Gordon; Obaro, Stephen

    2016-01-01

    Background The burden of typhoid in sub-Saharan African (SSA) countries has been difficult to estimate, in part, due to suboptimal laboratory diagnostics. However, surveillance blood cultures at two sites in Nigeria have identified typhoid associated with Salmonella enterica serovar Typhi (S. Typhi) as an important cause of bacteremia in children. Methods A total of 128 S. Typhi isolates from these studies in Nigeria were whole-genome sequenced, and the resulting data was used to place these Nigerian isolates into a worldwide context based on their phylogeny and carriage of molecular determinants of antibiotic resistance. Results Several distinct S. Typhi genotypes were identified in Nigeria that were related to other clusters of S. Typhi isolates from north, west and central regions of Africa. The rapidly expanding S. Typhi clade 4.3.1 (H58) previously associated with multiple antimicrobial resistances in Asia and in east, central and southern Africa, was not detected in this study. However, antimicrobial resistance was common amongst the Nigerian isolates and was associated with several plasmids, including the IncHI1 plasmid commonly associated with S. Typhi. Conclusions These data indicate that typhoid in Nigeria was established through multiple independent introductions into the country, with evidence of regional spread. MDR typhoid appears to be evolving independently of the haplotype H58 found in other typhoid endemic countries. This study highlights an urgent need for routine surveillance to monitor the epidemiology of typhoid and evolution of antimicrobial resistance within the bacterial population as a means to facilitate public health interventions to reduce the substantial morbidity and mortality of typhoid. PMID:27657909

  5. Enhancement of signal denoising and multiple fault signatures detecting in rotating machinery using dual-tree complex wavelet transform

    NASA Astrophysics Data System (ADS)

    Wang, Yanxue; He, Zhengjia; Zi, Yanyang

    2010-01-01

    In order to enhance the desired features related to some special type of machine fault, a technique based on the dual-tree complex wavelet transform (DTCWT) is proposed in this paper. It is demonstrated that DTCWT enjoys better shift invariance and reduced spectral aliasing than second-generation wavelet transform (SGWT) and empirical mode decomposition by means of numerical simulations. These advantages of the DTCWT arise from the relationship between the two dual-tree wavelet basis functions, instead of the matching of the used single wavelet basis function to the signal being analyzed. Since noise inevitably exists in the measured signals, an enhanced vibration signals denoising algorithm incorporating DTCWT with NeighCoeff shrinkage is also developed. Denoising results of vibration signals resulting from a crack gear indicate the proposed denoising method can effectively remove noise and retain the valuable information as much as possible compared to those DWT- and SGWT-based NeighCoeff shrinkage denoising methods. As is well known, excavation of comprehensive signatures embedded in the vibration signals is of practical importance to clearly clarify the roots of the fault, especially the combined faults. In the case of multiple features detection, diagnosis results of rolling element bearings with combined faults and an actual industrial equipment confirm that the proposed DTCWT-based method is a powerful and versatile tool and consistently outperforms SGWT and fast kurtogram, which are widely used recently. Moreover, it must be noted, the proposed method is completely suitable for on-line surveillance and diagnosis due to its good robustness and efficient algorithm.

  6. The nanomechanical signature of liver cancer tissues and its molecular origin

    NASA Astrophysics Data System (ADS)

    Tian, Mengxin; Li, Yiran; Liu, Weiren; Jin, Lei; Jiang, Xifei; Wang, Xinyan; Ding, Zhenbin; Peng, Yuanfei; Zhou, Jian; Fan, Jia; Cao, Yi; Wang, Wei; Shi, Yinghong

    2015-07-01

    Patients with cirrhosis are at higher risk of developing hepatocellular carcinoma (HCC), the second most frequent cause of cancer-related deaths. Although HCC diagnosis based on conventional morphological characteristics serves as the ``gold standard'' in the clinic, there is a high demand for more convenient and effective diagnostic methods that employ new biophysical perspectives. Here, we show that the nanomechanical signature of liver tissue is directly correlated with the development of HCC. Using indentation-type atomic force microscopy (IT-AFM), we demonstrate that the lowest elasticity peak (LEP) in the Young's modulus distribution of surgically removed liver cancer tissues can serve as a mechanical fingerprint to evaluate the malignancy of liver cancer. Cirrhotic tissues shared the same LEP as normal tissues. However, a noticeable downward shift in the LEP was detected when the cirrhotic tissues progressed to a malignant state, making the tumor tissues more prone to microvascular invasion. Cell-level mechanistic studies revealed that the expression level of a Rho-family effector (mDia1) was consistent with the mechanical trend exhibited by the tissue. Our findings indicate that the mechanical profiles of liver cancer tissues directly varied with tumor progression, providing an additional platform for the future diagnosis of HCC.Patients with cirrhosis are at higher risk of developing hepatocellular carcinoma (HCC), the second most frequent cause of cancer-related deaths. Although HCC diagnosis based on conventional morphological characteristics serves as the ``gold standard'' in the clinic, there is a high demand for more convenient and effective diagnostic methods that employ new biophysical perspectives. Here, we show that the nanomechanical signature of liver tissue is directly correlated with the development of HCC. Using indentation-type atomic force microscopy (IT-AFM), we demonstrate that the lowest elasticity peak (LEP) in the Young's modulus

  7. Molecular Signatures in Arabidopsis thaliana in Response to Insect Attack and Bacterial Infection

    PubMed Central

    Barah, Pankaj; Winge, Per; Kusnierczyk, Anna; Tran, Diem Hong; Bones, Atle M.

    2013-01-01

    Background Under the threat of global climatic change and food shortages, it is essential to take the initiative to obtain a comprehensive understanding of common and specific defence mechanisms existing in plant systems for protection against different types of biotic invaders. We have implemented an integrated approach to analyse the overall transcriptomic reprogramming and systems-level defence responses in the model plant species Arabidopsis thaliana (A. thaliana henceforth) during insect Brevicoryne brassicae (B. brassicae henceforth) and bacterial Pseudomonas syringae pv. tomato strain DC3000 (P. syringae henceforth) attacks. The main aim of this study was to identify the attacker-specific and general defence response signatures in A. thaliana when attacked by phloem-feeding aphids or pathogenic bacteria. Results The obtained annotated networks of differentially expressed transcripts indicated that members of transcription factor families, such as WRKY, MYB, ERF, BHLH and bZIP, could be crucial for stress-specific defence regulation in Arabidopsis during aphid and P. syringae attack. The defence response pathways, signalling pathways and metabolic processes associated with aphid attack and P. syringae infection partially overlapped. Components of several important biosynthesis and signalling pathways, such as salicylic acid (SA), jasmonic acid (JA), ethylene (ET) and glucosinolates, were differentially affected during the two the treatments. Several stress-regulated transcription factors were known to be associated with stress-inducible microRNAs. The differentially regulated gene sets included many signature transcription factors, and our co-expression analysis showed that they were also strongly co-expressed during 69 other biotic stress experiments. Conclusions Defence responses and functional networks that were unique and specific to aphid or P. syringae stresses were identified. Furthermore, our analysis revealed a probable link between biotic stress and

  8. Neural Plasticity in Multiple Sclerosis: The Functional and Molecular Background

    PubMed Central

    Ksiazek-Winiarek, Dominika Justyna; Szpakowski, Piotr; Glabinski, Andrzej

    2015-01-01

    Multiple sclerosis is an autoimmune neurodegenerative disorder resulting in motor dysfunction and cognitive decline. The inflammatory and neurodegenerative changes seen in the brains of MS patients lead to progressive disability and increasing brain atrophy. The most common type of MS is characterized by episodes of clinical exacerbations and remissions. This suggests the presence of compensating mechanisms for accumulating damage. Apart from the widely known repair mechanisms like remyelination, another important phenomenon is neuronal plasticity. Initially, neuroplasticity was connected with the developmental stages of life; however, there is now growing evidence confirming that structural and functional reorganization occurs throughout our lifetime. Several functional studies, utilizing such techniques as fMRI, TBS, or MRS, have provided valuable data about the presence of neuronal plasticity in MS patients. CNS ability to compensate for neuronal damage is most evident in RR-MS; however it has been shown that brain plasticity is also preserved in patients with substantial brain damage. Regardless of the numerous studies, the molecular background of neuronal plasticity in MS is still not well understood. Several factors, like IL-1β, BDNF, PDGF, or CB1Rs, have been implicated in functional recovery from the acute phase of MS and are thus considered as potential therapeutic targets. PMID:26229689

  9. Many Multiple Myelomas: Making More of the Molecular Mayhem

    PubMed Central

    Chesi, Marta; Bergsagel, P. Leif

    2014-01-01

    Multiple myeloma (MM) is malignancy of isotype-switched, BM-localized plasma cells that frequently results in bone destruction, BM failure, and death. Important molecular subgroups are identified by three classes of recurrent immunoglobulin gene translocations and hyperdiploidy, both of which affect disease course. From a clinical standpoint, it is critical to identify MM patients carrying the t(4;14) translocation, which is present in 15% of myelomas and is associated with dysregulation of WHSC1/MMSET and often FGFR3. These patients should all receive bortezomib as part of their initial induction treatment because this has been shown to significantly prolong survival. In contrast, patients with translocations affecting the MAF family of transcription factors, del17p, or gene-expression profiling (GEP)–defined high-risk disease appear to have a worse prognosis that is not dramatically improved by any intervention. These patients should be enrolled in innovative clinical trials. The remaining patients with cyclin D translocations or hyperdiploidy do well with most therapies, and the goal should be to control disease while minimizing toxicity. PMID:22160056

  10. Neural Plasticity in Multiple Sclerosis: The Functional and Molecular Background.

    PubMed

    Ksiazek-Winiarek, Dominika Justyna; Szpakowski, Piotr; Glabinski, Andrzej

    2015-01-01

    Multiple sclerosis is an autoimmune neurodegenerative disorder resulting in motor dysfunction and cognitive decline. The inflammatory and neurodegenerative changes seen in the brains of MS patients lead to progressive disability and increasing brain atrophy. The most common type of MS is characterized by episodes of clinical exacerbations and remissions. This suggests the presence of compensating mechanisms for accumulating damage. Apart from the widely known repair mechanisms like remyelination, another important phenomenon is neuronal plasticity. Initially, neuroplasticity was connected with the developmental stages of life; however, there is now growing evidence confirming that structural and functional reorganization occurs throughout our lifetime. Several functional studies, utilizing such techniques as fMRI, TBS, or MRS, have provided valuable data about the presence of neuronal plasticity in MS patients. CNS ability to compensate for neuronal damage is most evident in RR-MS; however it has been shown that brain plasticity is also preserved in patients with substantial brain damage. Regardless of the numerous studies, the molecular background of neuronal plasticity in MS is still not well understood. Several factors, like IL-1β, BDNF, PDGF, or CB1Rs, have been implicated in functional recovery from the acute phase of MS and are thus considered as potential therapeutic targets.

  11. Integrated molecular profiling of SOD2 expression in multiple myeloma.

    PubMed

    Hurt, Elaine M; Thomas, Suneetha B; Peng, Benjamin; Farrar, William L

    2007-05-01

    Reactive oxygen species are known to be involved in several cellular processes, including cell signaling. SOD2 is a key enzyme in the conversion of reactive oxygen species and has been implicated in a host of disease states, including cancer. Using an integrated, whole-cell approach encompassing epigenetics, genomics, and proteomics, we have defined the role of SOD2 in multiple myeloma. We show that the SOD2 promoter is methylated in several cell lines and there is a correlative decrease in expression. Furthermore, myeloma patient samples have decreased SOD2 expression compared with healthy donors. Overexpression of SOD2 results in decreased proliferation and altered sensitivity to 2-methoxyestradiol-induced DNA damage and apoptosis. Genomic profiling revealed regulation of 65 genes, including genes involved in tumorigenesis, and proteomic analysis identified activation of the JAK/STAT pathway. Analysis of nearly 400 activated transcription factors identified 31 transcription factors with altered DNA binding activity, including XBP1, NFAT, forkhead, and GAS binding sites. Integration of data from our gestalt molecular analysis has defined a role for SOD2 in cellular proliferation, JAK/STAT signaling, and regulation of several transcription factors.

  12. DNA methylation signatures define molecular subtypes of diffuse large B-cell lymphoma

    PubMed Central

    Shaknovich, Rita; Geng, Huimin; Johnson, Nathalie A.; Tsikitas, Lucas; Cerchietti, Leandro; Greally, John M.

    2010-01-01

    Expression profiling has shown 2 main and clinically distinct subtypes of diffuse large B-cell lymphomas (DLBCLs): germinal-center B cell–like (GCB) and activated B cell–like (ABC) DLBCLs. Further work has shown that these subtypes are partially characterized by distinct genetic alterations and different survival. Here, we show with the use of an assay that measures DNA methylation levels of 50 000 CpG motifs distributed among more than 14 000 promoters that these 2 DLBCL subtypes are also characterized by distinct epigenetic profiles. DNA methylation and gene expression profiling were performed on a cohort of 69 patients with DLBCL. After assigning ABC or GCB labels with a Bayesian expression classifier trained on an independent dataset, a supervised analysis identified 311 differentially methylated probe sets (263 unique genes) between ABC and GCB DLBCLs. Integrated analysis of methylation and gene expression showed a core tumor necrosis factor-α signaling pathway as the principal differentially perturbed gene network. Sixteen genes overlapped between the core ABC/GCB methylation and expression signatures and encoded important proteins such as IKZF1. This reduced gene set was an accurate predictor of ABC and GCB subtypes. Collectively, the data suggest that epigenetic patterning contributes to the ABC and GCB DLBCL phenotypes and could serve as useful biomarker. PMID:20610814

  13. The nanomechanical signature of liver cancer tissues and its molecular origin.

    PubMed

    Tian, Mengxin; Li, Yiran; Liu, Weiren; Jin, Lei; Jiang, Xifei; Wang, Xinyan; Ding, Zhenbin; Peng, Yuanfei; Zhou, Jian; Fan, Jia; Cao, Yi; Wang, Wei; Shi, Yinghong

    2015-08-14

    Patients with cirrhosis are at higher risk of developing hepatocellular carcinoma (HCC), the second most frequent cause of cancer-related deaths. Although HCC diagnosis based on conventional morphological characteristics serves as the "gold standard" in the clinic, there is a high demand for more convenient and effective diagnostic methods that employ new biophysical perspectives. Here, we show that the nanomechanical signature of liver tissue is directly correlated with the development of HCC. Using indentation-type atomic force microscopy (IT-AFM), we demonstrate that the lowest elasticity peak (LEP) in the Young's modulus distribution of surgically removed liver cancer tissues can serve as a mechanical fingerprint to evaluate the malignancy of liver cancer. Cirrhotic tissues shared the same LEP as normal tissues. However, a noticeable downward shift in the LEP was detected when the cirrhotic tissues progressed to a malignant state, making the tumor tissues more prone to microvascular invasion. Cell-level mechanistic studies revealed that the expression level of a Rho-family effector (mDia1) was consistent with the mechanical trend exhibited by the tissue. Our findings indicate that the mechanical profiles of liver cancer tissues directly varied with tumor progression, providing an additional platform for the future diagnosis of HCC.

  14. Emergence of canine distemper virus strains with modified molecular signature and enhanced neuronal tropism leading to high mortality in wild carnivores.

    PubMed

    Origgi, F C; Plattet, P; Sattler, U; Robert, N; Casaubon, J; Mavrot, F; Pewsner, M; Wu, N; Giovannini, S; Oevermann, A; Stoffel, M H; Gaschen, V; Segner, H; Ryser-Degiorgis, M-P

    2012-11-01

    An ongoing canine distemper epidemic was first detected in Switzerland in the spring of 2009. Compared to previous local canine distemper outbreaks, it was characterized by unusually high morbidity and mortality, rapid spread over the country, and susceptibility of several wild carnivore species. Here, the authors describe the associated pathologic changes and phylogenetic and biological features of a multiple highly virulent canine distemper virus (CDV) strain detected in and/or isolated from red foxes (Vulpes vulpes), Eurasian badgers (Meles meles), stone (Martes foina) and pine (Martes martes) martens, from a Eurasian lynx (Lynx lynx), and a domestic dog. The main lesions included interstitial to bronchointerstitial pneumonia and meningopolioencephalitis, whereas demyelination--the classic presentation of CDV infection--was observed in few cases only. In the brain lesions, viral inclusions were mainly in the nuclei of the neurons. Some significant differences in brain and lung lesions were observed between foxes and mustelids. Swiss CDV isolates shared together with a Hungarian CDV strain detected in 2004. In vitro analysis of the hemagglutinin protein from one of the Swiss CDV strains revealed functional and structural differences from that of the reference strain A75/17, with the Swiss strain showing increased surface expression and binding efficiency to the signaling lymphocyte activation molecule (SLAM). These features might be part of a novel molecular signature, which might have contributed to an increase in virus pathogenicity, partially explaining the high morbidity and mortality, the rapid spread, and the large host spectrum observed in this outbreak.

  15. Gene expression profiling of CD34+ cells identifies a molecular signature of chronic myeloid leukemia blast crisis.

    PubMed

    Zheng, C; Li, L; Haak, M; Brors, B; Frank, O; Giehl, M; Fabarius, A; Schatz, M; Weisser, A; Lorentz, C; Gretz, N; Hehlmann, R; Hochhaus, A; Seifarth, W

    2006-06-01

    Despite recent success in the treatment of early-stage disease, blastic phase (BP) of chronic myeloid leukemia (CML) that is characterized by rapid expansion of therapy-refractory and differentiation-arrested blasts, remains a therapeutic challenge. The development of resistance upon continuous administration of imatinib mesylate is associated with poor prognosis pointing to the need for alternative therapeutic strategies and a better understanding of the molecular mechanisms underlying disease progression. To identify transcriptional signatures that may explain pathological characteristics and aggressive behavior of BP blasts, we performed comparative gene expression profiling on CD34+ Ph+ cells purified from patients with untreated newly diagnosed chronic phase CML (CP, n=11) and from patients in BP (n=9) using Affymetrix oligonucleotide arrays. Supervised microarray data analysis revealed 114 differentially expressed genes (P<10(-4)), 34 genes displaying more than two-fold transcriptional changes when comparing CP and BP groups. While 24 of these genes were downregulated, 10 genes, especially suppressor of cytokine signalling 2 (SOCS2), CAMPATH-1 antigen (CD52), and four human leukocyte antigen-related genes were strongly overexpressed in BP. Expression of selected genes was validated by real-time-polymerase chain reaction and flow cytometry. Our data suggest the existence of a common gene expression profile of CML-BP and provide new insight into the molecular phenotype of blasts associated with disease progression and high malignancy.

  16. Kinematic Results From a Systematic Search for Infall Signatures Towards the Starless Core Population in the Perseus Molecular Cloud

    NASA Astrophysics Data System (ADS)

    Walker-LaFollette, Amanda; Shirley, Y. L.; Amaya, H.; Becker, S. L.; Biddle, L. I.; Lichtenberger, M.; Nieberding, M. N.; Raphael, B. A.; Romine, J. M.; Small, L.; Stanford-Jones, C.; Smith, C.; Thompson, R.; Towner, A. P.; Turner, J.; Watson, Z.; Cates, I.; McGraw, A. M.; Pearson, K.; Robertson, A.; Tombleson, R.

    2014-01-01

    We present the results of a survey searching for infall signatures toward 72 starless cores in the Perseus molecular cloud. Observations of the ground state rotational transitions of HCN, HNC, and H13CN were carried out using the 12-m radio telescope on Kitt Peak operated by the Arizona Radio Observatory. All three molecules are tracers of dense molecular gas. HCN 1-0 is an excellent infall tracer, with its three hyperfine lines probing different optical depths. We examined the spectra for signs of infall by comparing observed line asymmetries with the velocity peak of the optically thin isotopologue H13CN. We find that there is an excess of blue asymmetries, but clearly self-absorbed profiles are rare (< 20%). We compare typical measures of asymmetry such as δv and skewness. By comparing the number of blue asymmetric and blue skewed profiles to the number of class II protostars, we find a range for the observable collapse lifetime of 6x10^4-2x10^5yrs, which is commensurate with the gravitational free-fall time (5x10^4yrs) for the observed central densities of Perseus starless cores. The best infall candidates all have observed masses that are above the Jeans mass. We calculate the infall speeds for the best collapse candidates and compare their dynamics to other known collapsing starless cores. This project was observed by The University of Arizona Undergraduate Astronomy Club.

  17. Signature of an Intermediate-Mass Black Hole in the Central Molecular Zone of Our Galaxy

    NASA Astrophysics Data System (ADS)

    Oka, Tomoharu; Mizuno, Reiko; Miura, Kodai; Takekawa, Shunya

    2017-01-01

    The high-velocity compact cloud CO-0.40-0.22 was mapped in 22 molecular lines with the NRO 45 m radio telescope and the ASTE 10 m telescope. The map of each detected line shows that this cloud has a compact appearance (d~=3 pc) and extremely broad velocity width (Δ V~=100 km s-1). The representative position-velocity map along the major axis shows that CO-0.40-0.22 consists of an intense region with a shallow velocity gradient and a less intense high-velocity wing. This kinematical structure can be attributed to a gravitational kick to the molecular cloud caused by an invisible compact object with a mass of ~105 M ⊙. Its compactness and the absence of a counterpart at other wavelengths suggest that this massive object is an intermediate-mass black hole.

  18. X-ray absorption signatures of the molecular environment in water and ice.

    PubMed

    Chen, Wei; Wu, Xifan; Car, Roberto

    2010-07-02

    The x-ray absorption spectra of water and ice are calculated with a many-body approach for electron-hole excitations. The experimental features, including the effects of temperature change in the liquid, are reproduced from configurations generated by ab initio molecular dynamics. The spectral difference between the solid and the liquid is due to two major short-range order effects. One, due to breaking of hydrogen bonds, enhances the pre-edge intensity in the liquid. The other, due to a nonbonded molecular fraction in the first coordination shell, affects the main spectral edge in the conversion of ice to water. This effect may not involve hydrogen bond breaking as shown by experiment in high-density amorphous ice.

  19. Imaging Molecular Signatures of Breast Cancer with X-ray-Activated Nanophosphors

    DTIC Science & Technology

    2014-01-01

    and are working on RLI. 15. SUBJECT TERMS BREAST CANCER , IMAGING, MOLECULAR IMAGING, X-RAY, NANOPARTICLES 16. SECURITY CLASSIFICATION OF: 17...it is important to recognize that cancer nanotechnology is a major venture in the National Cancer Institute, and this technique will benefit from...Kortum, “Real-time vital optical imaging of precancer using anti-epidermal growth factor receptor antibodies conjugated to gold nanoparticles ,” Cancer

  20. The molecular signature and cis-regulatory architecture of a C. elegans gustatory neuron

    PubMed Central

    Etchberger, John F.; Lorch, Adam; Sleumer, Monica C.; Zapf, Richard; Jones, Steven J.; Marra, Marco A.; Holt, Robert A.; Moerman, Donald G.; Hobert, Oliver

    2007-01-01

    Taste receptor cells constitute a highly specialized cell type that perceives and conveys specific sensory information to the brain. The detailed molecular composition of these cells and the mechanisms that program their fate are, in general, poorly understood. We have generated serial analysis of gene expression (SAGE) libraries from two distinct populations of single, isolated sensory neuron classes, the gustatory neuron class ASE and the thermosensory neuron class AFD, from the nematode Caenorhabditis elegans. By comparing these two libraries, we have identified >1000 genes that define the ASE gustatory neuron class on a molecular level. This set of genes contains determinants of the differentiated state of the ASE neuron, such as a surprisingly complex repertoire of transcription factors (TFs), ion channels, neurotransmitters, and receptors, as well as seven-transmembrane receptor (7TMR)-type putative gustatory receptor genes. Through the in vivo dissection of the cis-regulatory regions of several ASE-expressed genes, we identified a small cis-regulatory motif, the “ASE motif,” that is required for the expression of many ASE-expressed genes. We demonstrate that the ASE motif is a binding site for the C2H2 zinc finger TF CHE-1, which is essential for the correct differentiation of the ASE gustatory neuron. Taken together, our results provide a unique view of the molecular landscape of a single neuron type and reveal an important aspect of the regulatory logic for gustatory neuron specification in C. elegans. PMID:17606643

  1. A molecular signature of an arrest of descent in human parturition

    PubMed Central

    MITTAL, Pooja; ROMERO, Roberto; TARCA, Adi L.; DRAGHICI, Sorin; NHAN-CHANG, Chia-Ling; CHAIWORAPONGSA, Tinnakorn; HOTRA, John; GOMEZ, Ricardo; KUSANOVIC, Juan Pedro; LEE, Deug-Chan; KIM, Chong Jai; HASSAN, Sonia S.

    2010-01-01

    Objective This study was undertaken to identify the molecular basis of an arrest of descent. Study Design Human myometrium was obtained from women in term labor (TL; n=29) and arrest of descent (AODes, n=21). Gene expression was characterized using Illumina® HumanHT-12 microarrays. A moderated t-test and false discovery rate adjustment were applied for analysis. Confirmatory qRT-PCR and immunoblot was performed in an independent sample set. Results 400 genes were differentially expressed between women with an AODes compared to those with TL. Gene Ontology analysis indicated enrichment of biological processes and molecular functions related to inflammation and muscle function. Impacted pathways included inflammation and the actin cytoskeleton. Overexpression of HIF1A, IL-6, and PTGS2 in AODES was confirmed. Conclusion We have identified a stereotypic pattern of gene expression in the myometrium of women with an arrest of descent. This represents the first study examining the molecular basis of an arrest of descent using a genome-wide approach. PMID:21284969

  2. Molecular Signature of a Right Heart Failure Program in Chronic Severe Pulmonary Hypertension

    PubMed Central

    Drake, Jennifer I.; Bogaard, Herman J.; Mizuno, Shiro; Clifton, Berrick; Xie, Bin; Gao, Yuan; Dumur, Catherine I.; Fawcett, Paul; Natarajan, Ramesh

    2011-01-01

    Right heart failure is the cause of death of most patients with severe pulmonary arterial hypertensive (PAH) disorders, yet little is known about the cellular and molecular causes of right ventricular failure (RVF). We first showed a differential gene expression pattern between normal rat right and left ventricles, and postulated the existence of a molecular right heart failure program that distinguishes RVF from adaptive right ventricular hypertrophy (RVH), and that may differ in some respects from a left heart failure program. By means of microarrays and transcriptional sequencing strategies, we used two models of adaptive RVH to characterize a gene expression pattern reflective of growth and the maintenance of myocardial structure. Moreover, two models of RVF were associated with fibrosis, capillary rarefaction, the decreased expression of genes encoding the angiogenesis factors vascular endothelial growth factor, insulin-like growth factor 1, apelin, and angiopoeitin-1, and the increased expression of genes encoding a set of glycolytic enzymes. The treatment of established RVF with a β-adrenergic receptor blocker reversed RVF, and partly reversed the molecular RVF program. We conclude that normal right and left ventricles demonstrate clearly discernable differences in the expression of mRNA and microRNA, and that RVH and RVF are characterized by distinct patterns of gene expression that relate to cell growth, angiogenesis, and energy metabolism. PMID:21719795

  3. Genome-wide transcriptional profiling reveals molecular signatures of secondary xylem differentiation in Populus tomentosa.

    PubMed

    Yang, X H; Li, X G; Li, B L; Zhang, D Q

    2014-11-11

    Wood formation occurs via cell division, primary cell wall and secondary wall formation, and programmed cell death in the vascular cambium. Transcriptional profiling of secondary xylem differentiation is essential for understanding the molecular mechanisms underlying wood formation. Differential gene expression in secondary xylem differentiation of Populus has been previously investigated using cDNA microarray analysis. However, little is known about the molecular mechanisms from a genome-wide perspective. In this study, the Affymetrix poplar genome chips containing 61,413 probes were used to investigate the changes in the transcriptome during secondary xylem differentiation in Chinese white poplar (Populus tomentosa). Two xylem tissues (newly formed and lignified) were sampled for genome-wide transcriptional profiling. In total, 6843 genes (~11%) were identified with differential expression in the two xylem tissues. Many genes involved in cell division, primary wall modification, and cellulose synthesis were preferentially expressed in the newly formed xylem. In contrast, many genes, including 4-coumarate:cinnamate-4-hydroxylase (C4H), 4-coumarate:CoA ligase (4CL), cinnamyl alcohol dehydrogenase (CAD), and caffeoyl CoA 3-O-methyltransferase (CCoAOMT), associated with lignin biosynthesis were more transcribed in the lignified xylem. The two xylem tissues also showed differential expression of genes related to various hormones; thus, the secondary xylem differentiation could be regulated by hormone signaling. Furthermore, many transcription factor genes were preferentially expressed in the lignified xylem, suggesting that wood lignification involves extensive transcription regulation. The genome-wide transcriptional profiling of secondary xylem differentiation could provide additional insights into the molecular basis of wood formation in poplar species.

  4. Striatal Molecular Signature of Subchronic Subthalamic Nucleus High Frequency Stimulation in Parkinsonian Rat

    PubMed Central

    Lortet, Sylviane; Lacombe, Emilie; Boulanger, Nicolas; Rihet, Pascal; Nguyen, Catherine; Goff, Lydia Kerkerian-Le; Salin, Pascal

    2013-01-01

    This study addresses the molecular mechanisms underlying the action of subthalamic nucleus high frequency stimulation (STN-HFS) in the treatment of Parkinson's disease and its interaction with levodopa (L-DOPA), focusing on the striatum. Striatal gene expression profile was assessed in rats with nigral dopamine neuron lesion, either treated or not, using agilent microarrays and qPCR verification. The treatments consisted in anti-akinetic STN-HFS (5 days), chronic L-DOPA treatment inducing dyskinesia (LIDs) or the combination of the two treatments that exacerbated LIDs. STN-HFS modulated 71 striatal genes. The main biological processes associated with the differentially expressed gene products include regulation of growth, of apoptosis and of synaptic transmission, and extracellular region is a major cellular component implicated. In particular, several of these genes have been shown to support survival or differentiation of striatal or of dopaminergic neurons. These results indicate that STN HFS may induce widespread anatomo-functional rearrangements in the striatum and create a molecular environment favorable for neuroprotection and neuroplasticity. STN-HFS and L-DOPA treatment share very few common gene regulation features indicating that the molecular substrates underlying their striatal action are mostly different; among the common effects is the down-regulation of Adrb1, which encodes the adrenergic beta-1- receptor, supporting a major role of this receptor in Parkinson's disease. In addition to genes already reported to be associated with LIDs (preprodynorphin, thyrotropin-releasing hormone, metabotropic glutamate receptor 4, cannabinoid receptor 1), the comparison between DOPA and DOPA/HFS identifies immunity-related genes as potential players in L-DOPA side effects. PMID:23593219

  5. A molecular signature in blood identifies early Parkinson’s disease

    PubMed Central

    2012-01-01

    Background The search for biomarkers in Parkinson’s disease (PD) is crucial to identify the disease early and monitor the effectiveness of neuroprotective therapies. We aim to assess whether a gene signature could be detected in blood from early/mild PD patients that could support the diagnosis of early PD, focusing on genes found particularly altered in the substantia nigra of sporadic PD. Results The transcriptional expression of seven selected genes was examined in blood samples from 62 early stage PD patients and 64 healthy age-matched controls. Stepwise multivariate logistic regression analysis identified five genes as optimal predictors of PD: p19 S-phase kinase-associated protein 1A (odds ratio [OR] 0.73; 95% confidence interval [CI] 0.60–0.90), huntingtin interacting protein-2 (OR 1.32; CI 1.08–1.61), aldehyde dehydrogenase family 1 subfamily A1 (OR 0.86; 95% CI 0.75–0.99), 19 S proteasomal protein PSMC4 (OR 0.73; 95% CI 0.60–0.89) and heat shock 70-kDa protein 8 (OR 1.39; 95% CI 1.14–1.70). At a 0.5 cut-off the gene panel yielded a sensitivity and specificity in detecting PD of 90.3 and 89.1 respectively and the area under the receiving operating curve (ROC AUC) was 0.96. The performance of the five-gene classifier on the de novo PD individuals alone composing the early PD cohort (n = 38), resulted in a similar ROC with an AUC of 0.95, indicating the stability of the model and also, that patient medication had no significant effect on the predictive probability (PP) of the classifier for PD risk. The predictive ability of the model was validated in an independent cohort of 30 patients at advanced stage of PD, classifying correctly all cases as PD (100% sensitivity). Notably, the nominal average value of the PP for PD (0.95 (SD = 0.09)) in this cohort was higher than that of the early PD group (0.83 (SD = 0.22)), suggesting a potential for the model to assess disease severity. Lastly, the gene panel fully discriminated between PD

  6. Extending Molecular Signatures of Climatic and Environmental Change to the Mesozoic

    NASA Astrophysics Data System (ADS)

    Brassell, S. C.

    2007-12-01

    The distributions, abundances and isotopic compositions of molecular constituents in sediments depend on their source organisms and the combination of environmental and climatic parameters that constrain or control their biosynthesis. Many such relationships are well documented and understood, thereby providing proxies of proven utility in paleoclimatic reconstructions. Thus, the temperature dependence in the extent of unsaturation in alkenones derived from prymnesiophyte algae, and in the proportion of ring structures in glycerol dibiphytanyl glycerol tetraethers (GDGTs) synthesized by crenarchaeota enables determination of sea surface paleotemperatures from sedimentary records. This molecular approach presumes temporal uniformity in the controlling factors on biosynthesis of these lipids, and their survival in the geological record, notwithstanding the challenge of establishing ancient calibrations for such proxies. Thus, alkenone records from marine sediments document cooling at the Eocene/Oligocene boundary but cannot assess changes in ocean temperatures during the Cretaceous, unlike GDGTs, which record fluctuations in ocean temperatures during the Early Cretaceous, and even survive in Jurassic strata. Other molecular measures offer less precise, yet informative, indications of climate. For example, the occurrence of sterol ethers in Valanginian sediments from the mid-Pacific suggests some cooling at that time, since these compounds are only known to occur elsewhere in cold waters or upwelling systems. Molecular compositions can also attest to levels of oxygenation in marine systems. In particular, the occurrence of 13C-depleted isorenieratane indicates the presence of photosynthetic green sulfur bacteria, and therefore anoxic conditions, albeit perhaps short-lived. Intermittent occurrences of isorenieratane often alternate with the appearance of 2-methylhopanoids, which provide separate distinct evidence for variations in oxygenation, linked to circumstances

  7. Signatures of Molecular Orbital Structure in Lateral Electron Momentum Distributions from Strong-Field Ionization

    NASA Astrophysics Data System (ADS)

    Petersen, Ingo; Henkel, Jost; Lein, Manfred

    2015-03-01

    Strong-field ionization of aligned diatomic and polyatomic molecules such as O2, N2, C2H4, and others in circularly polarized laser fields is investigated theoretically. By calculating the emission-angle-resolved lateral width of the momentum distribution perpendicular to the polarization plane, we show that nodal planes in molecular orbitals are directly imprinted on the angular dependence of the width. We demonstrate that orbital symmetries can be distinguished with the information obtained by observing the lateral width in addition to the angular distributions.

  8. Outcome-based profiling of astrocytic tumours identifies prognostic gene expression signatures which link molecular and morphology-based pathology.

    PubMed

    Beetz, Christian; Bergner, Sven; Brodoehl, Stefan; Brodhun, Michael; Ewald, Christian; Kalff, Rolf; Krüger, Jutta; Patt, Stephan; Kiehntopf, Michael; Deufel, Thomas

    2006-11-01

    Astrocytomas are intracranial malignancies for which invasive growth and high motility of tumour cells preclude total resection; the tumours usually recur in a more aggressive and, eventually, lethal form. Clinical outcome is highly variable and the accuracy of morphology-based prognostic statements is limited. In order to identify novel molecular markers for prognosis we obtained expression profiles of: i) tumours associated with particularly long recurrence-free intervals, ii) tumours which led to rapid patient death, and iii) tumour-free control brain. Unsupervised data analysis completely separated the three sample entities indicating a strong impact of the selection criteria on general gene expression. Consequently, significant numbers of specifically expressed genes could be identified for each entity. An extended set of tumours was then investigated by RT-PCR targeting 12 selected genes. Data from these experiments were summarised into a sample-specific index which assigns tumours to high- and low-risk groups as successfully as does morphology-based grading. Moreover, this index directly correlates with definite survival suggesting that integrated gene expression data allow individualised prognostic statements. We also analysed localisation of selected marker transcripts by in situ hybridization. Our finding of cell-specificity for some of these outcome-determining genes relates global expression data to the presence of morphological correlates of tumour behaviour and, thus, provides a link between morphology-based and molecular pathology. Our identification of expression signatures that are associated individually with clinical outcome confirms the prognostic relevance of gene expression data and, thus, represents a step towards eventually implementing molecular diagnosis into clinical practice in neuro-oncology.

  9. SIGNATURE OF AN INTERMEDIATE-MASS BLACK HOLE IN THE CENTRAL MOLECULAR ZONE OF OUR GALAXY

    SciTech Connect

    Oka, Tomoharu; Mizuno, Reiko; Miura, Kodai; Takekawa, Shunya

    2016-01-01

    We mapped the high-velocity compact cloud CO–0.40–0.22 in 21 molecular lines in the 3 mm band using the Nobeyama Radio Observatory 45 m radio telescope. Eighteen lines were detected from CO–0.40–0.22. The map of each detected line shows that this cloud has a compact appearance (d ≃ 3 pc) and extremely broad velocity width (ΔV ≃ 100 km s{sup −1}). The mass and kinetic energy of CO–0.40–0.22 are estimated to be 10{sup 3.6} M{sub ⊙} and 10{sup 49.7} erg, respectively. The representative position–velocity map along the major axis shows that CO–0.40–0.22 consists of an intense region with a shallow velocity gradient and a less intense high-velocity wing. Here, we show that this kinematical structure can be attributed to a gravitational kick to the molecular cloud caused by an invisible compact object with a mass of ∼10{sup 5} M{sub ⊙}. Its compactness and the absence of counterparts at other wavelengths suggest that this massive object is an intermediate-mass black hole.

  10. Atypical scrapie isolates involve a uniform prion species with a complex molecular signature.

    PubMed

    Götte, Dorothea R; Benestad, Sylvie L; Laude, Hubert; Zurbriggen, Andreas; Oevermann, Anna; Seuberlich, Torsten

    2011-01-01

    The pathobiology of atypical scrapie, a prion disease affecting sheep and goats, is still poorly understood. In a previous study, we demonstrated that atypical scrapie affecting small ruminants in Switzerland differs in the neuroanatomical distribution of the pathological prion protein (PrP(d)). To investigate whether these differences depend on host-related vs. pathogen-related factors, we transmitted atypical scrapie to transgenic mice over-expressing the ovine prion protein (tg338). The clinical, neuropathological, and molecular phenotype of tg338 mice is similar between mice carrying the Swiss atypical scrapie isolates and the Nor98, an atypical scrapie isolate from Norway. Together with published data, our results suggest that atypical scrapie is caused by a uniform type of prion, and that the observed phenotypic differences in small ruminants are likely host-dependant. Strikingly, by using a refined SDS-PAGE technique, we established that the prominent proteinase K-resistant prion protein fragment in atypical scrapie consists of two separate, unglycosylated peptides with molecular masses of roughly 5 and 8 kDa. These findings show similarities to those for other prion diseases in animals and humans, and lay the groundwork for future comparative research.

  11. A boosting approach for adapting the sparsity of risk prediction signatures based on different molecular levels.

    PubMed

    Sariyar, Murat; Schumacher, Martin; Binder, Harald

    2014-06-01

    Risk prediction models can link high-dimensional molecular measurements, such as DNA methylation, to clinical endpoints. For biological interpretation, often a sparse fit is desirable. Different molecular aggregation levels, such as considering DNA methylation at the CpG, gene, or chromosome level, might demand different degrees of sparsity. Hence, model building and estimation techniques should be able to adapt their sparsity according to the setting. Additionally, underestimation of coefficients, which is a typical problem of sparse techniques, should also be addressed. We propose a comprehensive approach, based on a boosting technique that allows a flexible adaptation of model sparsity and addresses these problems in an integrative way. The main motivation is to have an automatic sparsity adaptation. In a simulation study, we show that this approach reduces underestimation in sparse settings and selects more adequate model sizes than the corresponding non-adaptive boosting technique in non-sparse settings. Using different aggregation levels of DNA methylation data from a study in kidney carcinoma patients, we illustrate how automatically selected values of the sparsity tuning parameter can reflect the underlying structure of the data. In addition to that, prediction performance and variable selection stability is compared to the non-adaptive boosting approach.

  12. Conserved molecular signatures of neurogenesis in the hippocampal subgranular zone of rodents and primates

    PubMed Central

    Miller, Jeremy A.; Nathanson, Jason; Franjic, Daniel; Shim, Sungbo; Dalley, Rachel A.; Shapouri, Sheila; Smith, Kimberly A.; Sunkin, Susan M.; Bernard, Amy; Bennett, Jeffrey L.; Lee, Chang-Kyu; Hawrylycz, Michael J.; Jones, Allan R.; Amaral, David G.; Sestan, Nenad; Gage, Fred H.; Lein, Ed S.

    2013-01-01

    The neurogenic potential of the subgranular zone (SGZ) of the hippocampal dentate gyrus is likely to be regulated by molecular cues arising from its complex heterogeneous cellular environment. Through transcriptome analysis using laser microdissection coupled with DNA microarrays, in combination with analysis of genome-wide in situ hybridization data, we identified 363 genes selectively enriched in adult mouse SGZ. These genes reflect expression in the different constituent cell types, including progenitor and dividing cells, immature granule cells, astrocytes, oligodendrocytes and GABAergic interneurons. Similar transcriptional profiling in the rhesus monkey dentate gyrus across postnatal development identified a highly overlapping set of SGZ-enriched genes, which can be divided based on temporal profiles to reflect maturation of glia versus granule neurons. Furthermore, we identified a neurogenesis-related gene network with decreasing postnatal expression that is highly correlated with the declining number of proliferating cells in dentate gyrus over postnatal development. Many of the genes in this network showed similar postnatal downregulation in mouse, suggesting a conservation of molecular mechanisms underlying developmental and adult neurogenesis in rodents and primates. Conditional deletion of Sox4 and Sox11, encoding two neurogenesis-related transcription factors central in this network, produces a mouse with no hippocampus, confirming the crucial role for these genes in regulating hippocampal neurogenesis. PMID:24154525

  13. Mid-infrared, long wave infrared (4-12 μm) molecular emission signatures from pharmaceuticals using laser-induced breakdown spectroscopy (LIBS).

    PubMed

    Yang, Clayton S-C; Brown, Ei E; Kumi-Barimah, Eric; Hommerich, Uwe H; Jin, Feng; Trivedi, Sudhir B; Samuels, Alan C; Snyder, A Peter

    2014-01-01

    In an effort to augment the atomic emission spectra of conventional laser-induced breakdown spectroscopy (LIBS) and to provide an increase in selectivity, mid-wave to long-wave infrared (IR), LIBS studies were performed on several organic pharmaceuticals. Laser-induced breakdown spectroscopy signature molecular emissions of target organic compounds are observed for the first time in the IR fingerprint spectral region between 4-12 μm. The IR emission spectra of select organic pharmaceuticals closely correlate with their respective standard Fourier transform infrared spectra. Intact and/or fragment sample molecular species evidently survive the LIBS event. The combination of atomic emission signatures derived from conventional ultraviolet-visible-near-infrared LIBS with fingerprints of intact molecular entities determined from IR LIBS promises to be a powerful tool for chemical detection.

  14. The molecular signatures of Taxodiaceae / Cupressaceae / Taxaceae (TCT) leaf waxes in modern and ancient samples

    NASA Astrophysics Data System (ADS)

    Ho, M.; Zinniker, D.; Green Nylen, N.; Moldowan, J. M.; Denisevich, P.

    2005-12-01

    optimized for the synthesis of C34 and C36 fatty acids. The bimodal distribution of n-alkanes (abundant C25 and C27 and abundant C33 and C35) in some Cupressus species indicates that the expression of this VLCFA elongase may be spatially or temporally limited in some taxa. Examples of fossil TCT leaf waxes have been observed in Pleistocene coastal sediments from California and Washington and in Jurassic coals from the Turpan basin in western China. These wax contributions can be identified by their unique n-alkane and diterpenoid signatures and their relationship with macrofossil and/or microfossil remains tied to members of the TCT complex. The carbon isotopic composition of Pleistocene waxes is consistent with a rainforest or marsh adapted TCT taxon (possibly Thuja plicata), while the isotopic composition of the Jurassic waxes is indicative of a highly water stressed taxon. Unique enzymes for very long chain n-alkane biosynthesis in the core group of TCT taxa listed above may have arisen during the early Mesozoic in a desert or salt marsh adapted species in response to extreme temperatures or water stress.

  15. Tannin signatures of barks, needles, leaves, cones, and wood at the molecular level

    NASA Astrophysics Data System (ADS)

    Hernes, Peter J.; Hedges, John I.

    2004-03-01

    We analyzed 117 tissues from 77 different plant species for molecular tannin. Tannin was measured in 89 tissues (as high as 10.5 wt.% total tannin), including procyanidin (PC) tannin in 88 tissues, prodelphinidin (PD) tannin in 50, and propelargonidin (PP) tannin in 24. In addition to tannin, several flavones, flavanones, and triterpenoids were measured, the latter which yielded as much as 4.5 wt.%. Compositions varied considerably between species, including several that yielded comparatively rare tannin or triterpenoids. Conifer needles were distinguished by high yields of PD tannin overall and relative to PC tannin. Dicotyledon leaves were characterized by the presence of flavones and triterpenoids. Barks were marked by flavanones and tetracosanoic acid. Based on these trends, relationships that could be useful as geochemical parameters were developed for distinguishing needles, leaves, and barks as possible components of litter, soil, or sedimentary mixtures.

  16. Emissions of molecular hydrogen (H2) and its isotopic signature from residential heaters and waste incinerators

    NASA Astrophysics Data System (ADS)

    Vollmer, M. K.; Walter, S.; Mohn, J.; Steinbacher, M.; Bond, S. W.; Roeckmann, T.; Reimann, S.

    2011-12-01

    Atmospheric molecular hydrogen (H2) has recently received increased interest in the scientific community because of a potential shift to a global hydrogen energy economy which could potentially alter the atmospheric budget of H2 due to substantial leakage. This calls for an improved understanding of the present day's atmospheric H2 budget. One of the major sources of H2 are emissions from incomplete combustion of fossil fuel. While emissions of H2 from car exhaust have been studied extensively, those from fossil fuel based heating systems have remained a matter of speculation. Here we present results from measurements of a variety of residential heating systems covering oil, gas, and wood heating with various burner capacities. For oil and gas heating systems we surprisingly find no net H2 emissions, i.e. the exhaust air contains H2 at or below the mole fractions of the intake air (approx. 0.5 ppm). While H2 emissions are virtually absent, those of carbon monoxide (CO) are not. As a consequence, caution has to be exercised when modeling H2 emissions based on assumed H2/CO ratios and using CO emission inventories. We also find that the molecular hydrogen in the approx. 0.5 ppm exhaust air is isotopically strongly depleted (-20 permil to -200 permil) compared to the ambient air (+130 permil). This suggests that H2 is involved in the combustion processes, and therefore the H2 of the intake air is not the same H2 in the exhaust air. Exhausts from waste incinerator plants are generally also depleted in H2 mole fractions and in their H/D isotopic composition.

  17. Molecular signatures in rainbow darter (Etheostoma caeruleum) inhabiting an urbanized river reach receiving wastewater effluents.

    PubMed

    Bahamonde, P A; Tetreault, G R; McMaster, M E; Servos, M R; Martyniuk, C J; Munkittrick, K R

    2014-03-01

    darter, with emphasis on the differences in transcript abundance between sexes and how these changes relate to exposures to MWWEs. Molecular approaches are being investigated for their potential application to field ecotoxicology, and molecular bioassays for relevant, sentinel species in environmental monitoring programs are required to better understand the impact of anthropogenic impacts on species at risk in river systems.

  18. The Biophysical Probes 2-fluorohistidine and 4-fluorohistidine: Spectroscopic Signatures and Molecular Properties

    NASA Astrophysics Data System (ADS)

    Kasireddy, Chandana; Ellis, Jonathan M.; Bann, James G.; Mitchell-Koch, Katie R.

    2017-02-01

    Fluorinated amino acids serve as valuable biological probes, by reporting on local protein structure and dynamics through 19F NMR chemical shifts. 2-fluorohistidine and 4-fluorohistidine, studied here with DFT methods, have even more capabilities for biophysical studies, as their altered pKa values, relative to histidine, allow for studies of the role of proton transfer and tautomeric state in enzymatic mechanisms. Considering the two tautomeric forms of histidine, it was found that 2-fluorohistidine primarily forms the common (for histidine) τ-tautomer at neutral pH, while 4-fluorohistidine exclusively forms the less common π-tautomer. This suggests the two isomers of fluorohistidine can also serve as probes of tautomeric form within biomolecules, both by monitoring NMR chemical shifts and by potential perturbation of the tautomeric equilibrium within biomolecules. Fluorine also enables assignment of tautomeric states in crystal structures. The differences in experimental pKa values between the isomers was found to arise from solvation effects, providing insight into the polarization and molecular properties of each isomer. Results also encompass 13C and 19F NMR chemical shifts, from both tautomers of 2-fluorohistidine and 4-fluorohistidine in a number of different environments. This work can serve as a guide for interpretation of spectroscopic results in biophysical studies employing 2-fluorohistidine and 4-fluorohistidine.

  19. Molecular profiling of prostate cancer derived exosomes may reveal a predictive signature for response to docetaxel

    PubMed Central

    Kharaziha, Pedram; Chioureas, Dimitris; Rutishauser, Dorothea; Baltatzis, George; Lennartsson, Lena; Fonseca, Pedro; Azimi, Alireza; Hultenby, Kjell; Zubarev, Roman; Ullén, Anders; Yachnin, Jeffrey; Nilsson, Sten; Panaretakis, Theocharis

    2015-01-01

    Docetaxel is a cornerstone treatment for metastatic, castration resistant prostate cancer (CRPC) which remains a leading cause of cancer-related deaths, worldwide. The clinical usage of docetaxel has resulted in modest gains in survival, primarily due to the development of resistance. There are currently no clinical biomarkers available that predict whether a CRPC patient will respond or acquire resistance to this therapy. Comparative proteomics analysis of exosomes secreted from DU145 prostate cancer cells that are sensitive (DU145 Tax-Sen) or have acquired resistance (DU145 Tax-Res) to docetaxel, demonstrated significant differences in the amount of exosomes secreted and in their molecular composition. A panel of proteins was identified by proteomics to be differentially enriched in DU145 Tax-Res compared to DU145 Tax-Sen exosomes and was validated by western blotting. Importantly, we identified MDR-1, MDR-3, Endophilin-A2 and PABP4 that were enriched only in DU145 Tax-Res exosomes. We validated the presence of these proteins in the serum of a small cohort of patients. DU145 cells that have uptaken DU145 Tax-Res exosomes show properties of increased matrix degradation. In summary, exosomes derived from DU145 Tax-Res cells may be a valuable source of biomarkers for response to therapy. PMID:25844599

  20. The Biophysical Probes 2-fluorohistidine and 4-fluorohistidine: Spectroscopic Signatures and Molecular Properties

    PubMed Central

    Kasireddy, Chandana; Ellis, Jonathan M.; Bann, James G.; Mitchell-Koch, Katie R.

    2017-01-01

    Fluorinated amino acids serve as valuable biological probes, by reporting on local protein structure and dynamics through 19F NMR chemical shifts. 2-fluorohistidine and 4-fluorohistidine, studied here with DFT methods, have even more capabilities for biophysical studies, as their altered pKa values, relative to histidine, allow for studies of the role of proton transfer and tautomeric state in enzymatic mechanisms. Considering the two tautomeric forms of histidine, it was found that 2-fluorohistidine primarily forms the common (for histidine) τ-tautomer at neutral pH, while 4-fluorohistidine exclusively forms the less common π-tautomer. This suggests the two isomers of fluorohistidine can also serve as probes of tautomeric form within biomolecules, both by monitoring NMR chemical shifts and by potential perturbation of the tautomeric equilibrium within biomolecules. Fluorine also enables assignment of tautomeric states in crystal structures. The differences in experimental pKa values between the isomers was found to arise from solvation effects, providing insight into the polarization and molecular properties of each isomer. Results also encompass 13C and 19F NMR chemical shifts, from both tautomers of 2-fluorohistidine and 4-fluorohistidine in a number of different environments. This work can serve as a guide for interpretation of spectroscopic results in biophysical studies employing 2-fluorohistidine and 4-fluorohistidine. PMID:28198426

  1. Molecular modeling, spectroscopic signature and NBO analysis of some building blocks of organic conductors.

    PubMed

    Mukherjee, V

    2014-11-11

    Vibrational spectra with IR and Raman intensities in optimum state have been calculated for 2,2'-Bi-1,3-diselenole (commonly known as tetraselenafulvalene) and its halogen derivatives. All these calculations have been done by employing density functional theory (DFT) and second order Moller-Plesset perturbation theory (MP2) methods incorporated with suitable functionals and basis sets. Normal coordinate analysis has also been performed to calculate potential energy distributions (PEDs) to make a conspicuous assignment. The vibrational frequencies of all the four molecules have been assigned using PEDs and the results are compared with available values for the most similar molecules like tetrathiafulvalene. The molecular stability and bond strength have investigated by applying the Natural Bond Orbital (NBO) analysis. The energy gap between HOMO and LUMO is 2.041 eV for tetraselenafulvalene and it is slightly less than 2eV for halogen derivatives which implies that these molecules fall in the wide band gap semiconductor groups.

  2. Nuclear RNA-seq of single neurons reveals molecular signatures of activation.

    PubMed

    Lacar, Benjamin; Linker, Sara B; Jaeger, Baptiste N; Krishnaswami, Suguna; Barron, Jerika; Kelder, Martijn; Parylak, Sarah; Paquola, Apuã; Venepally, Pratap; Novotny, Mark; O'Connor, Carolyn; Fitzpatrick, Conor; Erwin, Jennifer; Hsu, Jonathan Y; Husband, David; McConnell, Michael J; Lasken, Roger; Gage, Fred H

    2016-04-19

    Single-cell sequencing methods have emerged as powerful tools for identification of heterogeneous cell types within defined brain regions. Application of single-cell techniques to study the transcriptome of activated neurons can offer insight into molecular dynamics associated with differential neuronal responses to a given experience. Through evaluation of common whole-cell and single-nuclei RNA-sequencing (snRNA-seq) methods, here we show that snRNA-seq faithfully recapitulates transcriptional patterns associated with experience-driven induction of activity, including immediate early genes (IEGs) such as Fos, Arc and Egr1. SnRNA-seq of mouse dentate granule cells reveals large-scale changes in the activated neuronal transcriptome after brief novel environment exposure, including induction of MAPK pathway genes. In addition, we observe a continuum of activation states, revealing a pseudotemporal pattern of activation from gene expression alone. In summary, snRNA-seq of activated neurons enables the examination of gene expression beyond IEGs, allowing for novel insights into neuronal activation patterns in vivo.

  3. Nuclear RNA-seq of single neurons reveals molecular signatures of activation

    PubMed Central

    Lacar, Benjamin; Linker, Sara B.; Jaeger, Baptiste N.; Krishnaswami, Suguna; Barron, Jerika; Kelder, Martijn; Parylak, Sarah; Paquola, Apuã; Venepally, Pratap; Novotny, Mark; O'Connor, Carolyn; Fitzpatrick, Conor; Erwin, Jennifer; Hsu, Jonathan Y.; Husband, David; McConnell, Michael J.; Lasken, Roger; Gage, Fred H.

    2016-01-01

    Single-cell sequencing methods have emerged as powerful tools for identification of heterogeneous cell types within defined brain regions. Application of single-cell techniques to study the transcriptome of activated neurons can offer insight into molecular dynamics associated with differential neuronal responses to a given experience. Through evaluation of common whole-cell and single-nuclei RNA-sequencing (snRNA-seq) methods, here we show that snRNA-seq faithfully recapitulates transcriptional patterns associated with experience-driven induction of activity, including immediate early genes (IEGs) such as Fos, Arc and Egr1. SnRNA-seq of mouse dentate granule cells reveals large-scale changes in the activated neuronal transcriptome after brief novel environment exposure, including induction of MAPK pathway genes. In addition, we observe a continuum of activation states, revealing a pseudotemporal pattern of activation from gene expression alone. In summary, snRNA-seq of activated neurons enables the examination of gene expression beyond IEGs, allowing for novel insights into neuronal activation patterns in vivo. PMID:27090946

  4. Molecular Signatures of Nicotinoid-Pathogen Synergy in the Termite Gut

    PubMed Central

    Sen, Ruchira; Raychoudhury, Rhitoban; Cai, Yunpeng; Sun, Yijun; Lietze, Verena-Ulrike; Peterson, Brittany F.; Scharf, Michael E.; Boucias, Drion G.

    2015-01-01

    Previous studies in lower termites revealed unexpected synergies between nicotinoid insecticides and fungal entomopathogens. The present study investigated molecular mechanisms of nicotinoid-pathogen synergy in the lower termite Reticulitermes flavipes, using the nicotinoid, imidacloprid, in combination with fungal and bacterial entomopathogens. Particular focus was placed on metatranscriptome composition and microbial dynamics in the symbiont-rich termite gut, which houses diverse mixes of protists and bacteria. cDNA microarrays containing a mix of host and protist symbiont oligonucleotides were used to simultaneously assess termite and protist gene expression. Five treatments were compared that included single challenges with sublethal doses of fungi (Metharizium anisopliae), bacteria (Serratia marcescens) or imidacloprid, and dual challenges with fungi + imidacloprid or bacteria + imidacloprid. Our findings point towards protist dysbiosis and compromised social behavior, rather than suppression of stereotypical immune defense mechanisms, as the dominant factors underlying nicotinoid-pathogen synergy in termites. Also, greater impacts observed for the fungal pathogen than for the bacterial pathogen suggest that the rich bacterial symbiont community in the R. flavipes gut (>5000 species-level phylotypes) exists in an ecological balance that effectively excludes exogenous bacterial pathogens. These findings significantly advance our understanding of antimicrobial defenses in this important eusocial insect group, as well as provide novel insights into how nicotinoids can exert deleterious effects on social insect colonies. PMID:25837376

  5. Molecular Signature of HPV-Induced Carcinogenesis: pRb, p53 and Gene Expression Profiling

    PubMed Central

    Buitrago-Pérez, Águeda; Garaulet, Guillermo; Vázquez-Carballo, Ana; Paramio, Jesús M; García-Escudero, Ramón

    2009-01-01

    The infection by mucosal human papillomavirus (HPV) is causally associated with tumor development in cervix and oropharynx. The mechanisms responsible for this oncogenic potential are mainly due to the product activities of two early viral oncogenes: E6 and E7. Although a large number of cellular targets have been described for both oncoproteins, the interaction with tumor suppressors p53 and retinoblastoma protein (pRb) emerged as the key functional activities. E6 degrades tumor suppressor p53, thus inhibiting p53-dependent functions, whereas E7 binds and degrades pRb, allowing the transcription of E2F-dependent genes. Since these two tumor suppressors exert their actions through transcriptional modulation, functional genomics has provided a large body of data that reflects the altered gene expression of HPVinfected cells or tissues. Here we will review the similarities and differences of these findings, and we also compare them with those obtained with transgenic mouse models bearing the deletion of some of the viral oncogene targets. The comparative analysis supports molecular evidences about the role of oncogenes E6 and E7 in the interference with the mentioned cellular functions, and also suggests that the mentioned transgenic mice can be used as models for HPV-associated diseases such as human cervical, oropharynx, and skin carcinomas. PMID:19721808

  6. Molecular Signature of HPV-Induced Carcinogenesis: pRb, p53 and Gene Expression Profiling.

    PubMed

    Buitrago-Pérez, Agueda; Garaulet, Guillermo; Vázquez-Carballo, Ana; Paramio, Jesús M; García-Escudero, Ramón

    2009-03-01

    The infection by mucosal human papillomavirus (HPV) is causally associated with tumor development in cervix and oropharynx. The mechanisms responsible for this oncogenic potential are mainly due to the product activities of two early viral oncogenes: E6 and E7. Although a large number of cellular targets have been described for both oncoproteins, the interaction with tumor suppressors p53 and retinoblastoma protein (pRb) emerged as the key functional activities. E6 degrades tumor suppressor p53, thus inhibiting p53-dependent functions, whereas E7 binds and degrades pRb, allowing the transcription of E2F-dependent genes. Since these two tumor suppressors exert their actions through transcriptional modulation, functional genomics has provided a large body of data that reflects the altered gene expression of HPVinfected cells or tissues. Here we will review the similarities and differences of these findings, and we also compare them with those obtained with transgenic mouse models bearing the deletion of some of the viral oncogene targets. The comparative analysis supports molecular evidences about the role of oncogenes E6 and E7 in the interference with the mentioned cellular functions, and also suggests that the mentioned transgenic mice can be used as models for HPV-associated diseases such as human cervical, oropharynx, and skin carcinomas.

  7. Mining the mouse transcriptome of receptive endometrium reveals distinct molecular signatures for the luminal and glandular epithelium.

    PubMed

    Niklaus, Andrea L; Pollard, Jeffrey W

    2006-07-01

    Epithelia coat most tissues where they sense and respond to the environment and participate in innate immune responses. In the adult mouse uterus, columnar epithelium lines the central lumen and the glands that penetrate the underlying stroma. A nidatory surge of estrogen causes differentiation of the luminal epithelium to the receptive state that permits blastocyst attachment and allows subsequent implantation. Here, using laser-capture microdissection to isolate the luminal and glandular epithelia separately, we have profiled gene expression 2 h before embryo attachment to determine whether there are unique roles for these two epithelial structures in this process. Although most genes were expressed in both compartments, there was greater expression of 153 and 118 genes in the lumen and glands, respectively. In the luminal epithelium, there is enrichment in lipid, metal-ion binding, and carbohydrate-metabolizing enzymes, whereas in the glands, immune response genes are emphasized. In situ hybridization to uterine sections obtained from mice during the preimplantation period validated these data and indicated an array of previously undocumented genes expressed with unique patterns in these epithelia. The data show that each epithelial compartment has a distinct molecular signature and that they act differentially and synergistically to permit blastocyst implantation.

  8. Vibrational signatures of cation-anion hydrogen bonding in ionic liquids: a periodic density functional theory and molecular dynamics study.

    PubMed

    Mondal, Anirban; Balasubramanian, Sundaram

    2015-02-05

    Hydrogen bonding in alkylammonium based protic ionic liquids was studied using density functional theory (DFT) and ab initio molecular dynamics (AIMD) simulations. Normal-mode analysis within the harmonic approximation and power spectra of velocity autocorrelation functions were used as tools to obtain the vibrational spectra in both the gas phase and the crystalline phases of these protic ionic liquids. The hydrogen bond vibrational modes were identified in the 150-240 cm(-1) region of the far-infrared (far-IR) spectra. A blue shift in the far-IR mode was observed with an increasing number of hydrogen-bonding sites on the cation; the exact peak position is modulated by the cation-anion hydrogen bond strength. Sub-100 cm(-1) bands in the far-IR spectrum are assigned to the rattling motion of the anions. Calculated NMR chemical shifts of the acidic protons in the crystalline phase of these salts also exhibit the signature of cation-anion hydrogen bonding.

  9. A patient-derived, pan-cancer EMT signature identifies global molecular alterations and immune target enrichment following epithelial to mesenchymal transition

    PubMed Central

    Mak, Milena P.; Tong, Pan; Diao, Lixia; Cardnell, Robert J.; Gibbons, Don L.; William, William N.; Skoulidis, Ferdinandos; Parra, Edwin R.; Rodriguez-Canales, Jaime; Wistuba, Ignacio I.; Heymach, John V.; Weinstein, John N.; Coombes, Kevin R.; Wang, Jing; Byers, Lauren Averett

    2015-01-01

    Purpose We previously demonstrated the association between epithelial-to-mesenchymal transition (EMT) and drug response in lung cancer using an EMT signature derived in cancer cell lines. Given the contribution of tumor microenvironments to EMT, we extended our investigation of EMT to patient tumors from 11 cancer types to develop a pan-cancer EMT signature. Experimental Design Using the pan-cancer EMT signature, we conducted an integrated, global analysis of genomic and proteomic profiles associated with EMT across 1,934 tumors including breast, lung, colon, ovarian, and bladder cancers. Differences in outcome and in vitro drug response corresponding to expression of the pan-cancer EMT signature were also investigated. Results Compared to the lung cancer EMT signature, the patient-derived, pan-cancer EMT signature encompasses a set of core EMT genes that correlate even more strongly with known EMT markers across diverse tumor types and identifies differences in drug sensitivity and global molecular alterations at the DNA, RNA, and protein levels. Among those changes associated with EMT, pathway analysis revealed a strong correlation between EMT and immune activation. Further supervised analysis demonstrated high expression of immune checkpoints and other druggable immune targets such as PD1, PD-L1, CTLA4, OX40L, and PDL2, in tumors with the most mesenchymal EMT scores. Elevated PD-L1 protein expression in mesenchymal tumors was confirmed by immunohistochemistry in an independent lung cancer cohort. Conclusions This new signature provides a novel, patient-based, histology-independent tool for the investigation of EMT and offers insights into potential novel therapeutic targets for mesenchymal tumors, independent of cancer type, including immune checkpoints. PMID:26420858

  10. A molecular signature of normal breast epithelial and stromal cells from Li-Fraumeni syndrome mutation carriers

    PubMed Central

    Herbert, Brittney-Shea; Chanoux, Rebecca A.; Liu, Yunlong; Baenziger, Peter H.; Goswami, Chirayu P.; McClintick, Jeanette N.; Edenberg, Howard J.; Pennington, Robert E.; Lipkin, Steven M.; Kopelovich, Levy

    2010-01-01

    Specific changes in gene expression during cancer initiation should enable discovery of biomarkers for risk assessment, early detection and targets for chemoprevention. It has been previously demonstrated that altered mRNA and proteome signatures of morphologically normal cells bearing a single inherited “hit” in a tumor suppressor gene parallel many changes observed in the corresponding sporadic cancer. Here, we report on the global gene expression profile of morphologically normal, cultured primary breast epithelial and stromal cells from Li-Fraumeni syndrome (LFS) TP53 mutation carriers. Our analyses identified multiple changes in gene expression in both morphologically normal breast epithelial and stromal cells associated with TP53 haploinsufficiency, as well as interlocking pathways. Notably, a dysregulated p53 signaling pathway was readily detectable. Pharmacological intervention with the p53 rescue compounds CP-31398 and PRIMA-1 provided further evidence in support of the central role of p53 in affecting these changes in LFS cells and treatment for this cancer. Because loss of signaling mediated by TP53 is associated with the development and survival of many human tumors, identification of gene expression profiles in morphologically normal cells that carry “one-hit” p53 mutations may reveal novel biomarkers, enabling the discovery of potential targets for chemoprevention of sporadic tumors as well. PMID:21311097

  11. Molecular signature of salivary gland tumors: potential use as diagnostic and prognostic marker.

    PubMed

    Fonseca, Felipe Paiva; Sena Filho, Marcondes; Altemani, Albina; Speight, Paul M; Vargas, Pablo Agustin

    2016-02-01

    Salivary gland tumors are a highly heterogeneous group of lesions with diverse microscopic appearances and variable clinical behavior. The use of clinical and histological parameters to predict patient prognosis and survival rates has been of limited utility, and the search for new biomarkers that could not only aid in a better understanding of their pathogenesis but also be reliable auxiliaries for prognostic determination and useful diagnostic tools has been performed in the last decades with very exciting results. Hence, gene rearrangements such as CRTC1-MAML2 in mucoepidermoid carcinomas have shown excellent specificity, and more than that, it has been strongly correlated with low-grade tumors and consequently with an increased survival rate and better prognosis of patients affected by neoplasms carrying this translocation. Moreover, MYB-NFIB and EWSR1-ATF1 gene fusions were shown to be specifically found in cases of adenoid cystic carcinomas and hyalinizing clear cell carcinomas, respectively, in the context of salivary gland tumors, becoming reliable diagnostic tools for these entities and potential therapeutic targets for future therapeutic protocols. Finally, the identification of ETV6-NTRK3 in cases previously diagnosed as uncommon acinic cell carcinomas, cystadenocarcinomas, and adenocarcinomas not otherwise specified led to the characterization of a completely new and now widely accepted entity, including, therefore, mammary analogue secretory carcinoma in the list of well-recognized salivary gland carcinomas. Thus, further molecular investigations of salivary gland tumors are warranted, and the recognition of other genetic abnormalities can lead to the acknowledgment of new entities and the acquirement of reliable biomarkers.

  12. Antirheumatic drug response signatures in human chondrocytes: potential molecular targets to stimulate cartilage regeneration

    PubMed Central

    Andreas, Kristin; Häupl, Thomas; Lübke, Carsten; Ringe, Jochen; Morawietz, Lars; Wachtel, Anja; Sittinger, Michael; Kaps, Christian

    2009-01-01

    treatment with NSAIDs and the DMARD chloroquine phosphate had only moderate to minor effects. Treatment with the DMARDs azathioprine, gold sodium thiomalate, and methotrexate efficiently reverted chondrocyte RA-related gene expression toward the 'healthy' level. Pathways of cytokine-cytokine receptor interaction, transforming growth factor-beta/Toll-like receptor/Jak-STAT (signal transducer and activator of transcription) signalling and extracellular matrix receptor interaction were targeted by antirheumatics. Conclusions Our findings indicate that RA-relevant stimuli result in the molecular activation of catabolic and inflammatory processes in human chondrocytes that are reverted by antirheumatic treatment. Candidate genes that evolved in this study for new therapeutic approaches include suppression of specific immune responses (COX-2, IL-23A, and IL-6) and activation of cartilage regeneration (CTGF and CYR-61). PMID:19192274

  13. Characterization of key transcription factors as molecular signatures of HPV-positive and HPV-negative oral cancers.

    PubMed

    Verma, Gaurav; Vishnoi, Kanchan; Tyagi, Abhishek; Jadli, Mohit; Singh, Tejveer; Goel, Ankit; Sharma, Ankita; Agarwal, Kiran; Prasad, Subhash Chandra; Pandey, Durgatosh; Sharma, Shashi; Mehrotra, Ravi; Singh, Sukh Mahendra; Bharti, Alok Chandra

    2017-03-01

    Prior studies established constitutively active AP-1, NF-κB, and STAT3 signaling in oral cancer. Differential expression/activation of specific members of these transcription factors has been documented in HPV-positive oral lesions that respond better to therapy. We performed a comprehensive analysis of differentially expressed, transcriptionally active members of these pivotal signaling mediators to develop specific signatures of HPV-positive and HPV-negative oral lesions by immunohistochemical method that is applicable in low-resource settings. We examined a total of 31 prospective and 30 formalin-fixed, paraffin-embedded tissues from treatment-naïve, histopathologically and clinically confirmed cases diagnosed as oral or oropharyngeal squamous cell carcinoma (OSCC/OPSCC). Following determination of their HPV status by GP5 + /GP6 +  PCR, the sequential sections of the tissues were evaluated for expression of JunB, JunD, c-Fos, p50, p65, STAT3, and pSTAT3(Y705), along with two key regulatory proteins pEGFR and p16 by IHC. Independent analysis of JunB and p65 showed direct correlation with HPV positivity, whereas STAT3 and pSTAT3 were inversely correlated. A combined analysis of transcription factors revealed a more restrictive combination, characterized by the presence of AP-1 and NF-κB lacking involvement of STAT3 that strongly correlated with HPV-positive tumors. Presence of STAT3/pSTAT3 with NF-κB irrespective of the presence or absence of AP-1 members was present in HPV-negative lesions. Expression of pSTAT3 strongly correlated with all the AP-1/NF-κB members (except JunD), its upstream activator pEGFR(Y)(1092) , and HPV infection-related negative regulator p16. Overall, we show a simple combination of AP-1, NF-κB, and STAT3 members' expression that may serve as molecular signature of HPV-positive lesions or more broadly the tumors that show better prognosis.

  14. Molecular signatures (conserved indels) in protein sequences that are specific for the order Pasteurellales and distinguish two of its main clades.

    PubMed

    Naushad, Hafiz Sohail; Gupta, Radhey S

    2012-01-01

    The members of the order Pasteurellales are currently distinguished primarily on the basis of their branching in the rRNA trees and no convincing biochemical or molecular markers are known that distinguish them from all other bacteria. The genome sequences for 20 Pasteurellaceae species/strains are now publicly available. We report here detailed analyses of protein sequences from these genomes to identify conserved signature indels (CSIs) that are specific for either all Pasteurellales or its major clades. We describe more than 23 CSIs in widely distributed genes/proteins that are uniquely shared by all sequenced Pasteurellaceae species/strains but are not found in any other bacteria. Twenty-one additional CSIs are also specific for the Pasteurellales except in some of these cases homologues were not detected in a few species or the CSI was also present in an isolated non-Pasteurellaceae species. The sequenced Pasteurellaceae species formed two distinct clades in a phylogenetic tree based upon concatenated sequences for 10 conserved proteins. The first of these clades consisting of Aggregatibacter, Pasteurella, Actinobacillus succinogenes, Mannheimia succiniciproducens, Haemophilus influenzae and Haemophilus somnus was also independently supported by 13 uniquely shared CSIs that are not present in other Pasteurellaceae species or other bacteria. Another clade consisting of the remaining Pasteurellaceae species (viz. Actinobacillus pleuropneumoniae, Actinobacillus minor, Haemophilus ducryi, Mannheimia haemolytica and Haemophilus parasuis) was also strongly and independently supported by nine CSIs that are uniquely present in these bacteria. The order Pasteurellales is presently made up of a single family, Pasteurellaceae, that encompasses all of its genera. In this context, our identification of two distinct clades within the Pasteurellales, which are supported by both phylogenetic analyses and by multiple highly specific molecular markers, strongly argues for and

  15. Molecular Signatures of Natural Selection for Polymorphic Genes of the Human Dopaminergic and Serotonergic Systems: A Review

    PubMed Central

    Taub, Daniel R.; Page, Joshua

    2016-01-01

    A large body of research has examined the behavioral and mental health consequences of polymorphisms in genes of the dopaminergic and serotonergic systems. Along with this, there has been considerable interest in the possibility that these polymorphisms have developed and/or been maintained due to the action of natural selection. Episodes of natural selection on a gene are expected to leave molecular “footprints” in the DNA sequences of the gene and adjacent genomic regions. Here we review the research literature investigating molecular signals of selection for genes of the dopaminergic and serotonergic systems. The gene SLC6A4, which codes for a serotonin transport protein, was the one gene for which there was consistent support from multiple studies for a selective episode. Positive selection on SLC6A4 appears to have been initiated ∼ 20–25,000 years ago in east Asia and possibly in Europe. There are scattered reports of molecular signals of selection for other neurotransmitter genes, but these have generally failed at replication across studies. In spite of speculation in the literature about selection on these genes, current evidence from population genomic analyses supports selectively neutral processes, such as genetic drift and population dynamics, as the principal drivers of recent evolution in dopaminergic and serotonergic genes other than SLC6A4. PMID:27375535

  16. Phylogenetic analysis of canine distemper virus in South America clade 1 reveals unique molecular signatures of the local epidemic.

    PubMed

    Fischer, Cristine D B; Gräf, Tiago; Ikuta, Nilo; Lehmann, Fernanda K M; Passos, Daniel T; Makiejczuk, Aline; Silveira, Marcos A T; Fonseca, André S K; Canal, Cláudio W; Lunge, Vagner R

    2016-07-01

    Canine distemper virus (CDV) is a highly contagious pathogen for domestic dogs and several wild carnivore species. In Brazil, natural infection of CDV in dogs is very high due to the large non-vaccinated dog population, a scenario that calls for new studies on the molecular epidemiology. This study investigates the phylodynamics and amino-acid signatures of CDV epidemic in South America by analyzing a large dataset compiled from publicly available sequences and also by collecting new samples from Brazil. A population of 175 dogs with canine distemper (CD) signs was sampled, from which 89 were positive for CDV, generating 42 new CDV sequences. Phylogenetic analysis of the new and publicly available sequences revealed that Brazilian sequences mainly clustered in South America 1 (SA1) clade, which has its origin estimated to the late 1980's. The reconstruction of the demographic history in SA1 clade showed an epidemic expanding until the recent years, doubling in size every nine years. SA1 clade epidemic distinguished from the world CDV epidemic by the emergence of the R580Q strain, a very rare and potentially detrimental substitution in the viral genome. The R580Q substitution was estimated to have happened in one single evolutionary step in the epidemic history in SA1 clade, emerging shortly after introduction to the continent. Moreover, a high prevalence (11.9%) of the Y549H mutation was observed among the domestic dogs sampled here. This finding was associated (p<0.05) with outcome-death and higher frequency in mixed-breed dogs, the later being an indicator of a continuous exchange of CDV strains circulating among wild carnivores and domestic dogs. The results reported here highlight the diversity of the worldwide CDV epidemic and reveal local features that can be valuable for combating the disease.

  17. Ectomycorrhizal fungi increase soil carbon storage: molecular signatures of mycorrhizal competition driving soil C storage at global scale

    NASA Astrophysics Data System (ADS)

    Averill, C.; Barry, B. K.; Hawkes, C.

    2015-12-01

    Soil carbon storage and decay is regulated by the activity of free-living decomposer microbes, which can be limited by nitrogen availability. Many plants associate with symbiotic ectomycorrhizal fungi on their roots, which produce nitrogen-degrading enzymes and may be able to compete with free-living decomposers for soil organic nitrogen. By doing so, ectomycorrhizal fungi may able to induce nitrogen limitation and reduce activity of free-living microbial decomposition by mining soil organic nitrogen. The implication is that ectomycorrhizal-dominated systems should have increased soil carbon storage relative to non-ectomycorrhizal systems, which has been confirmed at a global scale. To investigate these effects, we analyzed 364 globally distributed observations of soil fungal communities using 454 sequencing of the ITS region, along with soil C and N concentrations, climate and chemical data. We assigned operational taxonomic units using the QIIME pipeline and UNITE fungal database and assigned fungal reads as ectomycorrhizal or non-mycorrhizal based on current taxonomic knowledge. We tested for associations between ectomycorrhizal abundance, climate, and soil carbon and nitrogen. Sites with greater soil carbon had quantitatively more ectomycorrhizal fungi within the soil microbial community based on fungal sequence abundance, after accounting for soil nitrogen availability. This is consistent with our hypothesis that ectomycorrhizal fungi induce nitrogen-limitation of free-living decomposers and thereby increase soil carbon storage. The strength of the mycorrhizal effect increased non-linearly with ectomycorrhizal abundance: the greater the abundance, the greater the effect size. Mean annual temperature, potential evapotranspiration, soil moisture and soil pH were also significant predictors in the final AIC selected model. This analysis suggests that molecular data on soil microbial communities can be used to make quantitative biogeochemical predictions. The

  18. Detection of molecular signatures of oral squamous cell carcinoma and normal epithelium – application of a novel methodology for unsupervised segmentation of imaging mass spectrometry data

    PubMed Central

    Mrukwa, Grzegorz; Kalinowska, Magdalena; Pietrowska, Monika; Chekan, Mykola; Wierzgon, Janusz; Gawin, Marta; Drazek, Grzegorz; Polanska, Joanna

    2016-01-01

    Intra‐tumor heterogeneity is a vivid problem of molecular oncology that could be addressed by imaging mass spectrometry. Here we aimed to assess molecular heterogeneity of oral squamous cell carcinoma and to detect signatures discriminating normal and cancerous epithelium. Tryptic peptides were analyzed by MALDI‐IMS in tissue specimens from five patients with oral cancer. Novel algorithm of IMS data analysis was developed and implemented, which included Gaussian mixture modeling for detection of spectral components and iterative k‐means algorithm for unsupervised spectra clustering performed in domain reduced to a subset of the most dispersed components. About 4% of the detected peptides showed significantly different abundances between normal epithelium and tumor, and could be considered as a molecular signature of oral cancer. Moreover, unsupervised clustering revealed two major sub‐regions within expert‐defined tumor areas. One of them showed molecular similarity with histologically normal epithelium. The other one showed similarity with connective tissue, yet was markedly different from normal epithelium. Pathologist's re‐inspection of tissue specimens confirmed distinct features in both tumor sub‐regions: foci of actual cancer cells or cancer microenvironment‐related cells prevailed in corresponding areas. Hence, molecular differences detected during automated segmentation of IMS data had an apparent reflection in real structures present in tumor. PMID:27168173

  19. A Simple and Convenient Method of Multiple Linear Regression to Calculate Iodine Molecular Constants

    ERIC Educational Resources Information Center

    Cooper, Paul D.

    2010-01-01

    A new procedure using a student-friendly least-squares multiple linear-regression technique utilizing a function within Microsoft Excel is described that enables students to calculate molecular constants from the vibronic spectrum of iodine. This method is advantageous pedagogically as it calculates molecular constants for ground and excited…

  20. Unique molecular signatures as a hallmark of patients with metastatic breast cancer: implications for current treatment paradigms.

    PubMed

    Wheler, Jennifer J; Parker, Barbara A; Lee, Jack J; Atkins, Johnique T; Janku, Filip; Tsimberidou, Apostolia M; Zinner, Ralph; Subbiah, Vivek; Fu, Siqing; Schwab, Richard; Moulder, Stacy; Valero, Vicente; Schwaederle, Maria; Yelensky, Roman; Miller, Vincent A; Stephens, M Philip J; Meric-Bernstam, Funda; Kurzrock, Razelle

    2014-05-15

    Our analysis of the tumors of 57 women with metastatic breast cancer with next generation sequencing (NGS) demonstrates that each patient's tumor is unique in its molecular fingerprint. We observed 216 somatic aberrations in 70 different genes, including 131 distinct aberrations. The most common gene alterations (in order of decreasing frequency) included: TP53, PIK3CA, CCND1, MYC, HER2 (ERBB2), MCL1, PTEN, FGFR1, GATA3, NF1, PIK3R1, BRCA2, EGFR, IRS2, CDH1, CDKN2A, FGF19, FGF3 and FGF4. Aberrations included mutations (46%), amplifications (45%), deletions (5%), splices (2%), truncations (1%), fusions (0.5%) and rearrangements (0.5%), with multiple distinct variants within the same gene. Many of these aberrations represent druggable targets, either through direct pathway inhibition or through an associated pathway (via 'crosstalk'). The 'molecular individuality' of these tumors suggests that a customized strategy, using an "N-of-One" model of precision medicine, may represent an optimal approach for the treatment of patients with advanced tumors.

  1. Multiple Point Dynamic Gas Density Measurements Using Molecular Rayleigh Scattering

    NASA Technical Reports Server (NTRS)

    Seasholtz, Richard; Panda, Jayanta

    1999-01-01

    A nonintrusive technique for measuring dynamic gas density properties is described. Molecular Rayleigh scattering is used to measure the time-history of gas density simultaneously at eight spatial locations at a 50 kHz sampling rate. The data are analyzed using the Welch method of modified periodograms to reduce measurement uncertainty. Cross-correlations, power spectral density functions, cross-spectral density functions, and coherence functions may be obtained from the data. The technique is demonstrated using low speed co-flowing jets with a heated inner jet.

  2. Notch signaling deregulation in multiple myeloma: A rational molecular target

    PubMed Central

    Garavelli, Silvia; Platonova, Natalia; Paoli, Alessandro; Basile, Andrea; Taiana, Elisa; Neri, Antonino; Chiaramonte, Raffaella

    2015-01-01

    Despite recent therapeutic advances, multiple myeloma (MM) is still an incurable neoplasia due to intrinsic or acquired resistance to therapy. Myeloma cell localization in the bone marrow milieu allows direct interactions between tumor cells and non-tumor bone marrow cells which promote neoplastic cell growth, survival, bone disease, acquisition of drug resistance and consequent relapse. Twenty percent of MM patients are at high-risk of treatment failure as defined by tumor markers or presentation as plasma cell leukemia. Cumulative evidences indicate a key role of Notch signaling in multiple myeloma onset and progression. Unlike other Notch-related malignancies, where the majority of patients carry gain-of-function mutations in Notch pathway members, in MM cell Notch signaling is aberrantly activated due to an increased expression of Notch receptors and ligands; notably, this also results in the activation of Notch signaling in surrounding stromal cells which contributes to myeloma cell proliferation, survival and migration, as well as to bone disease and intrinsic and acquired pharmacological resistance. Here we review the last findings on the mechanisms and the effects of Notch signaling dysregulation in MM and provide a rationale for a therapeutic strategy aiming at inhibiting Notch signaling, along with a complete overview on the currently available Notch-directed approaches. PMID:26308486

  3. Multiple molecular and neuropharmacological effects of MDMA (Ecstasy).

    PubMed

    Simantov, Rabi

    2004-01-02

    3,4-Methylenedioxymethamphetamine (MDMA), commonly referred to as Ecstasy, is a widely abused, psychoactive recreational drug, which induces short- and long-term neuropsychiatric behaviors. This drug is neurotoxic to serotonergic neurons in vivo, and induces programmed cell death in cultured human serotonergic cells and rat neocortical neurons. Over the years it has been shown that MDMA alters the release of several neurotransmitters in the brain, it induces recompartmentation of intracellular serotonin and c-fos, and modifies the expression of a few genes. Recently, we observed changes in gene expression in mice treated with MDMA, and cloned and sequenced 11 cDNAs thus affected (4 correspond to known and 7 to unknown genes). The effect of MDMA on two of these genes, GABA transporter 1 and synaptotagmin IV was studied in detail. Characterization of the relationship between a given gene and certain physiological or behavioral effects of MDMA could shed light on the mechanism of the drug's action. However, establishing such a connection is difficult for several reasons, including that serotonergic neurons are not the only cells affected by MDMA. In this review, molecular and neurochemical events that occur in the brain following exposure to MDMA, and link between the observed molecular changes with known physiological effects of the drug are discussed. It is indicated that MDMA alters the expression of several proteins involved in GABA neurotransmission, thus having critical effect on thermoregulation and MDMA acute toxicity. This analysis should facilitate development of novel approaches to prevent deleterious effects, especially mortality induced by MDMA and other abused psychostimulants.

  4. Molecular Genetic and Epigenetic Basis of Multiple Sclerosis.

    PubMed

    Hojati, Zohreh

    2017-01-01

    Multiple Sclerosis (MS) is a chronic immune-mediated disease of spinal cord and brain. The initial event in MS occurs when activated CD4(+) T cells in periphery exacerbates immune responses by stimulating immune cells such as B cells, CD8(+) cells, mast cells, granulocytes and monocytes. These proinflammatory cells pass blood brain barrier by secreting proinflammatory cytokines including TNF-α and INF-γ which activate adhesion factors. APCs (antigen-presenting cells) reactivate CD4(+) T cells after infiltrating the CNS and CD4(+) T cells produce cytokines and chemokines. These proinflammatory cytokines aggravate inflammation by inducing myelin phagocytosis through microglia and astrocytes activation. MS is believed to have a multifactorial origin that includes a combination of multiple genetic, environmental and stochastic factors. Although the exact component of MS risks that can be explained by these factors is difficult to determine, estimates based on genetic and epidemiological studies suggest that up to 60-70 % of the total risk of MS may be contribute to genetic factors. In continue, firstly we provide an overview of the current understanding of epigenetic mechanisms, and so present evidence of how the epigenetic modifications contribute to increased susceptibility of MS. We also explain how specified epigenetic modifications may influence the pathophysiology and key aspects of disease in MS (demyelination, remyelination, inflammation, and neurodegeneration). Finally, we tend to discuss how environmental factors and epigenetic mechanisms may interact to have an effect on MS risk and clinical outcome and recommend new therapeutic interventions that might modulate patients' epigenetic profiles.

  5. The PAX2-null immunophenotype defines multiple lineages with common expression signatures in benign and neoplastic oviductal epithelium

    PubMed Central

    Ning, Gang; Bijron, Jonathan G.; Yamamoto, Yusuke; Wang, Xia; Howitt, Brooke E.; Herfs, Michael; Yang, Eric; Hong, Yue; Cornille, Maxence; Wu, Lingyan; Hanamornroongruang, Suchanan; McKeon, Frank D.; Crum, Christopher P.; Xian, Wa

    2014-01-01

    The oviducts contain high grade serous cancer (HGSC) precursors (serous tubal intraepithelial neoplasia or STINs), which are γ-H2AXp- and TP53 mutation-positive. Although they express wild type p53, secretory cell outgrowths (SCOUTs) are associated with older age and serous cancer; moreover both STINs and SCOUTs share a loss of PAX2 expression (PAX2n). We evaluated PAX2 expression in proliferating adult and embryonic oviductal cells, normal mucosa, SCOUTs, Walthard cell nests (WCNs), STINs and HGSCs, and the expression of genes chosen empirically or from SCOUT expression arrays. Clones generated in vitro from embryonic gynecologic tract and adult fallopian tube were Krt7p/PAX2n/EZH2p and underwent ciliated (PAX2n/EZH2n/FOXJ1p) and basal (Krt7n/EZH2n/Krt5p) differentiation. Similarly non-ciliated cells in normal mucosa were PAX2p but became PAX2n in multilayered epithelium undergoing ciliated or basal (Walthard cell nests or WCN) cell differentiation. PAX2n SCOUTs fell into two groups; Type I were secretory or secretory/ciliated with a “tubal” phenotype and were ALDH1n and β-cateninmem (membraneous only). Type II displayed a columnar to pseudostratified (endometrioid) phenotype, with an EZH2p, ALDH1p, β-cateninnc (nuclear and cytoplasmic), stathminp, LEF1p, RCN1p and RUNX2p expression signature. STINs and HGSCs shared the Type I immunophenotype of PAX2n, ALDH1n, β-cateninmem, but highly expressed EZH2p, LEF1p, RCN1p, and stathminp. This study, for the first time, links PAX2n with proliferating fetal and adult oviductal cells undergoing basal and ciliated differentiation and shows that this expression state is maintained in SCOUTs, STINs and HGSCs. All three entities can demonstrate a consistent perturbation of genes involved in potential tumor suppressor gene silencing (EZH2), transcriptional regulation (LEF1), regulation of differentiation (RUNX2), calcium binding (RCN1) and oncogenesis (stathmin). This shared expression signature between benign and

  6. Infrared (1-12 μm) atomic and molecular emission signatures from energetic materials using laser-induced breakdown spectroscopy

    NASA Astrophysics Data System (ADS)

    Kumi Barimah, E.; Hömmerich, U.; Brown, E.; Yang, C. S.-C.; Trivedi, S. B.; Jin, F.; Wijewarnasuriya, P. S.; Samuels, A. C.; Snyder, A. P.

    2013-05-01

    Laser-induced breakdown spectroscopy (LIBS) is a powerful analytical technique to detect the elemental composition of solids, liquids, and gases in real time. For example, recent advances in UV-VIS LIBS have shown great promise for applications in chemical, biological, and explosive sensing. The extension of conventional UVVIS LIBS to the near-IR (NIR), mid-IR (MIR) and long wave infrared (LWIR) regions (~1-12 μm) offers the potential to provide additional information due to IR atomic and molecular signatures. In this work, a Q-switched Nd: YAG laser operating at 1064 nm was employed as the excitation source and focused onto several chlorate and nitrate compounds including KClO3, NaClO3, KNO3, and NaNO3 to produce intense plasma at the target surface. IR LIBS studies on background air, KCl , and NaCl were also included for comparison. All potassium and sodium containing samples revealed narrow-band, atomic-like emissions assigned to transitions of neutral alkali-metal atoms in accordance with the NIST atomic spectra database. In addition, first evidence of broad-band molecular LIBS signatures from chlorate and nitrate compounds were observed at ~10 μm and ~7.3 μm, respectively. The observed molecular emissions showed strong correlation with FTIR absorption spectra of the investigated materials.

  7. Gegenees: fragmented alignment of multiple genomes for determining phylogenomic distances and genetic signatures unique for specified target groups.

    PubMed

    Agren, Joakim; Sundström, Anders; Håfström, Therese; Segerman, Bo

    2012-01-01

    The rapid development of Next Generation Sequencing technologies leads to the accumulation of huge amounts of sequencing data. The scientific community faces an enormous challenge in how to deal with this explosion. Here we present a software tool, 'Gegenees', that uses a fragmented alignment approach to facilitate the comparative analysis of hundreds of microbial genomes. The genomes are fragmented and compared, all against all, by a multithreaded BLAST control engine. Ready-made alignments can be complemented with new genomes without recalculating the existing data points. Gegenees gives a phylogenomic overview of the genomes and the alignment can then be mined for genomic regions with conservation patterns matching a defined target group and absent from a background group. The genomic regions are given biomarker scores forming a uniqueness signature that can be viewed and explored, graphically and in tabular form. A primer/probe alignment tool is also included for specificity verification of currently used or new primers. We exemplify the use of Gegenees on the Bacillus cereus group, on Foot and Mouth Disease Viruses, and on strains from the 2011 Escherichia coli O104:H4 outbreak. Gegenees contributes towards an increased capacity of fast and efficient data mining as more and more genomes become sequenced.

  8. Gegenees: Fragmented Alignment of Multiple Genomes for Determining Phylogenomic Distances and Genetic Signatures Unique for Specified Target Groups

    PubMed Central

    Håfström, Therese; Segerman, Bo

    2012-01-01

    The rapid development of Next Generation Sequencing technologies leads to the accumulation of huge amounts of sequencing data. The scientific community faces an enormous challenge in how to deal with this explosion. Here we present a software tool, ‘Gegenees’, that uses a fragmented alignment approach to facilitate the comparative analysis of hundreds of microbial genomes. The genomes are fragmented and compared, all against all, by a multithreaded BLAST control engine. Ready-made alignments can be complemented with new genomes without recalculating the existing data points. Gegenees gives a phylogenomic overview of the genomes and the alignment can then be mined for genomic regions with conservation patterns matching a defined target group and absent from a background group. The genomic regions are given biomarker scores forming a uniqueness signature that can be viewed and explored, graphically and in tabular form. A primer/probe alignment tool is also included for specificity verification of currently used or new primers. We exemplify the use of Gegenees on the Bacillus cereus group, on Foot and Mouth Disease Viruses, and on strains from the 2011 Escherichia coli O104:H4 outbreak. Gegenees contributes towards an increased capacity of fast and efficient data mining as more and more genomes become sequenced. PMID:22723939

  9. A C(18)O survey of dense cores in the Taurus molecular cloud: Signatures of evolution and protostellar collapse

    NASA Technical Reports Server (NTRS)

    Zhou, Shudong; Evans, Neal J., II; Wang, Yangsheng; Peng, Ruisheng; Lo, K. Y.

    1994-01-01

    We have mapped 11 dense cores in the Taurus molecular cloud in the C(18)O J = 2 goes to 1 line at a linear resolution of 0.02 pc. The core masses derived from C(18)O range from 0.06 to 5 solar mass. Five of them have embedded infrared sources, and six do not. Dense cores without infrared sources show multiple emission peaks. In contrast, dense cores with infrared sources have a single peak and smaller sizes. The cores with infrared sources have line widths that are 2-3 times the value expected from correlations found in previous surveys. This enhancement may be accounted for by models of gravitational collapse. The data are consistent with the idea that dense cores evolve first toward smaller sizes and smaller line width along the line width-size relation, and then toward larger line width and constant or smaller sizes as an infrared source becomes observable. A good collapse candidate, L1527, is identified based on the shapes of C(18)O and H2CO lines.

  10. Noninvasive imaging of multiple myeloma using near infrared fluorescent molecular probe

    NASA Astrophysics Data System (ADS)

    Hathi, Deep; Zhou, Haiying; Bollerman-Nowlis, Alex; Shokeen, Monica; Akers, Walter J.

    2016-03-01

    Multiple myeloma is a plasma cell malignancy characterized by monoclonal gammopathy and osteolytic bone lesions. Multiple myeloma is most commonly diagnosed in late disease stages, presenting with pathologic fracture. Early diagnosis and monitoring of disease status may improve quality of life and long-term survival for multiple myeloma patients from what is now a devastating and fatal disease. We have developed a near-infrared targeted fluorescent molecular probe with high affinity to the α4β1 integrin receptor (VLA-4)overexpressed by a majority of multiple myeloma cells as a non-radioactive analog to PET/CT tracer currently being developed for human diagnostics. A near-infrared dye that emits about 700 nm was conjugated to a high affinity peptidomimmetic. Binding affinity and specificity for multiple myeloma cells was investigated in vitro by tissue staining and flow cytometry. After demonstration of sensitivity and specificity, preclinical optical imaging studies were performed to evaluate tumor specificity in murine subcutaneous and metastatic multiple myeloma models. The VLA-4-targeted molecular probe showed high affinity for subcutaneous MM tumor xenografts. Importantly, tumor cells specific accumulation in the bone marrow of metastatic multiple myeloma correlated with GFP signal from transfected cells. Ex vivo flow cytometry of tumor tissue and bone marrow further corroborated in vivo imaging data, demonstrating the specificity of the novel agent and potential for quantitative imaging of multiple myeloma burden in these models.

  11. Common immunogenetic profile in children with multiple autoimmune diseases: the signature of HLA-DQ pleiotropic genes.

    PubMed

    Larizza, Daniela; Calcaterra, Valeria; Klersy, Catherine; Badulli, Carla; Caramagna, Claudia; Ricci, Antonio; Brambilla, Paola; Salvaneschi, Laura; Martinetti, Miryam

    2012-09-01

    Type 1 diabetes mellitus (T1DM), celiac disease (CD) and autoimmune thyroid disease (ATD) are autoimmune conditions relatively common in paediatric age and frequently occur in association in the same subject. This event is not by chance and requires an explanation. Here, we studied the distribution of HLA-DQ αβ heterodimers in 334 Italian children with T1DM, ATD and CD alone or in association and in 224 Italian healthy controls. In particular, 164 patients had T1DM (133 alone, 20+ATD, 7+CD and 4+CD+ATD), 118 had ATD (110 alone, 8+CD) and 52 had CD (40 alone, 11+ATD and 1+T1DM). 51 patients suffered from multiple autoimmune diseases. The risk for multiple autoimmune diseases was significantly associated with the increased number of HLA-DQ markers of susceptibility for both T1DM (p = 0.003) and CD (p = 0.006). The presence of one or more diabetogenic DQ molecules significantly increased the probability of developing not only T1DM (p < 0.001) but also CD (p < 0.001) and ATD (p = 0.001). Similarly, the presence of one or more celiac HLA-DQ heterodimers significantly increased the likelihood of developing not only CD (p < 0.001), but also T1DM (p < 0.001) and ATD (p < 0.001). We confirm that the sharing of the immunogenetic background is responsible for the development of multiple autoimmune diseases although with a different risk according to the number and type of susceptible HLA-DQ heterodimers as reported in the algorithm proposed here. It is likely that combinations of DQA1 and DQB1 alleles are the real culprits of the progression towards multiple autoimmune diseases and HLA-DQ genomic typing will improve the capability to predict associated autoimmune diseases in infancy.

  12. Molecular signatures identify a candidate target of balancing selection in an arcD-like gene of Staphylococcus epidermidis.

    PubMed

    Zhang, Liangfen; Thomas, Jonathan C; Didelot, Xavier; Robinson, D Ashley

    2012-08-01

    A comparative population genetics study revealed high levels of nucleotide polymorphism and intermediate-frequency alleles in an arcC gene of Staphylococcus epidermidis, but not in a homologous gene of the more aggressive human pathogen, Staphylococcus aureus. Further investigation showed that the arcC genes used in the multilocus sequence typing schemes of these two species were paralogs. Phylogenetic analyses of arcC-containing loci, including the arginine catabolic mobile element, from both species, suggested that these loci had an eventful history involving gene duplications, rearrangements, deletions, and horizontal transfers. The peak signatures in the polymorphic S. epidermidis locus were traced to an arcD-like gene adjacent to arcC; these signatures consisted of unusually elevated Tajima's D and π/K ratios, which were robust to assumptions about recombination and species divergence time and among the most elevated in the S. epidermidis genome. Amino acid polymorphisms, including one that differed in polarity and hydropathy, were located in the peak signatures and defined two allelic lineages. Recombination events were detected between these allelic lineages and potential donors and recipients of S. epidermidis were identified in each case. By comparison, the orthologous gene of S. aureus showed no unusual signatures. The ArcD-like protein belonged to the unknown ion transporter 3 family and appeared to be unrelated to ArcD from the arginine deiminase pathway. These studies report the first comparative population genetics results for staphylococci and the first statistical evidence for a candidate target of balancing selection in S. epidermidis.

  13. Resolving Multiple Molecular Orbitals Using Two-Dimensional High-Harmonic Spectroscopy

    NASA Astrophysics Data System (ADS)

    Yun, Hyeok; Lee, Kyung-Min; Sung, Jae Hee; Kim, Kyung Taec; Kim, Hyung Taek; Nam, Chang Hee

    2015-04-01

    High-harmonic radiation emitted from molecules in a strong laser field contains information on molecular structure and dynamics. When multiple molecular orbitals participate in high-harmonic generation, resolving the contribution of each orbital is crucial for understanding molecular dynamics and for extending high-harmonic spectroscopy to more complicated molecules. We show that two-dimensional high-harmonic spectroscopy can resolve high-harmonic radiation emitted from the two highest-occupied molecular orbitals, HOMO and HOMO-1, of aligned molecules. By the application of an orthogonally polarized two-color laser field that consists of the fundamental and its second-harmonic fields to aligned CO2 molecules, the characteristics attributed to the two orbitals are found to be separately imprinted in odd and even harmonics. Two-dimensional high-harmonic spectroscopy may open a new route to investigate ultrafast molecular dynamics during chemical processes.

  14. Resolving multiple molecular orbitals using two-dimensional high-harmonic spectroscopy.

    PubMed

    Yun, Hyeok; Lee, Kyung-Min; Sung, Jae Hee; Kim, Kyung Taec; Kim, Hyung Taek; Nam, Chang Hee

    2015-04-17

    High-harmonic radiation emitted from molecules in a strong laser field contains information on molecular structure and dynamics. When multiple molecular orbitals participate in high-harmonic generation, resolving the contribution of each orbital is crucial for understanding molecular dynamics and for extending high-harmonic spectroscopy to more complicated molecules. We show that two-dimensional high-harmonic spectroscopy can resolve high-harmonic radiation emitted from the two highest-occupied molecular orbitals, HOMO and HOMO-1, of aligned molecules. By the application of an orthogonally polarized two-color laser field that consists of the fundamental and its second-harmonic fields to aligned CO2 molecules, the characteristics attributed to the two orbitals are found to be separately imprinted in odd and even harmonics. Two-dimensional high-harmonic spectroscopy may open a new route to investigate ultrafast molecular dynamics during chemical processes.

  15. Authentication of animal signatures in traditional Chinese medicine of Lingyang Qingfei Wan using routine molecular diagnostic assays.

    PubMed

    Cao, Meng; Wang, Jikun; Yao, Lu; Xie, Suhua; Du, Jing; Zhao, Xingbo

    2014-01-01

    Lingyang Qingfei Wan produced by Beijing TongRenTang is a long-standing and popular medicine in China and international pharmaceutical markets. Concerns continue to be raised about the legality of usage of saiga antelope, which was defined as endangered species by Convention on International Trade in Endangered Species of Wild Fauna and Flora legislation and internal legislation in China. Therefore, the alternative pill in which substitutes saiga antelope with goat in the formula of Lingyang Qingfei Wan was developed. In order to authenticate the origin of animal contents in Lingyang Qingfei Wan and its alternative pill, molecular diagnostic assay was utilized by mtDNA polymorphism analysis. Four universal primer pairs containing mtDNA 12SrRNA, 16SrRNA, cytochrome b gene and cytochrome oxidase I were employed to obtain species-specific sequences of saiga antelope and goat, and multiple species-specific primer pairs for saiga antelope and goat were used to identify the animal origin in patent pills according to nucleotide polymorphisms between the two species. In additions, alternative techniques were attempted surrounding dilemmas of low concentration of target DNAs and presence of PCR-inhibitory substances in organic ingredients within complex pill. Results revealed that all species-specific primers could be successfully used for authentication of animal origin within complex pill, and sample preprocessing was critical during experimental manipulation. Internal positive control was an efficient and cost-effective way to assist in monitoring the potential interference from inhibitory substances which existed in the highly processed pills.

  16. A phylogenomic and molecular signature based approach for characterization of the phylum Spirochaetes and its major clades: proposal for a taxonomic revision of the phylum.

    PubMed

    Gupta, Radhey S; Mahmood, Sharmeen; Adeolu, Mobolaji

    2013-01-01

    The Spirochaetes species cause many important diseases including syphilis and Lyme disease. Except for their containing a distinctive endoflagella, no other molecular or biochemical characteristics are presently known that are specific for either all Spirochaetes or its different families. We report detailed comparative and phylogenomic analyses of protein sequences from Spirochaetes genomes to understand their evolutionary relationships and to identify molecular signatures for this group. These studies have identified 38 conserved signature indels (CSIs) that are specific for either all members of the phylum Spirochaetes or its different main clades. Of these CSIs, a 3 aa insert in the FlgC protein is uniquely shared by all sequenced Spirochaetes providing a molecular marker for this phylum. Seven, six, and five CSIs in different proteins are specific for members of the families Spirochaetaceae, Brachyspiraceae, and Leptospiraceae, respectively. Of the 19 other identified CSIs, 3 are uniquely shared by members of the genera Sphaerochaeta, Spirochaeta, and Treponema, whereas 16 others are specific for the genus Borrelia. A monophyletic grouping of the genera Sphaerochaeta, Spirochaeta, and Treponema distinct from the genus Borrelia is also strongly supported by phylogenetic trees based upon concatenated sequences of 22 conserved proteins. The molecular markers described here provide novel and more definitive means for identification and demarcation of different main groups of Spirochaetes. To accommodate the extensive genetic diversity of the Spirochaetes as revealed by different CSIs and phylogenetic analyses, it is proposed that the four families of this phylum should be elevated to the order level taxonomic ranks (viz. Spirochaetales, Brevinematales ord. nov., Brachyspiriales ord. nov., and Leptospiriales ord. nov.). It is further proposed that the genera Borrelia and Cristispira be transferred to a new family Borreliaceae fam. nov. within the order

  17. Signature control

    NASA Astrophysics Data System (ADS)

    Pyati, Vittal P.

    The reduction of vehicle radar signature is accomplished by means of vehicle shaping, the use of microwave frequencies-absorbent materials, and either passive or active cancellation techniques; such techniques are also useful in the reduction of propulsion system-associated IR emissions. In some anticipated scenarios, the objective is not signature-reduction but signature control, for deception, via decoy vehicles that mimic the signature characteristics of actual weapons systems. As the stealthiness of airframes and missiles increases, their propulsion systems' exhaust plumes assume a more important role in detection by an adversary.

  18. MULTIPLE FAST MOLECULAR OUTFLOWS IN THE PRE-PLANETARY NEBULA CRL 618

    SciTech Connect

    Lee, Chin-Fei; Huang, Po-Sheng; Sahai, Raghvendra; Sánchez Contreras, Carmen; Tay, Jeremy Jian Hao

    2013-11-01

    CRL 618 is a well-studied pre-planetary nebula. It has multiple highly collimated optical lobes, fast molecular outflows along the optical lobes, and an extended molecular envelope that consists of a dense torus in the equator and a tenuous round halo. Here we present our observations of this source in CO J = 3-2 and HCN J = 4-3 obtained with the Submillimeter Array at up to ∼0.''3 resolutions. We spatially resolve the fast molecular outflow region previously detected in CO near the central star and find it to be composed of multiple outflows that have similar dynamical ages and are oriented along the different optical lobes. We also detect fast molecular outflows further away from the central star near the tips of the extended optical lobes and a pair of equatorial outflows inside the dense torus. We find that two episodes of bullet ejections in different directions are needed, one producing the fast molecular outflows near the central star and one producing the fast molecular outflows near the tips of the extended optical lobes. One possibility to launch these bullets is a magneto-rotational explosion of the stellar envelope.

  19. Primary multiple sulfur isotopic compositions of pyrite in 2.7 Ga shales from the Joy Lake sequence (Superior Province) show felsic volcanic array-like signature

    NASA Astrophysics Data System (ADS)

    Li, Jianghanyang; Zhang, Zhe; Stern, Richard A.; Hannah, Judith L.; Stein, Holly J.; Yang, Gang; Li, Long

    2017-04-01

    Multiple sulfur isotopes provide a powerful tool to study photochemical and biological processes controlling the Archean sulfur cycle and infer related atmospheric and marine environments. However, our understanding of early Earth's environment remains limited by the availability of well-preserved geological samples, as most Archean sedimentary rocks have experienced some degree of metamorphic alteration. To evaluate sulfur isotopic behavior during post-depositional processes and elucidate the sulfur cycle at 2.7 Ga, we use high-resolution in situ analytical techniques (EPMA and SIMS) to determine elemental compositions and multiple sulfur isotopic compositions of large diagenetic pyrite nodules and fine-grained secondary pyrite disseminated in quartz veins (formed during a lower greenschist metamorphic event) in shales from the 2.7 Ga Joy Lake sequence in the southwest Superior Province. Results show that trace metals and sulfur in the secondary pyrite were derived from both metamorphic fluid and pre-existing diagenetic pyrite. Diagenetic pyrite nodules could have been partially dissolved by metamorphic fluid. But the surviving nodules show elemental and isotopic features different from those of the deduced metamorphic fluid endmember, suggesting the nodules were not geochemically altered by metamorphism, and thus preserve primary isotopic signatures acquired during diagenesis. The sulfur isotopic ratios of pyrite nodules show strong variations, with decreasing δ34S values and increasing Δ33S values from cores to rims. This negative Δ33S-δ34S relationship is different from the commonly observed 'Archean reference line' defined by most Archean pyrite data, but similar to the 'felsic volcanic array'. Our observation provides a first possible case from 2.7 Ga, the age of peak crustal growth in the Archean, to support the hypothesis that photochemical pathways could be different under conditions of intense volcanic emission. This study also shows that high

  20. Switchable Multiple Spin States in the Kondo description of Doped Molecular Magnets.

    PubMed

    Ray, Rajyavardhan; Kumar, Sanjeev

    2017-02-08

    We show that introducing electrons in magnetic clusters and molecular magnets lead to rich phase diagrams with a variety of low-spin and high-spin states allowing for multiple switchability. The analysis is carried out for a quantum spin-fermion model using the exact diagonalization, and the cluster mean-field approach. The model is relevant for a number of molecular magnets with triangular motifs consisting of transition metal ions such as Cr, Cu and V. Re-entrant spin-state behavior and chirality on-off transitions exist over a wide parameter regime. A subtle competition among geometrical frustration effects, electron itinerancy, and Kondo coupling at the molecular level is highlighted. Our results demonstrate that electron doping provides a viable mean to tame the magnetic properties of molecular magnets towards potential technological applications.

  1. Switchable Multiple Spin States in the Kondo description of Doped Molecular Magnets

    PubMed Central

    Ray, Rajyavardhan; Kumar, Sanjeev

    2017-01-01

    We show that introducing electrons in magnetic clusters and molecular magnets lead to rich phase diagrams with a variety of low-spin and high-spin states allowing for multiple switchability. The analysis is carried out for a quantum spin-fermion model using the exact diagonalization, and the cluster mean-field approach. The model is relevant for a number of molecular magnets with triangular motifs consisting of transition metal ions such as Cr, Cu and V. Re-entrant spin-state behavior and chirality on-off transitions exist over a wide parameter regime. A subtle competition among geometrical frustration effects, electron itinerancy, and Kondo coupling at the molecular level is highlighted. Our results demonstrate that electron doping provides a viable mean to tame the magnetic properties of molecular magnets towards potential technological applications. PMID:28176869

  2. Switchable Multiple Spin States in the Kondo description of Doped Molecular Magnets

    NASA Astrophysics Data System (ADS)

    Ray, Rajyavardhan; Kumar, Sanjeev

    2017-02-01

    We show that introducing electrons in magnetic clusters and molecular magnets lead to rich phase diagrams with a variety of low-spin and high-spin states allowing for multiple switchability. The analysis is carried out for a quantum spin-fermion model using the exact diagonalization, and the cluster mean-field approach. The model is relevant for a number of molecular magnets with triangular motifs consisting of transition metal ions such as Cr, Cu and V. Re-entrant spin-state behavior and chirality on-off transitions exist over a wide parameter regime. A subtle competition among geometrical frustration effects, electron itinerancy, and Kondo coupling at the molecular level is highlighted. Our results demonstrate that electron doping provides a viable mean to tame the magnetic properties of molecular magnets towards potential technological applications.

  3. SignS: a parallelized, open-source, freely available, web-based tool for gene selection and molecular signatures for survival and censored data

    PubMed Central

    Diaz-Uriarte, Ramon

    2008-01-01

    Background Censored data are increasingly common in many microarray studies that attempt to relate gene expression to patient survival. Several new methods have been proposed in the last two years. Most of these methods, however, are not available to biomedical researchers, leading to many re-implementations from scratch of ad-hoc, and suboptimal, approaches with survival data. Results We have developed SignS (Signatures for Survival data), an open-source, freely-available, web-based tool and R package for gene selection, building molecular signatures, and prediction with survival data. SignS implements four methods which, according to existing reviews, perform well and, by being of a very different nature, offer complementary approaches. We use parallel computing via MPI, leading to large decreases in user waiting time. Cross-validation is used to asses predictive performance and stability of solutions, the latter an issue of increasing concern given that there are often several solutions with similar predictive performance. Biological interpretation of results is enhanced because genes and signatures in models can be sent to other freely-available on-line tools for examination of PubMed references, GO terms, and KEGG and Reactome pathways of selected genes. Conclusion SignS is the first web-based tool for survival analysis of expression data, and one of the very few with biomedical researchers as target users. SignS is also one of the few bioinformatics web-based applications to extensively use parallelization, including fault tolerance and crash recovery. Because of its combination of methods implemented, usage of parallel computing, code availability, and links to additional data bases, SignS is a unique tool, and will be of immediate relevance to biomedical researchers, biostatisticians and bioinformaticians. PMID:18208605

  4. Communication: Multiple-timestep ab initio molecular dynamics with electron correlation.

    PubMed

    Steele, Ryan P

    2013-07-07

    A time-reversible, multiple-timestep protocol is presented for ab initio molecular dynamics simulations using correlated, wavefunction-based underlying potentials. The method is motivated by the observation that electron correlation contributions to forces vary on a slower timescale than their Hartree-Fock counterparts. An efficient dynamics algorithm, involving short-timestep Hartree-Fock and long-timestep Moøller-Plesset perturbation theory, is presented and tested. Results indicate stable trajectories and relative speedups comparable to those seen in force field-based multiple-timestep schemes, with the highest efficiency improvement occurring for large systems.

  5. Communication: Multiple-timestep ab initio molecular dynamics with electron correlation

    NASA Astrophysics Data System (ADS)

    Steele, Ryan P.

    2013-07-01

    A time-reversible, multiple-timestep protocol is presented for ab initio molecular dynamics simulations using correlated, wavefunction-based underlying potentials. The method is motivated by the observation that electron correlation contributions to forces vary on a slower timescale than their Hartree-Fock counterparts. An efficient dynamics algorithm, involving short-timestep Hartree-Fock and long-timestep Møller-Plesset perturbation theory, is presented and tested. Results indicate stable trajectories and relative speedups comparable to those seen in force field-based multiple-timestep schemes, with the highest efficiency improvement occurring for large systems.

  6. Complete protection against aflatoxin B(1)-induced liver cancer with a triterpenoid: DNA adduct dosimetry, molecular signature, and genotoxicity threshold.

    PubMed

    Johnson, Natalie M; Egner, Patricia A; Baxter, Victoria K; Sporn, Michael B; Wible, Ryan S; Sutter, Thomas R; Groopman, John D; Kensler, Thomas W; Roebuck, Bill D

    2014-07-01

    In experimental animals and humans, aflatoxin B1 (AFB1) is a potent hepatic toxin and carcinogen. The synthetic oleanane triterpenoid 1-[2-cyano-3-,12-dioxooleana-1,9(11)-dien-28-oyl]imidazole (CDDO-Im), a powerful activator of Keap1-Nrf2 signaling, protects against AFB1-induced toxicity and preneoplastic lesion formation (GST-P-positive foci). This study assessed and mechanistically characterized the chemoprotective efficacy of CDDO-Im against AFB1-induced hepatocellular carcinoma (HCC). A lifetime cancer bioassay was undertaken in F344 rats dosed with AFB1 (200 μg/kg rat/day) for four weeks and receiving either vehicle or CDDO-Im (three times weekly), one week before and throughout the exposure period. Weekly, 24-hour urine samples were collected for analysis of AFB1 metabolites. In a subset of rats, livers were analyzed for GST-P foci. The comparative response of a toxicogenomic RNA expression signature for AFB1 was examined. CDDO-Im completely protected (0/20) against AFB1-induced liver cancer compared with a 96% incidence (22/23) observed in the AFB1 group. With CDDO-Im treatment, integrated level of urinary AFB1-N(7)-guanine was significantly reduced (66%) and aflatoxin-N-acetylcysteine, a detoxication product, was consistently elevated (300%) after the first AFB1 dose. In AFB1-treated rats, the hepatic burden of GST-P-positive foci increased substantially (0%-13.8%) over the four weeks, but was largely absent with CDDO-Im intervention. The toxicogenomic RNA expression signature characteristic of AFB1 was absent in the AFB1 + CDDO-Im-treated rats. The remarkable efficacy of CDDO-Im as an anticarcinogen is established even in the face of a significant aflatoxin adduct burden. Consequently, the absence of cancer requires a concept of a threshold for DNA damage for cancer development.

  7. Epidemic and maintenance of rabies in Chinese ferret badgers (Melogale moschata) indicated by epidemiology and the molecular signatures of rabies viruses.

    PubMed

    Zhang, Shoufeng; Liu, Ye; Hou, Yanli; Zhao, Jinghui; Zhang, Fei; Wang, Ying; Hu, Rongliang

    2013-06-01

    An epidemic of Chinese ferret badger-associated human rabies was investigated in Wuyuan county, Jiangxi province and rabies viruses isolates from ferret badgers in different districts in Jiangxi and Zhejiang provinces were sequenced with their nucleotides and amino acids and aligned for epidemiological analysis. The results showed that the human rabies in Wuyuan are only associated with ferret badger bites; the rabies virus can be isolated in a high percentage of ferret badgers in the epidemic areas in Jiangxi and Zhejiang provinces; the isolates share the same molecular features in nucleotides and have characteristic amino acid signatures, i.e., 2 sites in the nucleoprotein and 3 sites in the glycoprotein, that are distinct from virus isolates from dogs in the same region. We conclude that rabies in Chinese ferret badgers has formed an independent transmission cycle and ferret badgers may serve as another important rabies reservoir independent of dog rabies in China.

  8. The VLA Nascent Disk and Multiplicity Survey of Perseus Protostars (VANDAM). II. Multiplicity of Protostars in the Perseus Molecular Cloud

    NASA Astrophysics Data System (ADS)

    Tobin, John J.; Looney, Leslie W.; Li, Zhi-Yun; Chandler, Claire J.; Dunham, Michael M.; Segura-Cox, Dominique; Sadavoy, Sarah I.; Melis, Carl; Harris, Robert J.; Kratter, Kaitlin; Perez, Laura

    2016-02-01

    We present a multiplicity study of all known protostars (94) in the Perseus molecular cloud from a Karl G. Jansky Very Large Array survey at Ka-band (8 mm and 1 cm) and C-band (4 and 6.6 cm). The observed sample has a bolometric luminosity range between 0.1 L⊙ and ˜33 L⊙, with a median of 0.7 L⊙. This multiplicity study is based on the Ka-band data, having a best resolution of ˜0.″065 (15 au) and separations out to ˜43″ (10,000 au) can be probed. The overall multiplicity fraction (MF) is found to be 0.40 ± 0.06 and the companion star fraction (CSF) is 0.71 ± 0.06. The MF and CSF of the Class 0 protostars are 0.57 ± 0.09 and 1.2 ± 0.2, and the MF and CSF of Class I protostars are both 0.23 ± 0.08. The distribution of companion separations appears bi-modal, with a peak at ˜75 au and another peak at ˜3000 au. Turbulent fragmentation is likely the dominant mechanism on >1000 au scales and disk fragmentation is likely to be the dominant mechanism on <200 au scales. Toward three Class 0 sources we find companions separated by <30 au. These systems have the smallest separations of currently known Class 0 protostellar binary systems. Moreover, these close systems are embedded within larger (50-400 au) structures and may be candidates for ongoing disk fragmentation.

  9. THE VLA NASCENT DISK AND MULTIPLICITY SURVEY OF PERSEUS PROTOSTARS (VANDAM). II. MULTIPLICITY OF PROTOSTARS IN THE PERSEUS MOLECULAR CLOUD

    SciTech Connect

    Tobin, John J.; Harris, Robert J.; Looney, Leslie W.; Segura-Cox, Dominique; Li, Zhi-Yun; Chandler, Claire J.; Perez, Laura; Dunham, Michael M.; Sadavoy, Sarah I.; Melis, Carl; Kratter, Kaitlin

    2016-02-10

    We present a multiplicity study of all known protostars (94) in the Perseus molecular cloud from a Karl G. Jansky Very Large Array survey at Ka-band (8 mm and 1 cm) and C-band (4 and 6.6 cm). The observed sample has a bolometric luminosity range between 0.1 L{sub ⊙} and ∼33 L{sub ⊙}, with a median of 0.7 L{sub ⊙}. This multiplicity study is based on the Ka-band data, having a best resolution of ∼0.″065 (15 au) and separations out to ∼43″ (10,000 au) can be probed. The overall multiplicity fraction (MF) is found to be 0.40 ± 0.06 and the companion star fraction (CSF) is 0.71 ± 0.06. The MF and CSF of the Class 0 protostars are 0.57 ± 0.09 and 1.2 ± 0.2, and the MF and CSF of Class I protostars are both 0.23 ± 0.08. The distribution of companion separations appears bi-modal, with a peak at ∼75 au and another peak at ∼3000 au. Turbulent fragmentation is likely the dominant mechanism on >1000 au scales and disk fragmentation is likely to be the dominant mechanism on <200 au scales. Toward three Class 0 sources we find companions separated by <30 au. These systems have the smallest separations of currently known Class 0 protostellar binary systems. Moreover, these close systems are embedded within larger (50–400 au) structures and may be candidates for ongoing disk fragmentation.

  10. May Diet and Dietary Supplements Improve the Wellness of Multiple Sclerosis Patients? A Molecular Approach

    PubMed Central

    Riccio, Paolo; Rossano, Rocco; Liuzzi, Grazia Maria

    2010-01-01

    Multiple sclerosis is a complex and multifactorial neurological disease, and nutrition is one of the environmental factors possibly involved in its pathogenesis. At present, the role of nutrition is unclear, and MS therapy is not associated to a particular diet. MS clinical trials based on specific diets or dietary supplements are very few and in some cases controversial. To understand how diet can influence the course of MS and improve the wellness of MS patients, it is necessary to identify the dietary molecules, their targets and the molecular mechanisms involved in the control of the disease. The aim of this paper is to provide a molecular basis for the nutritional intervention in MS by evaluating at molecular level the effect of dietary molecules on the inflammatory and autoimmune processes involved in the disease. PMID:21461338

  11. Multispectral excitation based multiple fluorescent targets resolving in fluorescence molecular tomography

    NASA Astrophysics Data System (ADS)

    Zhou, Yuan; Guang, Huizhi; Pu, Huangsheng; Zhang, Jiulou; Bai, Jing; Luo, Jianwen

    2016-04-01

    Fluorescence molecular tomography (FMT) can visualize biological activities at cellular and molecular levels in vivo, and has been extensively used in drug delivery and tumor detection research of small animals. The ill-posedness of the FMT inverse problem makes it difficult to reconstruct and resolve multiple adjacent fluorescent targets that have different functional features but are labeled with the same fluorochrome. An algorithm based on independent component analysis (ICA) for multispectral excited FMT is proposed to resolve multiple fluorescent targets in this study. Fluorescent targets are excited by multispectral excitation, and the three-dimensional distribution of fluorescent yields under the excitation spectrum is reconstructed by an iterative Tikhonov regularization algorithm. Subsequently, multiple fluorescent targets are resolved from mixed fluorescence signals by employing ICA. Simulations were performed and the results demonstrate that multiple adjacent fluorescent targets can be resolved if the number of excitation wavelengths is not smaller than that of fluorescent targets with different concentrations. The algorithm obtains both independent components that provide spatial information of different fluorescent targets and spectral courses that reflect variation trends of fluorescent yields along with the excitation spectrum. By using this method, it is possible to visualize the metabolism status of drugs in different structure organs, and quantitatively depict the variation trends of fluorescent yields of each functional organ under the excitation spectrum. This method may provide a pattern for tumor detection, drug delivery and treatment monitoring in vivo.

  12. Robust Selection of Cancer Survival Signatures from High-Throughput Genomic Data Using Two-Fold Subsampling

    PubMed Central

    Lee, Sangkyun; Rahnenführer, Jörg; Lang, Michel; De Preter, Katleen; Mestdagh, Pieter; Koster, Jan; Versteeg, Rogier; Stallings, Raymond L.; Varesio, Luigi; Asgharzadeh, Shahab; Schulte, Johannes H.; Fielitz, Kathrin; Schwermer, Melanie; Morik, Katharina; Schramm, Alexander

    2014-01-01

    Identifying relevant signatures for clinical patient outcome is a fundamental task in high-throughput studies. Signatures, composed of features such as mRNAs, miRNAs, SNPs or other molecular variables, are often non-overlapping, even though they have been identified from similar experiments considering samples with the same type of disease. The lack of a consensus is mostly due to the fact that sample sizes are far smaller than the numbers of candidate features to be considered, and therefore signature selection suffers from large variation. We propose a robust signature selection method that enhances the selection stability of penalized regression algorithms for predicting survival risk. Our method is based on an aggregation of multiple, possibly unstable, signatures obtained with the preconditioned lasso algorithm applied to random (internal) subsamples of a given cohort data, where the aggregated signature is shrunken by a simple thresholding strategy. The resulting method, RS-PL, is conceptually simple and easy to apply, relying on parameters automatically tuned by cross validation. Robust signature selection using RS-PL operates within an (external) subsampling framework to estimate the selection probabilities of features in multiple trials of RS-PL. These probabilities are used for identifying reliable features to be included in a signature. Our method was evaluated on microarray data sets from neuroblastoma, lung adenocarcinoma, and breast cancer patients, extracting robust and relevant signatures for predicting survival risk. Signatures obtained by our method achieved high prediction performance and robustness, consistently over the three data sets. Genes with high selection probability in our robust signatures have been reported as cancer-relevant. The ordering of predictor coefficients associated with signatures was well-preserved across multiple trials of RS-PL, demonstrating the capability of our method for identifying a transferable consensus signature

  13. Identifying molecular signatures of hypoxia adaptation from sex chromosomes: A case for Tibetan Mastiff based on analyses of X chromosome.

    PubMed

    Wu, Hong; Liu, Yan-Hu; Wang, Guo-Dong; Yang, Chun-Tao; Otecko, Newton O; Liu, Fei; Wu, Shi-Fang; Wang, Lu; Yu, Li; Zhang, Ya-Ping

    2016-10-07

    Genome-wide studies on high-altitude adaptation have received increased attention as a classical case of organismal evolution under extreme environment. However, the current genetic understanding of high-altitude adaptation emanated mainly from autosomal analyses. Only a few earlier genomic studies paid attention to the allosome. In this study, we performed an intensive scan of the X chromosome of public genomic data generated from Tibetan Mastiff (TM) and five other dog populations for indications of high-altitude adaptation. We identified five genes showing signatures of selection on the X chromosome. Notable among these genes was angiomotin (AMOT), which is related to the process of angiogenesis. We sampled additional 11 dog populations (175 individuals in total) at continuous altitudes in China from 300 to 4,000 meters to validate and test the association between the haplotype frequency of AMOT gene and altitude adaptation. The results suggest that AMOT gene may be a notable candidate gene for the adaptation of TM to high-altitude hypoxic conditions. Our study shows that X chromosome deserves consideration in future studies of adaptive evolution.

  14. Identifying molecular signatures of hypoxia adaptation from sex chromosomes: A case for Tibetan Mastiff based on analyses of X chromosome

    PubMed Central

    Wu, Hong; Liu, Yan-Hu; Wang, Guo-Dong; Yang, Chun-Tao; Otecko, Newton O.; Liu, Fei; Wu, Shi-Fang; Wang, Lu; Yu, Li; Zhang, Ya-Ping

    2016-01-01

    Genome-wide studies on high-altitude adaptation have received increased attention as a classical case of organismal evolution under extreme environment. However, the current genetic understanding of high-altitude adaptation emanated mainly from autosomal analyses. Only a few earlier genomic studies paid attention to the allosome. In this study, we performed an intensive scan of the X chromosome of public genomic data generated from Tibetan Mastiff (TM) and five other dog populations for indications of high-altitude adaptation. We identified five genes showing signatures of selection on the X chromosome. Notable among these genes was angiomotin (AMOT), which is related to the process of angiogenesis. We sampled additional 11 dog populations (175 individuals in total) at continuous altitudes in China from 300 to 4,000 meters to validate and test the association between the haplotype frequency of AMOT gene and altitude adaptation. The results suggest that AMOT gene may be a notable candidate gene for the adaptation of TM to high-altitude hypoxic conditions. Our study shows that X chromosome deserves consideration in future studies of adaptive evolution. PMID:27713520

  15. A Novel Molecular and Functional Stemness Signature Assessing Human Cord Blood-Derived Endothelial Progenitor Cell Immaturity

    PubMed Central

    Pascaud, Juliette; Driancourt, Catherine; Boyer-Di-Ponio, Julie; Uzan, Georges

    2016-01-01

    Endothelial Colony Forming Cells (ECFCs), a distinct population of Endothelial Progenitor Cells (EPCs) progeny, display phenotypic and functional characteristics of endothelial cells while retaining features of stem/progenitor cells. Cord blood-derived ECFCs (CB-ECFCs) have a high clonogenic and proliferative potentials and they can acquire different endothelial phenotypes, this requiring some plasticity. These properties provide angiogenic and vascular repair capabilities to CB-ECFCs for ischemic cell therapies. However, the degree of immaturity retained by EPCs is still confused and poorly defined. Consequently, to better characterize CB-ECFC stemness, we quantified their clonogenic potential and demonstrated that they were reprogrammed into induced pluripotent stem cells (iPSCs) more efficiently and rapidly than adult endothelial cells. Moreover, we analyzed the transcriptional profile of a broad gene panel known to be related to stem cells. We showed that, unlike mature endothelial cells, CB-ECFCs expressed genes involved in the maintenance of embryonic stem cell properties such as DNMT3B, GDF3 or SOX2. Thus, these results provide further evidence and tools to appreciate EPC-derived cell stemness. Moreover this novel stem cell transcriptional signature of ECFCs could help better characterizing and ranging EPCs according to their immaturity profile. PMID:27043207

  16. Molecular Scale Theoretical Studies of Energy Deposition and Redistribution in Crystalline High Explosives to Stimulate Enhanced Detectable Signatures

    DTIC Science & Technology

    2012-06-07

    T» .1 15. SUBJECT TERMS Terahertz spectroscopy, Pentaerythritol Tetranitrate, PETN, Molecular dynamics, Vibrational energy transfer, Infrared...2009). Terahertz spectrum and normal- mode relaxation in pentaerythritol tetranitrate: Effect of changes in bond-stretching force field terms. Andrey...Pereverzev and Thomas D. Sewell. Journal of Chemical Physics 134, 224502 (2011). Terahertz spectrum and normal- mode relaxation in pentaerythritol

  17. Multiple sulfur isotope signatures of sulfite and thiosulfate reduction by the model dissimilatory sulfate-reducer, Desulfovibrio alaskensis str. G20

    PubMed Central

    Leavitt, William D.; Cummins, Renata; Schmidt, Marian L.; Sim, Min S.; Ono, Shuhei; Bradley, Alexander S.; Johnston, David T.

    2014-01-01

    Dissimilatory sulfate reduction serves as a key metabolic carbon remineralization process in anoxic marine environments. Sulfate reducing microorganisms can impart a wide range in mass-dependent sulfur isotopic fractionation. As such, the presence and relative activity of these organisms is identifiable from geological materials. By extension, sulfur isotope records are used to infer the redox balance of marine sedimentary environments, and the oxidation state of Earth's oceans and atmosphere. However, recent work suggests that our understanding of microbial sulfate reduction (MSRs) may be missing complexity associated with the presence and role of key chemical intermediates in the reductive process. This study provides a test of proposed metabolic models of sulfate reduction by growing an axenic culture of the well-studied MSRs, Desulfovibrio alaskensis strain G20, under electron donor limited conditions on the terminal electron acceptors sulfate, sulfite or thiosulfate, and tracking the multiple S isotopic consequences of each condition set. The dissimilatory reduction of thiosulfate and sulfite produce unique minor isotope effects, as compared to the reduction of sulfate. Further, these experiments reveal a complex biochemistry associated with sulfite reduction. That is, under high sulfite concentrations, sulfur is shuttled to an intermediate pool of thiosulfate. Site-specific isotope fractionation (within thiosulfate) is very large (34ε ~ 30‰) while terminal product sulfide carries only a small fractionation from the initial sulfite (34ε < 10‰): a signature similar in magnitude to sulfate and thiosulfate reduction. Together these findings show that microbial sulfate reduction (MSR) is highly sensitive to the concentration of environmentally important sulfur-cycle intermediates (sulfite and thiosulfate), especially when thiosulfate and the large site-specific isotope effects are involved. PMID:25505449

  18. Multiple sulfur isotope signatures of sulfite and thiosulfate reduction by the model dissimilatory sulfate-reducer, Desulfovibrio alaskensis str. G20.

    PubMed

    Leavitt, William D; Cummins, Renata; Schmidt, Marian L; Sim, Min S; Ono, Shuhei; Bradley, Alexander S; Johnston, David T

    2014-01-01

    Dissimilatory sulfate reduction serves as a key metabolic carbon remineralization process in anoxic marine environments. Sulfate reducing microorganisms can impart a wide range in mass-dependent sulfur isotopic fractionation. As such, the presence and relative activity of these organisms is identifiable from geological materials. By extension, sulfur isotope records are used to infer the redox balance of marine sedimentary environments, and the oxidation state of Earth's oceans and atmosphere. However, recent work suggests that our understanding of microbial sulfate reduction (MSRs) may be missing complexity associated with the presence and role of key chemical intermediates in the reductive process. This study provides a test of proposed metabolic models of sulfate reduction by growing an axenic culture of the well-studied MSRs, Desulfovibrio alaskensis strain G20, under electron donor limited conditions on the terminal electron acceptors sulfate, sulfite or thiosulfate, and tracking the multiple S isotopic consequences of each condition set. The dissimilatory reduction of thiosulfate and sulfite produce unique minor isotope effects, as compared to the reduction of sulfate. Further, these experiments reveal a complex biochemistry associated with sulfite reduction. That is, under high sulfite concentrations, sulfur is shuttled to an intermediate pool of thiosulfate. Site-specific isotope fractionation (within thiosulfate) is very large ((34)ε ~ 30‰) while terminal product sulfide carries only a small fractionation from the initial sulfite ((34)ε < 10‰): a signature similar in magnitude to sulfate and thiosulfate reduction. Together these findings show that microbial sulfate reduction (MSR) is highly sensitive to the concentration of environmentally important sulfur-cycle intermediates (sulfite and thiosulfate), especially when thiosulfate and the large site-specific isotope effects are involved.

  19. Positional isomers of cyanostilbene: two-component molecular assembly and multiple-stimuli responsive luminescence

    PubMed Central

    Fan, Guoling; Yan, Dongpeng

    2014-01-01

    An understanding of the aggregates and properties of positional isomers can not only uncover how a slight difference in molecular structure alter crystal packing and bulk solid-state properties, but also plays an important role in developing new types of molecule-based functional materials. Herein, we report a study of the molecular packing and static/dynamic luminescence properties of three cyanostilbene (CS)-based isomers (CS1, CS2, CS3) within their single- and two-component molecular solids. Changing the positions of the cyano substitutents in the CS isomers has a marked influence on their packing modes and luminescent properties. Moreover, two-component CS-based materials have been constructed, which exhibit tunable conformations and packing fashions, as well as fluorescence properties, which differ from the pristine CS solids. The CS-based two-component molecular materials show solvent-responsive luminescence due to the dynamic disassembly of the samples. Moreover, it was found that the system based on CS2 and octafluoronaphthalene shows reversible photochromic fluorescence upon alternating light illumination and grinding. Such co-assembly procedures provide a facile way to fabricate patterned luminescent film materials. Therefore, this work not only affords new insight into the relationship between isomers and luminescence from molecular and supramolecular perspectives, but provides an effective strategy to develop multiple-stimuli-responsive luminescent materials. PMID:24816686

  20. Positional isomers of cyanostilbene: two-component molecular assembly and multiple-stimuli responsive luminescence

    NASA Astrophysics Data System (ADS)

    Fan, Guoling; Yan, Dongpeng

    2014-05-01

    An understanding of the aggregates and properties of positional isomers can not only uncover how a slight difference in molecular structure alter crystal packing and bulk solid-state properties, but also plays an important role in developing new types of molecule-based functional materials. Herein, we report a study of the molecular packing and static/dynamic luminescence properties of three cyanostilbene (CS)-based isomers (CS1, CS2, CS3) within their single- and two-component molecular solids. Changing the positions of the cyano substitutents in the CS isomers has a marked influence on their packing modes and luminescent properties. Moreover, two-component CS-based materials have been constructed, which exhibit tunable conformations and packing fashions, as well as fluorescence properties, which differ from the pristine CS solids. The CS-based two-component molecular materials show solvent-responsive luminescence due to the dynamic disassembly of the samples. Moreover, it was found that the system based on CS2 and octafluoronaphthalene shows reversible photochromic fluorescence upon alternating light illumination and grinding. Such co-assembly procedures provide a facile way to fabricate patterned luminescent film materials. Therefore, this work not only affords new insight into the relationship between isomers and luminescence from molecular and supramolecular perspectives, but provides an effective strategy to develop multiple-stimuli-responsive luminescent materials.

  1. Modeling Stochastic Kinetics of Molecular Machines at Multiple Levels: From Molecules to Modules

    PubMed Central

    Chowdhury, Debashish

    2013-01-01

    A molecular machine is either a single macromolecule or a macromolecular complex. In spite of the striking superficial similarities between these natural nanomachines and their man-made macroscopic counterparts, there are crucial differences. Molecular machines in a living cell operate stochastically in an isothermal environment far from thermodynamic equilibrium. In this mini-review we present a catalog of the molecular machines and an inventory of the essential toolbox for theoretically modeling these machines. The tool kits include 1), nonequilibrium statistical-physics techniques for modeling machines and machine-driven processes; and 2), statistical-inference methods for reverse engineering a functional machine from the empirical data. The cell is often likened to a microfactory in which the machineries are organized in modular fashion; each module consists of strongly coupled multiple machines, but different modules interact weakly with each other. This microfactory has its own automated supply chain and delivery system. Buoyed by the success achieved in modeling individual molecular machines, we advocate integration of these models in the near future to develop models of functional modules. A system-level description of the cell from the perspective of molecular machinery (the mechanome) is likely to emerge from further integrations that we envisage here. PMID:23746505

  2. Modeling stochastic kinetics of molecular machines at multiple levels: from molecules to modules.

    PubMed

    Chowdhury, Debashish

    2013-06-04

    A molecular machine is either a single macromolecule or a macromolecular complex. In spite of the striking superficial similarities between these natural nanomachines and their man-made macroscopic counterparts, there are crucial differences. Molecular machines in a living cell operate stochastically in an isothermal environment far from thermodynamic equilibrium. In this mini-review we present a catalog of the molecular machines and an inventory of the essential toolbox for theoretically modeling these machines. The tool kits include 1), nonequilibrium statistical-physics techniques for modeling machines and machine-driven processes; and 2), statistical-inference methods for reverse engineering a functional machine from the empirical data. The cell is often likened to a microfactory in which the machineries are organized in modular fashion; each module consists of strongly coupled multiple machines, but different modules interact weakly with each other. This microfactory has its own automated supply chain and delivery system. Buoyed by the success achieved in modeling individual molecular machines, we advocate integration of these models in the near future to develop models of functional modules. A system-level description of the cell from the perspective of molecular machinery (the mechanome) is likely to emerge from further integrations that we envisage here.

  3. Integrated Molecular Signature of Disease: Analysis of Influenza Virus-Infected Macaques through Functional Genomics and Proteomics

    SciTech Connect

    Baas, T.; Baskin, C. R.; Diamond, Deborah L.; Garcia-Sastre, A.; Bielefeldt-Ohmann, H.; Tumpey, T. M.; Thomas, M. J.; Carter, V. S.; Teal, T. H.; Van Hoven, N.; Proll, Sean; Jacobs, Jon M.; Caldwell, Z.; Gritsenko, Marina A.; Hukkanen, R.; Camp, David G.; Smith, Richard D.; Katze, Michael G.

    2006-11-01

    Recent outbreaks of avian influenza in humans have stressed the need for an improved non-human primate model of influenza pathogenesis. In order to develop our macaque model, we expanded our in vivo and functional genomics experiments: We focused on the innate immune response at day 2 post-inoculation and on gene expression in affected lung tissue with viral genetic material present; finally, we sought to identify signature genes for early infection in whole blood. For these purposes, we infected six pigtailed macaques with 107 TCID50 of influenza A/Texas/36/91 virus and three control animals with a sham inoculate. We sacrificed one control and two experimental animals at day 2, 4, and 7 and lung tissue was harvested for pathology, gene expression profiling, and proteomics. Additionally, blood was collected for genomics every other day from each animal until its endpoint. Gross and microscopic pathology, immunohistochemistry, viral gene expression by arrays and/or quantitative real-time RT-PCR confirmed successful yet mild infection in all experimental animals. Genomic experiments were performed using second generation macaque-specific oligonucleotide arrays and high-throughput proteomics revealed host response to infection at the protein level. Our data showed dramatic differences in gene expression within the same influenza-induced lesion based on the presence or absence of viral mRNA. We also identified genes tightly co-regulated in peripheral white blood cells and in lung tissue at day 2 post-inoculation. This latter finding opens the possibility of using gene expression arrays on whole blood to detect infection after exposure but prior to onset of symptoms or shedding.

  4. Multiple-Time Step Ab Initio Molecular Dynamics Based on Two-Electron Integral Screening.

    PubMed

    Fatehi, Shervin; Steele, Ryan P

    2015-03-10

    A multiple-timestep ab initio molecular dynamics scheme based on varying the two-electron integral screening method used in Hartree-Fock or density functional theory calculations is presented. Although screening is motivated by numerical considerations, it is also related to separations in the length- and timescales characterizing forces in a molecular system: Loose thresholds are sufficient to describe fast motions over short distances, while tight thresholds may be employed for larger length scales and longer times, leading to a practical acceleration of ab initio molecular dynamics simulations. Standard screening approaches can lead, however, to significant discontinuities in (and inconsistencies between) the energy and gradient when the screening threshold is loose, making them inappropriate for use in dynamics. To remedy this problem, a consistent window-screening method that smooths these discontinuities is devised. Further algorithmic improvements reuse electronic-structure information within the dynamics step and enhance efficiency relative to a naı̈ve multiple-timestepping protocol. The resulting scheme is shown to realize meaningful reductions in the cost of Hartree-Fock and B3LYP simulations of a moderately large system, the protonated sarcosine/glycine dipeptide embedded in a 19-water cluster.

  5. DNA extraction methods and multiple sampling to improve molecular diagnosis of Sarcocystis spp. in cattle hearts.

    PubMed

    Bräunig, Patrícia; Portella, Luiza Pires; Cezar, Alfredo Skrebsky; Libardoni, Felipe; Sangioni, Luis Antonio; Vogel, Fernanda Silveira Flores; Gonçalves, Paulo Bayard Dias

    2016-10-01

    Molecular detection of Sarcocystis spp. in tissue samples can be useful for experimental and diagnostic purposes. However, the parasite spreads unevenly through tissues, forming tissue cysts, and the cystic wall is an obstacle in DNA extraction protocols. Therefore, adequate sampling and effective disruption of the cysts are essential to improve the accuracy of DNA detection by PCR. The aims of this study were to evaluate the suitability of four protocols for DNA extraction from cysts of Sarcocystis spp. present in bovine myocardium samples or after their harvest in phosphate-buffered saline (PBS) solution as well as determine the effects of single or multiple sampling on the accuracy of molecular diagnosis of sarcocystosis in cattle hearts. Cysts and myocardium samples from nine bovine hearts were randomly distributed to four DNA extraction protocols: kit, kit with modification, DNAzol, and cetyl-trimethyl ammonium bromide (CTAB). Samples were submitted to DNA extraction and PCR as replicates of each heart (simplicate, duplicate, and triplicate), and the probability of a true positive diagnostic was calculated. Among the protocols tested, the kit with modification was determined to be the most suitable for DNA extraction from cysts in PBS solution (92.6 % of DNA detection by PCR); DNAzol resulted in higher DNA detection frequency from bovine myocardium samples (48.1 %). Multiple sampling improved the molecular diagnosis of Sarcocystis spp. infection in cattle hearts, increasing at 22.2 % the rate of true positive diagnostic.

  6. Tumor suppressive microRNAs (miR-222 and miR-31) regulate molecular pathways based on microRNA expression signature in prostate cancer.

    PubMed

    Fuse, Miki; Kojima, Satoko; Enokida, Hideki; Chiyomaru, Takeshi; Yoshino, Hirofumi; Nohata, Nijiro; Kinoshita, Takashi; Sakamoto, Shinichi; Naya, Yukio; Nakagawa, Masayuki; Ichikawa, Tomohiko; Seki, Naohiko

    2012-11-26

    microRNAs (miRNAs) have key roles in human tumorigenesis, tumor progression and metastasis. miRNAs are aberrantly expressed in many human cancers and can function as tumor suppressors or oncogenes that target many cancer-related genes. This study seeks to identify novel miRNA-regulated molecular pathways in prostate cancer (PCa). The miRNA expression signature in clinical specimens of PCa showed that 56 miRNAs were significantly downregulated in PCa compared with non-PCa tissues. We focused on the top four downregulated miRNAs (miR-187, miR-205, miR-222 and miR-31) to investigate their functional significance in PCa cells. Expression levels of these four miRNAs were validated in PCa specimens (15 PCa tissues and 17 non-PCa tissues) to confirm that they were significantly reduced in these PCa tissues. Gain-of-function analysis demonstrated that miR-222 and miR-31 inhibited cell proliferation, invasion and migration in PCa cell lines (PC3 and DU145), suggesting that miR-222 and miR-31 may act as tumor suppressors in PCa. Genome-wide gene expression analysis using miR-222 or miR-31 transfectants to identify the pathways they affect showed that many cancer-related genes are regulated by these miRNAs in PC3 cells. Identification and categorization of the molecular pathways regulated by tumor suppressive miRNAs could provide new information about the molecular mechanisms of PCa tumorigenesis.

  7. Signature of coexistence of superconductivity and ferromagnetism in two-dimensional NbSe2 triggered by surface molecular adsorption.

    PubMed

    Zhu, Xiaojiao; Guo, Yuqiao; Cheng, Hao; Dai, Jun; An, Xingda; Zhao, Jiyin; Tian, Kangzhen; Wei, Shiqiang; Cheng Zeng, Xiao; Wu, Changzheng; Xie, Yi

    2016-04-04

    Ferromagnetism is usually deemed incompatible with superconductivity. Consequently, the coexistence of superconductivity and ferromagnetism is usually observed only in elegantly designed multi-ingredient structures in which the two competing electronic states originate from separate structural components. Here we report the use of surface molecular adsorption to induce ferromagnetism in two-dimensional superconducting NbSe2, representing the freestanding case of the coexistence of superconductivity and ferromagnetism in one two-dimensional nanomaterial. Surface-structural modulation of the ultrathin superconducting NbSe2 by polar reductive hydrazine molecules triggers a slight elongation of the covalent Nb-Se bond, which weakens the covalent interaction and enhances the ionicity of the tetravalent Nb with unpaired electrons, yielding ferromagnetic ordering. The induced ferromagnetic momentum couples with conduction electrons generating unique correlated effects of intrinsic negative magnetoresistance and the Kondo effect. We anticipate that the surface molecular adsorption will be a powerful tool to regulate spin ordering in the two-dimensional paradigm.

  8. Signature of coexistence of superconductivity and ferromagnetism in two-dimensional NbSe2 triggered by surface molecular adsorption

    NASA Astrophysics Data System (ADS)

    Zhu, Xiaojiao; Guo, Yuqiao; Cheng, Hao; Dai, Jun; An, Xingda; Zhao, Jiyin; Tian, Kangzhen; Wei, Shiqiang; Cheng Zeng, Xiao; Wu, Changzheng; Xie, Yi

    2016-04-01

    Ferromagnetism is usually deemed incompatible with superconductivity. Consequently, the coexistence of superconductivity and ferromagnetism is usually observed only in elegantly designed multi-ingredient structures in which the two competing electronic states originate from separate structural components. Here we report the use of surface molecular adsorption to induce ferromagnetism in two-dimensional superconducting NbSe2, representing the freestanding case of the coexistence of superconductivity and ferromagnetism in one two-dimensional nanomaterial. Surface-structural modulation of the ultrathin superconducting NbSe2 by polar reductive hydrazine molecules triggers a slight elongation of the covalent Nb-Se bond, which weakens the covalent interaction and enhances the ionicity of the tetravalent Nb with unpaired electrons, yielding ferromagnetic ordering. The induced ferromagnetic momentum couples with conduction electrons generating unique correlated effects of intrinsic negative magnetoresistance and the Kondo effect. We anticipate that the surface molecular adsorption will be a powerful tool to regulate spin ordering in the two-dimensional paradigm.

  9. A systems biology pipeline identifies new immune and disease related molecular signatures and networks in human cells during microgravity exposure

    NASA Astrophysics Data System (ADS)

    Mukhopadhyay, Sayak; Saha, Rohini; Palanisamy, Anbarasi; Ghosh, Madhurima; Biswas, Anupriya; Roy, Saheli; Pal, Arijit; Sarkar, Kathakali; Bagh, Sangram

    2016-05-01

    Microgravity is a prominent health hazard for astronauts, yet we understand little about its effect at the molecular systems level. In this study, we have integrated a set of systems-biology tools and databases and have analysed more than 8000 molecular pathways on published global gene expression datasets of human cells in microgravity. Hundreds of new pathways have been identified with statistical confidence for each dataset and despite the difference in cell types and experiments, around 100 of the new pathways are appeared common across the datasets. They are related to reduced inflammation, autoimmunity, diabetes and asthma. We have identified downregulation of NfκB pathway via Notch1 signalling as new pathway for reduced immunity in microgravity. Induction of few cancer types including liver cancer and leukaemia and increased drug response to cancer in microgravity are also found. Increase in olfactory signal transduction is also identified. Genes, based on their expression pattern, are clustered and mathematically stable clusters are identified. The network mapping of genes within a cluster indicates the plausible functional connections in microgravity. This pipeline gives a new systems level picture of human cells under microgravity, generates testable hypothesis and may help estimating risk and developing medicine for space missions.

  10. Signature of coexistence of superconductivity and ferromagnetism in two-dimensional NbSe2 triggered by surface molecular adsorption

    PubMed Central

    Zhu, Xiaojiao; Guo, Yuqiao; Cheng, Hao; Dai, Jun; An, Xingda; Zhao, Jiyin; Tian, Kangzhen; Wei, Shiqiang; Cheng Zeng, Xiao; Wu, Changzheng; Xie, Yi

    2016-01-01

    Ferromagnetism is usually deemed incompatible with superconductivity. Consequently, the coexistence of superconductivity and ferromagnetism is usually observed only in elegantly designed multi-ingredient structures in which the two competing electronic states originate from separate structural components. Here we report the use of surface molecular adsorption to induce ferromagnetism in two-dimensional superconducting NbSe2, representing the freestanding case of the coexistence of superconductivity and ferromagnetism in one two-dimensional nanomaterial. Surface-structural modulation of the ultrathin superconducting NbSe2 by polar reductive hydrazine molecules triggers a slight elongation of the covalent Nb–Se bond, which weakens the covalent interaction and enhances the ionicity of the tetravalent Nb with unpaired electrons, yielding ferromagnetic ordering. The induced ferromagnetic momentum couples with conduction electrons generating unique correlated effects of intrinsic negative magnetoresistance and the Kondo effect. We anticipate that the surface molecular adsorption will be a powerful tool to regulate spin ordering in the two-dimensional paradigm. PMID:27039840

  11. A systems biology pipeline identifies new immune and disease related molecular signatures and networks in human cells during microgravity exposure

    PubMed Central

    Mukhopadhyay, Sayak; Saha, Rohini; Palanisamy, Anbarasi; Ghosh, Madhurima; Biswas, Anupriya; Roy, Saheli; Pal, Arijit; Sarkar, Kathakali; Bagh, Sangram

    2016-01-01

    Microgravity is a prominent health hazard for astronauts, yet we understand little about its effect at the molecular systems level. In this study, we have integrated a set of systems-biology tools and databases and have analysed more than 8000 molecular pathways on published global gene expression datasets of human cells in microgravity. Hundreds of new pathways have been identified with statistical confidence for each dataset and despite the difference in cell types and experiments, around 100 of the new pathways are appeared common across the datasets. They are related to reduced inflammation, autoimmunity, diabetes and asthma. We have identified downregulation of NfκB pathway via Notch1 signalling as new pathway for reduced immunity in microgravity. Induction of few cancer types including liver cancer and leukaemia and increased drug response to cancer in microgravity are also found. Increase in olfactory signal transduction is also identified. Genes, based on their expression pattern, are clustered and mathematically stable clusters are identified. The network mapping of genes within a cluster indicates the plausible functional connections in microgravity. This pipeline gives a new systems level picture of human cells under microgravity, generates testable hypothesis and may help estimating risk and developing medicine for space missions. PMID:27185415

  12. Molecular Signatures of Self-Renewal, Differentiation, and Lineage Choice in Multipotential Hemopoietic Progenitor Cells In Vitro

    PubMed Central

    Bruno, Ludovica; Hoffmann, Reinhard; McBlane, Fraser; Brown, John; Gupta, Rajeev; Joshi, Chirag; Pearson, Stella; Seidl, Thomas; Heyworth, Clare; Enver, Tariq

    2004-01-01

    The molecular mechanisms governing self-renewal, differentiation, and lineage specification remain unknown. Transcriptional profiling is likely to provide insight into these processes but, as yet, has been confined to “static” molecular profiles of stem and progenitors cells. We now provide a comprehensive, statistically robust, and “dynamic” analysis of multipotent hemopoietic progenitor cells undergoing self-renewal in response to interleukin-3 (IL-3) and multilineage differentiation in response to lineage-affiliated cytokines. Cells undergoing IL-3-dependent proliferative self-renewal displayed striking complexity, including expression of genes associated with different lineage programs, suggesting a highly responsive compartment poised to rapidly execute intrinsically or extrinsically initiated cell fate decisions. A remarkable general feature of early differentiation was a resolution of complexity through the downregulation of gene expression. Although effector genes characteristic of mature cells were upregulated late, coincident with morphological changes, lineage-specific changes in gene expression were observed prior to this, identifying genes which may provide early harbingers of unilineage commitment. Of particular interest were genes that displayed differential behavior irrespective of the lineage elaborated, many of which were rapidly downregulated within 4 to 8 h after exposure to a differentiation cue. These are likely to include genes important in self-renewal, the maintenance of multipotentiality, or the negative regulation of differentiation per se. PMID:14701746

  13. Diffusion-coupled molecular assembly: structuring of coordination polymers across multiple length scales.

    PubMed

    Hirai, Kenji; Reboul, Julien; Morone, Nobuhiro; Heuser, John E; Furukawa, Shuhei; Kitagawa, Susumu

    2014-10-22

    Porous coordination polymers (PCPs) are an intriguing class of molecular-based materials because of the designability of framework scaffolds, pore sizes and pore surface functionalities. Besides the structural designability at the molecular scale, the structuring of PCPs into mesoscopic/macroscopic morphologies has attracted much attention due to the significance for the practical applications. The structuring of PCPs at the mesoscopic/macroscopic scale has been so far demonstrated by the spatial localization of coordination reactions on the surface of templates or at the phase boundaries. However, these methodologies have never been applied to the fabrication of solid-solution or multivariate metal-organic frameworks (MOFs), in which multiple components are homogeneously mixed. Herein, we demonstrate the structuring of a box-type superstructure comprising of a solid-solution PCP by integrating a bidirectional diffusion of multiple organic ligands into molecular assembly. The parent crystals of [Zn2(ndc)2(bpy)]n were placed in the DMF solution of additional organic component of H2bdc, and the temperature was rapidly elevated up to 80 °C (ndc = 1,4-naphthalenedicarboxylate, bpy = 4,4'-bipyridyl, bdc = 1,4-benzenedicarboxylate). The dissolution of the parent crystals induced the outward diffusion of components; contrariwise, the accumulation of the other organic ligand of H2bdc induced the inward diffusion toward the surface of the parent crystals. This bidirectional diffusion of multiple components spatially localized the recrystallization at the surface of cuboid parent crystals; therefore, the nanocrystals of a solid-solution PCP ([Zn2(bdc)1.5(ndc)0.5(bpy)]n) were organized into a mesoscopic box superstructure. Furthermore, we demonstrated that the box superstructures enhanced the mass transfer kinetics for the separation of hydrocarbons.

  14. Multiple exciton generation in quantum dots versus singlet fission in molecular chromophores for solar photon conversion.

    PubMed

    Beard, Matthew C; Johnson, Justin C; Luther, Joseph M; Nozik, Arthur J

    2015-06-28

    Both multiple exciton generation (MEG) in semiconductor nanocrystals and singlet fission (SF) in molecular chromophores have the potential to greatly increase the power conversion efficiency of solar cells for the production of solar electricity (photovoltaics) and solar fuels (artificial photosynthesis) when used in solar photoconverters. MEG creates two or more excitons per absorbed photon, and SF produces two triplet states from a single singlet state. In both cases, multiple charge carriers from a single absorbed photon can be extracted from the cell and used to create higher power conversion efficiencies for a photovoltaic cell or a cell that produces solar fuels, like hydrogen from water splitting or reduced carbon fuels from carbon dioxide and water (analogous to biological photosynthesis). The similarities and differences in the mechanisms and photoconversion cell architectures between MEG and SF are discussed.

  15. A Targeted "Capture" and "Removal" Scavenger toward Multiple Pollutants for Water Remediation based on Molecular Recognition.

    PubMed

    Wang, Jie; Shen, Haijing; Hu, Xiaoxia; Li, Yan; Li, Zhihao; Xu, Jinfan; Song, Xiufeng; Zeng, Haibo; Yuan, Quan

    2016-03-01

    For the water remediation techniques based on adsorption, the long-standing contradictories between selectivity and multiple adsorbability, as well as between affinity and recyclability, have put it on weak defense amid more and more severe environment crisis. Here, a pollutant-targeting hydrogel scavenger is reported for water remediation with both high selectivity and multiple adsorbability for several pollutants, and with strong affinity and good recyclability through rationally integrating the advantages of multiple functional materials. In the scavenger, aptamers fold into binding pockets to accommodate the molecular structure of pollutants to afford perfect selectivity, and Janus nanoparticles with antibacterial function as well as anisotropic surfaces to immobilize multiple aptamers allow for simultaneously handling different kinds of pollutants. The scavenger exhibits high efficiencies in removing pollutants from water and it can be easily recycled for many times without significant loss of loading capacities. Moreover, the residual concentrations of each contaminant are well below the drinking water standards. Thermodynamic behavior of the adsorption process is investigated and the rate-controlling process is determined. Furthermore, a point of use device is constructed and it displays high efficiency in removing pollutants from environmental water. The scavenger exhibits great promise to be applied in the next generation of water purification systems.

  16. Marked influence of the nature of the chemical bond on CP-violating signature in molecular ions HBr(+) and HI(+).

    PubMed

    Ravaine, Boris; Porsev, Sergey G; Derevianko, Andrei

    2005-01-14

    Heavy polar molecules offer a great sensitivity to the electron electric dipole moment (EDM). To guide emerging searches for EDMs with molecular ions, we estimate the EDM-induced energy corrections for hydrogen halide ions HBr(+) and HI(+) in their respective ground X (2)Pi(3/2) states. We find that the energy corrections due to EDM for the two ions differ by an unexpectedly large factor of 15. We demonstrate that a major part of this enhancement is due to a dissimilarity in the nature of the chemical bond for the two ions: the bond that is nearly of ionic character in HBr(+) exhibits predominantly a covalent nature in HI(+). We conclude that because of this enhancement the HI(+) ion may be a potentially competitive candidate for the EDM search.

  17. Molecularly Imprinted Polymers for Selective Analysis of Chemical Warfare Surrogate and Nuclear Signature Compounds in Complex Matrices

    SciTech Connect

    Harvey, Scott D.

    2005-08-01

    This paper describes the preparation and evaluation of molecularly imprinted polymers (MIPs) that display specificity toward diisopropyl methylphosphonate (DIMP) and tributyl phosphate (TBP). Polymer activity was assessed by solid-phase extraction and high-performance liquid chromatography experiments. Both DIMP- and TBP-specific MIPs selectively retained their targets relative to a nonimprinted control. Proof-of-principle experiments demonstrated highly selective analysis of the targets from fortified complex matrix samples (diesel fuel, gasoline, and air extract concentrate). The retained MIP fractions gave near quantitative recovery of the target analytes with very low matrix background content. The same fraction from the control sorbent was less pure and recovered only about half of the analyte.

  18. Multiple outflows in the bipolar planetary nebula M1-16: A molecular line study

    NASA Technical Reports Server (NTRS)

    Sahai, Raghvendra; Wootten, Alwyn; Schwarz, Hugo E.; Wild, W.

    1994-01-01

    Extensive observations of the molecular gas in the young, compact planetary nebula M1-16 have been made, using the Swedish-ESO-Submillimeter Telescope. A map of the CO J = 2-1 emission shows that the molecular envelope contains both a slow and a fast outflow with expansion velocities of 19 km/s and greater than 34 km/s, respectively. The slow outflow is mildly elliptical, while the fast molecular outflow is bipolar. This fast outflow is roughly aligned with the very fast outflows recently found in the optical, while the long axis of the slow elliptical outflow is roughly orthogonal to the optical outflow axis. The kinematic timescales for the CO fast outflow and the optical very fast outflow agree closely, supporting the view that the former represents material in the slow outflow accelerated by the very fast outflow. The kinematic signature of a disk expanding with about 15.5 km/s can also be seen in the CO J = 2-1 data. The mass-loss rate (a) for the slow outflow is greater than or equal to 2.8 x 10(exp -5) solar mass/yr and possibly as large as 9 x 10(exp -5) solar mass/yr, (b) for the fast outflow is greater than or equal to 5 x 10(exp -6) solar mass/yr, and (c) for the very fast optically visible outflow is approximately equal 5 x 10(exp -7) solar mass/yr. The disk mass is approximately equal 6 x 10(exp -3) solar mass. Grain photoelectric heating results in temperatures of 20-70 K in molecular gas of the slow outflow. The (13)C/(12)C abundance ratio in M1-16 is found to be 0.33, quite possibly the highest found for any evolved object. Upper limits for the (18)O/(16)O and (17)O/(16)O ratios were found to be consistent with the values found in AGB stars. A search for other molecular species in M1-16 resulted in the detection of the high-excitation species HCN, CN, (13)CN, HCO(+), and H(13)CO(+) and possibly N2H(+). Both the HCO(+)/HCN and CN/HCN line-intensity ratios are enhanced, the former by a very large factor, over the values found in the envelopes of AGB

  19. Simulating Brain Tumor Heterogeneity with a Multiscale Agent-Based Model: Linking Molecular Signatures, Phenotypes and Expansion Rate

    PubMed Central

    Zhang, Le; Strouthos, Costas G.; Wang, Zhihui; Deisboeck, Thomas S.

    2008-01-01

    We have extended our previously developed 3D multi-scale agent-based brain tumor model to simulate cancer heterogeneity and to analyze its impact across the scales of interest. While our algorithm continues to employ an epidermal growth factor receptor (EGFR) gene-protein interaction network to determine the cells’ phenotype, it now adds an implicit treatment of tumor cell adhesion related to the model’s biochemical microenvironment. We simulate a simplified tumor progression pathway that leads to the emergence of five distinct glioma cell clones with different EGFR density and cell ‘search precisions’. The in silico results show that microscopic tumor heterogeneity can impact the tumor system’s multicellular growth patterns. Our findings further confirm that EGFR density results in the more aggressive clonal populations switching earlier from proliferation-dominated to a more migratory phenotype. Moreover, analyzing the dynamic molecular profile that triggers the phenotypic switch between proliferation and migration, our in silico oncogenomics data display spatial and temporal diversity in documenting the regional impact of tumorigenesis, and thus support the added value of multi-site and repeated assessments in vitro and in vivo. Potential implications from this in silico work for experimental and computational studies are discussed. PMID:20047002

  20. Molecular signatures of Pleistocene sea-level changes that affected connectivity among freshwater shrimp in Indo-Australian waters.

    PubMed

    De Bruyn, Mark; Mather, Peter B

    2007-10-01

    A major paradigm in evolutionary biology asserts that global climate change during the Pleistocene often led to rapid and extensive diversification in numerous taxa. Recent phylogenetic data suggest that past climatic oscillations may have promoted long-distance marine dispersal in some freshwater crustacea from the Indo-Australian Archipelago (IAA). Whether this pattern is common, and whether similar processes are acting on diversification below the species level is unknown. We used nuclear and mitochondrial molecular variation in a freshwater-dependent decapod crustacean (Macrobrachium rosenbergii), sampled widely from the IAA, to assess the impact of Pleistocene sea-level changes on lineage diversification in this species. Fitting of an isolation with migration model enabled us to reject ongoing migration among lineages, and results indicate that isolation among both mainland-mainland and mainland-island lineages arose during the mid-Pleistocene. Our data suggest a scenario of widespread marine dispersal during Pleistocene glacial maxima (in support of the 'Pleistocene marine dispersal hypothesis') when sea levels were low, and geographical distances between fresh watersheds were greatly reduced, followed by increased isolation as sea levels subsequently rose.

  1. Locally accessible conformations of proteins: multiple molecular dynamics simulations of crambin.

    PubMed Central

    Caves, L. S.; Evanseck, J. D.; Karplus, M.

    1998-01-01

    Multiple molecular dynamics (MD) simulations of crambin with different initial atomic velocities are used to sample conformations in the vicinity of the native structure. Individual trajectories of length up to 5 ns sample only a fraction of the conformational distribution generated by ten independent 120 ps trajectories at 300 K. The backbone atom conformational space distribution is analyzed using principal components analysis (PCA). Four different major conformational regions are found. In general, a trajectory samples only one region and few transitions between the regions are observed. Consequently, the averages of structural and dynamic properties over the ten trajectories differ significantly from those obtained from individual trajectories. The nature of the conformational sampling has important consequences for the utilization of MD simulations for a wide range of problems, such as comparisons with X-ray or NMR data. The overall average structure is significantly closer to the X-ray structure than any of the individual trajectory average structures. The high frequency (less than 10 ps) atomic fluctuations from the ten trajectories tend to be similar, but the lower frequency (100 ps) motions are different. To improve conformational sampling in molecular dynamics simulations of proteins, as in nucleic acids, multiple trajectories with different initial conditions should be used rather than a single long trajectory. PMID:9541397

  2. Three-dimensional molecular mapping of a multiple emulsion by means of CARS microscopy.

    PubMed

    Meyer, Tobias; Akimov, Denis; Tarcea, Nicolae; Chatzipapadopoulos, Susana; Muschiolik, Gerald; Kobow, Jens; Schmitt, Michael; Popp, Jürgen

    2008-02-07

    Multiple emulsions consisting of water droplets dispersed in an oil phase containing emulsifier which is emulsified in an outer water phase (W/O/W) are of great interest in pharmacology for developing new drugs, in the nutrition sciences for designing functional food, and in biology as model systems for cell organelles such as liposomes. In the food industry multiple emulsions with high sugar content in the aqueous phase can be used for the production of sweets, because the high sugar content prevents deterioration. However, for these emulsions the refractive indexes of oil and aqueous phase are very similar. This seriously impedes the analysis of these emulsions, e.g., for process monitoring, because microscopic techniques based on transmission or reflection do not provide sufficient contrast. We have characterized the inner dispersed phase of concentrated W/O/W emulsions with the same refractive index of the three phases by micro Raman spectroscopy and investigated the composition and molecular distribution in water-oil-water emulsions by means of three-dimensional laser scanning CARS (coherent anti-Stokes Raman scattering) microscopy. CARS microscopy has been used to study water droplets dispersed in oil droplets at different Raman resonances to visualize different molecular species. Water droplets with a diameter of about 700 nm could clearly be visualized. The advantages of CARS microscopy for studying this particular system are emphasized by comparing this microscopic technique with conventional confocal reflection and transmission microscopies.

  3. Meta-Analysis of Pulmonary Transcriptomes from Differently Primed Mice Identifies Molecular Signatures to Differentiate Immune Responses following Bordetella pertussis Challenge

    PubMed Central

    van Riet, Elly; Kersten, Gideon F. A.; Metz, Bernard

    2017-01-01

    Respiratory infection with Bordetella pertussis leads to severe effects in the lungs. The resulting immunity and also immunization with pertussis vaccines protect against disease, but the induced type of immunity and longevity of the response are distinct. In this study the effects of priming, by either vaccination or infection, on a subsequent pathogen encounter were studied. To that end, three postchallenge transcriptome datasets of previously primed mice were combined and compared to the responses in unprimed control mice. In total, 205 genes showed different transcription activity. A coexpression network analysis assembled these genes into 27 clusters, combined into six groups with overlapping biological function. Local pulmonary immunity was only present in mice with infection-induced immunity. Complement-mediated responses were more prominent in mice immunized with an outer membrane vesicle pertussis vaccine than in mice that received a whole-cell pertussis vaccine. Additionally, 46 genes encoding for secreted proteins may serve as markers in blood for the degree of protection (Cxcl9, Gp2, and Pla2g2d), intensity of infection (Retnla, Saa3, Il6, and Il1b), or adaptive recall responses (Ighg, C1qb). The molecular signatures elucidated in this study contribute to better understanding of functional interactions in challenge-induced responses in relation to pertussis immunity. PMID:28243609

  4. Molecular Signature of Pseudomonas aeruginosa with Simultaneous Nanomolar Detection of Quorum Sensing Signaling Molecules at a Boron-Doped Diamond Electrode

    PubMed Central

    Buzid, Alyah; Shang, Fengjun; Reen, F. Jerry; Muimhneacháin, Eoin Ó; Clarke, Sarah L.; Zhou, Lin; Luong, John H. T.; O’Gara, Fergal; McGlacken, Gerard P.; Glennon, Jeremy D.

    2016-01-01

    Electroanalysis was performed using a boron-doped diamond (BDD) electrode for the simultaneous detection of 2-heptyl-3-hydroxy-4-quinolone (PQS), 2-heptyl-4-hydroxyquinoline (HHQ) and pyocyanin (PYO). PQS and its precursor HHQ are two important signal molecules produced by Pseudomonas aeruginosa, while PYO is a redox active toxin involved in virulence and pathogenesis. This Gram-negative and opportunistic human pathogen is associated with a hospital-acquired infection particularly in patients with compromised immunity and is the primary cause of morbidity and mortality in cystic fibrosis (CF) patients. Early detection is crucial in the clinical management of this pathogen, with established infections entering a biofilm lifestyle that is refractory to conventional antibiotic therapies. Herein, a detection procedure was optimized and proven for the simultaneous detection of PYO, HHQ and PQS in standard mixtures, biological samples, and P. aeruginosa spiked CF sputum samples with remarkable sensitivity, down to nanomolar levels. Differential pulse voltammetry (DPV) scans were also applicable for monitoring the production of PYO, HHQ and PQS in P. aeruginosa PA14 over 8 h of cultivation. The simultaneous detection of these three compounds represents a molecular signature specific to this pathogen. PMID:27427496

  5. Molecular Signature of Pseudomonas aeruginosa with Simultaneous Nanomolar Detection of Quorum Sensing Signaling Molecules at a Boron-Doped Diamond Electrode

    NASA Astrophysics Data System (ADS)

    Buzid, Alyah; Shang, Fengjun; Reen, F. Jerry; Muimhneacháin, Eoin Ó.; Clarke, Sarah L.; Zhou, Lin; Luong, John H. T.; O’Gara, Fergal; McGlacken, Gerard P.; Glennon, Jeremy D.

    2016-07-01

    Electroanalysis was performed using a boron-doped diamond (BDD) electrode for the simultaneous detection of 2-heptyl-3-hydroxy-4-quinolone (PQS), 2-heptyl-4-hydroxyquinoline (HHQ) and pyocyanin (PYO). PQS and its precursor HHQ are two important signal molecules produced by Pseudomonas aeruginosa, while PYO is a redox active toxin involved in virulence and pathogenesis. This Gram-negative and opportunistic human pathogen is associated with a hospital-acquired infection particularly in patients with compromised immunity and is the primary cause of morbidity and mortality in cystic fibrosis (CF) patients. Early detection is crucial in the clinical management of this pathogen, with established infections entering a biofilm lifestyle that is refractory to conventional antibiotic therapies. Herein, a detection procedure was optimized and proven for the simultaneous detection of PYO, HHQ and PQS in standard mixtures, biological samples, and P. aeruginosa spiked CF sputum samples with remarkable sensitivity, down to nanomolar levels. Differential pulse voltammetry (DPV) scans were also applicable for monitoring the production of PYO, HHQ and PQS in P. aeruginosa PA14 over 8 h of cultivation. The simultaneous detection of these three compounds represents a molecular signature specific to this pathogen.

  6. Molecular and quantitative signatures of biparental inbreeding depression in the self-incompatible tree species Prunus avium.

    PubMed

    Jolivet, C; Rogge, M; Degen, B

    2013-05-01

    Genetic diversity strongly influences populations' adaptability to changing environments and therefore survival. Sustainable forest management practices have multiple roles including conservation of genetic resources and timber production. In this study, we aimed at better understanding the variation in genetic diversity among adult and offspring individuals, and the effects of mating system on offspring survival and growth in wild cherry, Prunus avium. We analysed adult trees and open pollinated seed-families from three stands in Germany at eight microsatellite loci and one incompatibility system locus and conducted paternity analyses. Seed viability testing and seed sowing in a nursery allowed further testing for the effects of pollen donor diversity and genetic similarity between mates on the offspring performance at the seed and seedling stages. Our results were contrasting across stands. Loss of genetic diversity from adult to seedling stages and positive effect of mate diversity on offspring performance occurred in one stand only, whereas biparental inbreeding depression and significant decrease in fixation index from adults to seedlings was detected in two stands. We discussed the effects of stand genetic diversity on the magnitude of biparental inbreeding depression at several life-stages and its consequences on the management of genetic resources in P. avium.

  7. BRCA1-like signature in triple negative breast cancer: Molecular and clinical characterization reveals subgroups with therapeutic potential.

    PubMed

    Severson, Tesa M; Peeters, Justine; Majewski, Ian; Michaut, Magali; Bosma, Astrid; Schouten, Philip C; Chin, Suet-Feung; Pereira, Bernard; Goldgraben, Mae A; Bismeijer, Tycho; Kluin, Roelof J C; Muris, Jettie J F; Jirström, Karin; Kerkhoven, Ron M; Wessels, Lodewyk; Caldas, Carlos; Bernards, René; Simon, Iris M; Linn, Sabine

    2015-10-01

    Triple negative (TN) breast cancers make up some 15% of all breast cancers. Approximately 10-15% are mutant for the tumor suppressor, BRCA1. BRCA1 is required for homologous recombination-mediated DNA repair and deficiency results in genomic instability. BRCA1-mutated tumors have a specific pattern of genomic copy number aberrations that can be used to classify tumors as BRCA1-like or non-BRCA1-like. BRCA1 mutation, promoter methylation, BRCA1-like status and genome-wide expression data was determined for 112 TN breast cancer samples with long-term follow-up. Mutation status for 21 known DNA repair genes and PIK3CA was assessed. Gene expression and mutation frequency in BRCA1-like and non-BRCA1-like tumors were compared. Multivariate survival analysis was performed using the Cox proportional hazards model. BRCA1 germline mutation was identified in 10% of patients and 15% of tumors were BRCA1 promoter methylated. Fifty-five percent of tumors classified as BRCA1-like. The functions of genes significantly up-regulated in BRCA1-like tumors included cell cycle and DNA recombination and repair. TP53 was found to be frequently mutated in BRCA1-like (P < 0.05), while PIK3CA was frequently mutated in non-BRCA1-like tumors (P < 0.05). A significant association with worse prognosis was evident for patients with BRCA1-like tumors (adjusted HR = 3.32, 95% CI = 1.30-8.48, P = 0.01). TN tumors can be further divided into two major subgroups, BRCA1-like and non-BRCA1-like with different mutation and expression patterns and prognoses. Based on these molecular patterns, subgroups may be more sensitive to specific targeted agents such as PI3K or PARP inhibitors.

  8. The Molecular Signature of HIV-1-Associated Lipomatosis Reveals Differential Involvement of Brown and Beige/Brite Adipocyte Cell Lineages.

    PubMed

    Cereijo, Rubén; Gallego-Escuredo, José Miguel; Moure, Ricardo; Villarroya, Joan; Domingo, Joan Carles; Fontdevila, Joan; Martínez, Esteban; Gutiérrez, Maria del Mar; Mateo, María Gracia; Giralt, Marta; Domingo, Pere; Villarroya, Francesc

    2015-01-01

    Highly active antiretroviral therapy has remarkably improved quality of life of HIV-1-infected patients. However, this treatment has been associated with the so-called lipodystrophic syndrome, which conveys a number of adverse metabolic effects and morphological alterations. Among them, lipoatrophy of subcutaneous fat in certain anatomical areas and hypertrophy of visceral depots are the most common. Less frequently, lipomatous enlargements of subcutaneous fat at distinct anatomic areas occur. Lipomatous adipose tissue in the dorso-cervical area ("buffalo hump") has been associated with a partial white-to-brown phenotype transition and with increased cell proliferation, but, to date, lipomatous enlargements arising in other parts of the body have not been characterized. In order to establish the main molecular events associated with the appearance of lipomatosis in HIV-1 patients, we analyzed biopsies of lipomatous tissue from "buffalo hump" and from other anatomical areas in patients, in comparison with healthy subcutaneous adipose tissue, using a marker gene expression approach. Both buffalo-hump and non-buffalo-hump lipomatous adipose tissues exhibited similar patterns of non-compromised adipogenesis, unaltered inflammation, non-fibrotic phenotype and proliferative activity. Shorter telomere length, prelamin A accumulation and SA-β-Gal induction, reminiscent of adipocyte senescence, were also common to both types of lipomatous tissues. Buffalo hump biopsies showed expression of marker genes of brown adipose tissue (e.g. UCP1) and, specifically, of "classical" brown adipocytes (e.g. ZIC1) but not of beige/brite adipocytes. No such brown fat-related gene expression occurred in lipomatous tissues at other anatomical sites. In conclusion, buffalo hump and other subcutaneous adipose tissue enlargements from HIV-1-infected patients share a similar lipomatous character. However, a distorted induction of white-to-"classical brown adipocyte" phenotype appears unique of

  9. Molecular signature and in vivo behavior of bone marrow endosteal and subendosteal stromal cell populations and their relevance to hematopoiesis

    SciTech Connect

    Balduino, Alex; Mello-Coelho, Valeria; Wang, Zhou; Taichman, Russell S.; Krebsbach, Paul H.; Weeraratna, Ashani T.; Becker, Kevin G.; Mello, Wallace de; Taub, Dennis D.; Borojevic, Radovan

    2012-11-15

    In the bone marrow cavity, hematopoietic stem cells (HSC) have been shown to reside in the endosteal and subendosteal perivascular niches, which play specific roles on HSC maintenance. Although cells with long-term ability to reconstitute full hematopoietic system can be isolated from both niches, several data support a heterogenous distribution regarding the cycling behavior of HSC. Whether this distinct behavior depends upon the role played by the stromal populations which distinctly create these two niches is a question that remains open. In the present report, we used our previously described in vivo assay to demonstrate that endosteal and subendosteal stromal populations are very distinct regarding skeletal lineage differentiation potential. This was further supported by a microarray-based analysis, which also demonstrated that these two stromal populations play distinct, albeit complementary, roles in HSC niche. Both stromal populations were preferentially isolated from the trabecular region and behave distinctly in vitro, as previously reported. Even though these two niches are organized in a very close range, in vivo assays and molecular analyses allowed us to identify endosteal stroma (F-OST) cells as fully committed osteoblasts and subendosteal stroma (F-RET) cells as uncommitted mesenchymal cells mainly represented by perivascular reticular cells expressing high levels of chemokine ligand, CXCL12. Interestingly, a number of cytokines and growth factors including interleukin-6 (IL-6), IL-7, IL-15, Hepatocyte growth factor (HGF) and stem cell factor (SCF) matrix metalloproteases (MMPs) were also found to be differentially expressed by F-OST and F-RET cells. Further microarray analyses indicated important mechanisms used by the two stromal compartments in order to create and coordinate the 'quiescent' and 'proliferative' niches in which hematopoietic stem cells and progenitors reside.

  10. The signature of seeds in resurrection plants: a molecular and physiological comparison of desiccation tolerance in seeds and vegetative tissues.

    PubMed

    Illing, Nicola; Denby, Katherine J; Collett, Helen; Shen, Arthur; Farrant, Jill M

    2005-11-01

    Desiccation-tolerance in vegetative tissues of angiosperms has a polyphyletic origin and could be due to 1) appropriation of the seed-specific program of gene expression that protects orthodox seeds against desiccation, and/or 2) a sustainable version of the abiotic stress response. We tested these hypotheses by comparing molecular and physiological data from the development of orthodox seeds, the response of desiccation-sensitive plants to abiotic stress, and the response of desiccation-tolerant plants to extreme water loss. Analysis of publicly-available gene expression data of 35 LEA proteins and 68 anti-oxidant enzymes in the desiccation-sensitive Arabidopsis thaliana identified 13 LEAs and 4 anti-oxidants exclusively expressed in seeds. Two (a LEA6 and 1-cys-peroxiredoxin) are not expressed in vegetative tissues in A. thaliana, but have orthologues that are specifically activated in desiccating leaves of Xerophyta humilis. A comparison of antioxidant enzyme activity in two desiccation-sensitive species of Eragrostis with the desiccation-tolerant E. nindensis showed equivalent responses upon initial dehydration, but activity was retained at low water content in E. nindensis only. We propose that these antioxidants are housekeeping enzymes and that they are protected from damage in the desiccation-tolerant species. Sucrose is considered an important protectant against desiccation in orthodox seeds, and we show that sucrose accumulates in drying leaves of E. nindensis, but not in the desiccation-sensitive Eragrostis species. The activation of "seed-specific" desiccation protection mechanisms (sucrose accumulation and expression of LEA6 and 1-cys-peroxiredoxin genes) in the vegetative tissues of desiccation-tolerant plants points towards acquisition of desiccation tolerance from seeds.

  11. Evidence for nucleosynthetic enrichment of the protosolar molecular cloud core by multiple supernova events.

    PubMed

    Schiller, Martin; Paton, Chad; Bizzarro, Martin

    2015-01-15

    The presence of isotope heterogeneity of nucleosynthetic origin amongst meteorites and their components provides a record of the diverse stars that contributed matter to the protosolar molecular cloud core. Understanding how and when the solar system's nucleosynthetic heterogeneity was established and preserved within the solar protoplanetary disk is critical for unraveling the earliest formative stages of the solar system. Here, we report calcium and magnesium isotope measurements of primitive and differentiated meteorites as well as various types of refractory inclusions, including refractory inclusions (CAIs) formed with the canonical (26)Al/(27)Al of ~5 × 10(-5) ((26)Al decays to (26)Mg with a half-life of ~0.73 Ma) and CAIs that show fractionated and unidentified nuclear effects (FUN-CAIs) to understand the origin of the solar system's nucleosynthetic heterogeneity. Bulk analyses of primitive and differentiated meteorites along with canonical and FUN-CAIs define correlated, mass-independent variations in (43)Ca, (46)Ca and (48)Ca. Moreover, sequential dissolution experiments of the Ivuna carbonaceous chondrite aimed at identifying the nature and number of presolar carriers of isotope anomalies within primitive meteorites have detected the presence of multiple carriers of the short-lived (26)Al nuclide as well as carriers of anomalous and uncorrelated (43)Ca, (46)Ca and (48)Ca compositions, which requires input from multiple and recent supernovae sources. We infer that the solar system's correlated nucleosynthetic variability reflects unmixing of old, galactically-inherited homogeneous dust from a new, supernovae-derived dust component formed shortly prior to or during the evolution of the giant molecular cloud parental to the protosolar molecular cloud core. This implies that similarly to (43)Ca, (46)Ca and (48)Ca, the short-lived (26)Al nuclide was heterogeneously distributed in the inner solar system at the time of CAI formation.

  12. Generalized Scalable Multiple Copy Algorithms for Molecular Dynamics Simulations in NAMD

    PubMed Central

    Jiang, Wei; Phillips, James C.; Huang, Lei; Fajer, Mikolai; Meng, Yilin; Gumbart, James C.; Luo, Yun; Schulten, Klaus; Roux, Benoît

    2014-01-01

    Computational methodologies that couple the dynamical evolution of a set of replicated copies of a system of interest offer powerful and flexible approaches to characterize complex molecular processes. Such multiple copy algorithms (MCAs) can be used to enhance sampling, compute reversible work and free energies, as well as refine transition pathways. Widely used examples of MCAs include temperature and Hamiltonian-tempering replica-exchange molecular dynamics (T-REMD and H-REMD), alchemical free energy perturbation with lambda replica-exchange (FEP/λ-REMD), umbrella sampling with Hamiltonian replica exchange (US/H-REMD), and string method with swarms-of-trajectories conformational transition pathways. Here, we report a robust and general implementation of MCAs for molecular dynamics (MD) simulations in the highly scalable program NAMD built upon the parallel programming system Charm++. Multiple concurrent NAMD instances are launched with internal partitions of Charm++ and located continuously within a single communication world. Messages between NAMD instances are passed by low-level point-to-point communication functions, which are accessible through NAMD’s Tcl scripting interface. The communication-enabled Tcl scripting provides a sustainable application interface for end users to realize generalized MCAs without modifying the source code. Illustrative applications of MCAs with fine-grained inter-copy communication structure, including global lambda exchange in FEP/λ-REMD, window swapping US/H-REMD in multidimensional order parameter space, and string method with swarms-of-trajectories were carried out on IBM Blue Gene/Q to demonstrate the versatility and massive scalability of the present implementation. PMID:24944348

  13. Evidence for nucleosynthetic enrichment of the protosolar molecular cloud core by multiple supernova events

    PubMed Central

    Schiller, Martin; Paton, Chad; Bizzarro, Martin

    2015-01-01

    The presence of isotope heterogeneity of nucleosynthetic origin amongst meteorites and their components provides a record of the diverse stars that contributed matter to the protosolar molecular cloud core. Understanding how and when the solar system’s nucleosynthetic heterogeneity was established and preserved within the solar protoplanetary disk is critical for unraveling the earliest formative stages of the solar system. Here, we report calcium and magnesium isotope measurements of primitive and differentiated meteorites as well as various types of refractory inclusions, including refractory inclusions (CAIs) formed with the canonical 26Al/27Al of ~5 × 10−5 (26Al decays to 26Mg with a half-life of ~0.73 Ma) and CAIs that show fractionated and unidentified nuclear effects (FUN-CAIs) to understand the origin of the solar system’s nucleosynthetic heterogeneity. Bulk analyses of primitive and differentiated meteorites along with canonical and FUN-CAIs define correlated, mass-independent variations in 43Ca, 46Ca and 48Ca. Moreover, sequential dissolution experiments of the Ivuna carbonaceous chondrite aimed at identifying the nature and number of presolar carriers of isotope anomalies within primitive meteorites have detected the presence of multiple carriers of the short-lived 26Al nuclide as well as carriers of anomalous and uncorrelated 43Ca, 46Ca and 48Ca compositions, which requires input from multiple and recent supernovae sources. We infer that the solar system’s correlated nucleosynthetic variability reflects unmixing of old, galactically-inherited homogeneous dust from a new, supernovae-derived dust component formed shortly prior to or during the evolution of the giant molecular cloud parental to the protosolar molecular cloud core. This implies that similarly to 43Ca, 46Ca and 48Ca, the short-lived 26Al nuclide was heterogeneously distributed in the inner solar system at the time of CAI formation. PMID:25684790

  14. Melt rheology and molecular weight degradation of amylopectin during multiple pass extrusion of starch

    SciTech Connect

    Willett, J.L.; Millard, M.M.; Jasberg, B.K.

    1996-12-31

    The degradation of starch during extrusion and the role of specific mechanical energy (SME) in this process have been widely studied for single pass extrusion, Multiple extrusion histories are not uncommon in the plastics industry, but little if any has been reported on their effects on starch. Native waxy maize starch (app. 98% amylopectin) was initially converted to a thermoplastic by twin screw extrusion. This extrudate was equilibrated to either 18% or 23% moisture content, and subsequently re-extruded in a single screw extruder (3:1 compression screw) at 110{degrees}C or 130{degrees}C. Melt viscosity data were calculated using the output-pressure data from the second pass. The melts exhibited shear thinning behavior; the power law index increased with temperature, and slightly with moisture content. Molecular weights of selected second-pass extrudates, as well as the native starch and the first-pass extrudate, were measured by light scattering in dimethyl sulfoxide/water. The initial extrusion pass reduced the molecular weight from 300 million to 50 million. Molecular weight reductions in the second pass increased with increasing SME. A first order expression was shown to fit the MW-SME data with a correlation coefficient of 0.91. Implications of the degradation on extrusion processing of starch and the use of single screw extruders for rheological characterization will be discussed.

  15. Multiple Time-Step Dual-Hamiltonian Hybrid Molecular Dynamics — Monte Carlo Canonical Propagation Algorithm

    PubMed Central

    Weare, Jonathan; Dinner, Aaron R.; Roux, Benoît

    2016-01-01

    A multiple time-step integrator based on a dual Hamiltonian and a hybrid method combining molecular dynamics (MD) and Monte Carlo (MC) is proposed to sample systems in the canonical ensemble. The Dual Hamiltonian Multiple Time-Step (DHMTS) algorithm is based on two similar Hamiltonians: a computationally expensive one that serves as a reference and a computationally inexpensive one to which the workload is shifted. The central assumption is that the difference between the two Hamiltonians is slowly varying. Earlier work has shown that such dual Hamiltonian multiple time-step schemes effectively precondition nonlinear differential equations for dynamics by reformulating them into a recursive root finding problem that can be solved by propagating a correction term through an internal loop, analogous to RESPA. Of special interest in the present context, a hybrid MD-MC version of the DHMTS algorithm is introduced to enforce detailed balance via a Metropolis acceptance criterion and ensure consistency with the Boltzmann distribution. The Metropolis criterion suppresses the discretization errors normally associated with the propagation according to the computationally inexpensive Hamiltonian, treating the discretization error as an external work. Illustrative tests are carried out to demonstrate the effectiveness of the method. PMID:26918826

  16. What Do Effective Treatments for Multiple Sclerosis Tell Us about the Molecular Mechanisms Involved in Pathogenesis?

    PubMed Central

    Buzzard, Katherine A.; Broadley, Simon A.; Butzkueven, Helmut

    2012-01-01

    Multiple sclerosis is a potentially debilitating disease of the central nervous system. A concerted program of research by many centers around the world has consistently demonstrated the importance of the immune system in its pathogenesis. This knowledge has led to the formal testing of a number of therapeutic agents in both animal models and humans. These clinical trials have shed yet further light on the pathogenesis of MS through their sometimes unexpected effects and by their differential effects in terms of impact on relapses, progression of the disease, paraclinical parameters (MRI) and the adverse events that are experienced. Here we review the currently approved medications for the commonest form of multiple sclerosis (relapsing-remitting) and the emerging therapies for which preliminary results from phase II/III clinical trials are available. A detailed analysis of the molecular mechanisms responsible for the efficacy of these medications in multiple sclerosis indicates that blockade or modulation of both T- and B-cell activation and migration pathways in the periphery or CNS can lead to amelioration of the disease. It is hoped that further therapeutic trials will better delineate the pathogenesis of MS, ultimately leading to even better treatments with fewer adverse effects. PMID:23202920

  17. The Molecular Signature of HIV-1-Associated Lipomatosis Reveals Differential Involvement of Brown and Beige/Brite Adipocyte Cell Lineages

    PubMed Central

    Cereijo, Rubén; Gallego-Escuredo, José Miguel; Moure, Ricardo; Villarroya, Joan; Domingo, Joan Carles; Fontdevila, Joan; Martínez, Esteban; Gutiérrez, Maria del Mar; Mateo, María Gracia; Giralt, Marta; Domingo, Pere; Villarroya, Francesc

    2015-01-01

    Highly active antiretroviral therapy has remarkably improved quality of life of HIV-1-infected patients. However, this treatment has been associated with the so-called lipodystrophic syndrome, which conveys a number of adverse metabolic effects and morphological alterations. Among them, lipoatrophy of subcutaneous fat in certain anatomical areas and hypertrophy of visceral depots are the most common. Less frequently, lipomatous enlargements of subcutaneous fat at distinct anatomic areas occur. Lipomatous adipose tissue in the dorso-cervical area (“buffalo hump”) has been associated with a partial white-to-brown phenotype transition and with increased cell proliferation, but, to date, lipomatous enlargements arising in other parts of the body have not been characterized. In order to establish the main molecular events associated with the appearance of lipomatosis in HIV-1 patients, we analyzed biopsies of lipomatous tissue from “buffalo hump” and from other anatomical areas in patients, in comparison with healthy subcutaneous adipose tissue, using a marker gene expression approach. Both buffalo-hump and non-buffalo-hump lipomatous adipose tissues exhibited similar patterns of non-compromised adipogenesis, unaltered inflammation, non-fibrotic phenotype and proliferative activity. Shorter telomere length, prelamin A accumulation and SA-β-Gal induction, reminiscent of adipocyte senescence, were also common to both types of lipomatous tissues. Buffalo hump biopsies showed expression of marker genes of brown adipose tissue (e.g. UCP1) and, specifically, of “classical” brown adipocytes (e.g. ZIC1) but not of beige/brite adipocytes. No such brown fat-related gene expression occurred in lipomatous tissues at other anatomical sites. In conclusion, buffalo hump and other subcutaneous adipose tissue enlargements from HIV-1-infected patients share a similar lipomatous character. However, a distorted induction of white-to-“classical brown adipocyte” phenotype

  18. Spatio-Temporal Gene Expression Profiling during In Vivo Early Ovarian Folliculogenesis: Integrated Transcriptomic Study and Molecular Signature of Early Follicular Growth

    PubMed Central

    Bonnet, Agnes; Servin, Bertrand; Mulsant, Philippe; Mandon-Pepin, Beatrice

    2015-01-01

    Background The successful achievement of early ovarian folliculogenesis is important for fertility and reproductive life span. This complex biological process requires the appropriate expression of numerous genes at each developmental stage, in each follicular compartment. Relatively little is known at present about the molecular mechanisms that drive this process, and most gene expression studies have been performed in rodents and without considering the different follicular compartments. Results We used RNA-seq technology to explore the sheep transcriptome during early ovarian follicular development in the two main compartments: oocytes and granulosa cells. We documented the differential expression of 3,015 genes during this phase and described the gene expression dynamic specific to these compartments. We showed that important steps occurred during primary/secondary transition in sheep. We also described the in vivo molecular course of a number of pathways. In oocytes, these pathways documented the chronology of the acquisition of meiotic competence, migration and cellular organization, while in granulosa cells they concerned adhesion, the formation of cytoplasmic projections and steroid synthesis. This study proposes the involvement in this process of several members of the integrin and BMP families. The expression of genes such as Kruppel-like factor 9 (KLF9) and BMP binding endothelial regulator (BMPER) was highlighted for the first time during early follicular development, and their proteins were also predicted to be involved in gene regulation. Finally, we selected a data set of 24 biomarkers that enabled the discrimination of early follicular stages and thus offer a molecular signature of early follicular growth. This set of biomarkers includes known genes such as SPO11 meiotic protein covalently bound to DSB (SPO11), bone morphogenetic protein 15 (BMP15) and WEE1 homolog 2 (S. pombe)(WEE2) which play critical roles in follicular development but other

  19. Molecular Grafting onto a Stable Framework Yields Novel Cyclic Peptides for the Treatment of Multiple Sclerosis

    PubMed Central

    2013-01-01

    Multiple sclerosis (MS) is an inflammatory disease of the central nervous system (CNS) and is characterized by the destruction of myelin and axons leading to progressive disability. Peptide epitopes from CNS proteins, such as myelin oligodendrocyte glycoprotein (MOG), possess promising immunoregulatory potential for treating MS; however, their instability and poor bioavailability is a major impediment for their use clinically. To overcome this problem, we used molecular grafting to incorporate peptide sequences from the MOG35–55 epitope onto a cyclotide, which is a macrocyclic peptide scaffold that has been shown to be intrinsically stable. Using this approach, we designed novel cyclic peptides that retained the structure and stability of the parent scaffold. One of the grafted peptides, MOG3, displayed potent ability to prevent disease development in a mouse model of MS. These results demonstrate the potential of bioengineered cyclic peptides for the treatment of MS. PMID:24147816

  20. Molecular and biologic markers of progression in monoclonal gammopathy of undetermined significance to multiple myeloma.

    PubMed

    Mailankody, Sham; Mena, Esther; Yuan, Constance M; Balakumaran, Arun; Kuehl, W Michael; Landgren, Ola

    2010-12-01

    Multiple myeloma (MM) is a malignant plasma cell dyscrasia localized in the bone marrow. Recent studies have shown that MM is preceded in virtually all cases by a premalignant state called monoclonal gammopathy of undetermined significance (MGUS). This review focuses on non-IgM MGUS and its progression to MM. Although certain clinical markers of MGUS progression have been identified, it currently is not possible to accurately determine individual risk of progression. This review focuses on the various biologic and molecular markers that could be used to determine the risk of MM progression. A better understanding of the pathogenesis will allow us to define the biological high-risk precursor disease and, ultimately, to develop early intervention strategies designed to delay and prevent full-blown MM.

  1. HIV-1 and HIV-2 LTR nucleotide sequences: assessment of the alignment by N-block presentation, "retroviral signatures" of overrepeated oligonucleotides, and a probable important role of scrambled stepwise duplications/deletions in molecular evolution.

    PubMed

    Laprevotte, I; Pupin, M; Coward, E; Didier, G; Terzian, C; Devauchelle, C; Hénaut, A

    2001-07-01

    Previous analyses of retroviral nucleotide sequences, suggest a so-called "scrambled duplicative stepwise molecular evolution" (many sectors with successive duplications/deletions of short and longer motifs) that could have stemmed from one or several starter tandemly repeated short sequence(s). In the present report, we tested this hypothesis by focusing on the long terminal repeats (LTRs) (and flanking sequences) of 24 human and 3 simian immunodeficiency viruses. By using a calculation strategy applicable to short sequences, we found consensus overrepresented motifs (often containing CTG or CAG) that were congruent with the previously defined "retroviral signature." We also show many local repetition patterns that are significant when compared with simply shuffled sequences. First- and second-order Markov chain analyses demonstrate that a major portion of the overrepresented oligonucleotides can be predicted from the dinucleotide compositions of the sequences, but by no means can biological mechanisms be deduced from these results: some of the listed local repetitions remain significant against dinucleotide-conserving shuffled sequences; together with previous results, this suggests that interspersed and/or local mononucleotide and oligonucleotide repetitions could have biased the dinucleotide compositions of the sequences. We searched for suggestive evolutionary patterns by scrutinizing a reliable multiple alignment of the 27 sequences. A manually constructed alignment based on homology blocks was in good agreement with the polypeptide alignment in the coding sectors and has been exhaustively assessed by using a multiplied alphabet obtained by the promising mathematical strategy called the N-block presentation (taking into account the environment of each nucleotide in a sequence). Sector by sector, we hypothesize many successive duplication/deletion scenarios that fit our previous evolutionary hypotheses. This suggests an important duplication/deletion role for

  2. Current and emerging strategies for the treatment and management of systemic lupus erythematosus based on molecular signatures of acute and chronic inflammation

    PubMed Central

    Das, Undurti N

    2010-01-01

    Lupus is a chronic, systemic inflammatory condition in which eicosanoids, cytokines, nitric oxide (NO), a deranged immune system, and genetics play a significant role. Our studies revealed that an imbalance in the pro- and antioxidants and NO and an alteration in the metabolism of essential fatty acids exist in lupus. The current strategy of management includes administration of nonsteroidal anti-inflammatory drugs such as hydroxychloroquine and immunosuppressive drugs such as corticosteroids. Investigational drugs include the following: 1) belimumab, a fully human monoclonal antibody that specifically recognizes and inhibits the biological activity of B-lymphocyte stimulator, also known as B-cell-activation factor of the TNF family; 2) stem cell transplantation; 3) rituximab, a chimeric monoclonal antibody against CD20, which is primarily found on the surface of B-cells and can therefore destroy B-cells; and 4) IL-27, which has potent anti-inflammatory actions. Our studies showed that a regimen of corticosteroids and cyclophosphamide, and methods designed to enhance endothelial NO synthesis and augment antioxidant defenses, led to induction of long-lasting remission of the disease. These results suggest that methods designed to modulate molecular signatures of the disease process and suppress inflammation could be of significant benefit in lupus. Some of these strategies could be vagal nerve stimulation, glucose–insulin infusion, and administration of lipoxins, resolvins, protectins, and nitrolipids by themselves or their stable synthetic analogs that are known to suppress inflammation and help in the resolution and healing of the inflammation-induced damage. These strategies are likely to be useful not only in lupus but also in other conditions, such as rheumatoid arthritis, scleroderma, ischemia-reperfusion injury to the myocardium, ischemic heart disease, and sepsis. PMID:22096364

  3. Existence of CD8α-like dendritic cells with a conserved functional specialization and a common molecular signature in distant mammalian species.

    PubMed

    Contreras, Vanessa; Urien, Céline; Guiton, Rachel; Alexandre, Yannick; Vu Manh, Thien-Phong; Andrieu, Thibault; Crozat, Karine; Jouneau, Luc; Bertho, Nicolas; Epardaud, Mathieu; Hope, Jayne; Savina, Ariel; Amigorena, Sebastian; Bonneau, Michel; Dalod, Marc; Schwartz-Cornil, Isabelle

    2010-09-15

    The mouse lymphoid organ-resident CD8alpha(+) dendritic cell (DC) subset is specialized in Ag presentation to CD8(+) T cells. Recent evidence shows that mouse nonlymphoid tissue CD103(+) DCs and human blood DC Ag 3(+) DCs share similarities with CD8alpha(+) DCs. We address here whether the organization of DC subsets is conserved across mammals in terms of gene expression signatures, phenotypic characteristics, and functional specialization, independently of the tissue of origin. We study the DC subsets that migrate from the skin in the ovine species that, like all domestic animals, belongs to the Laurasiatheria, a distinct phylogenetic clade from the supraprimates (human/mouse). We demonstrate that the minor sheep CD26(+) skin lymph DC subset shares significant transcriptomic similarities with mouse CD8alpha(+) and human blood DC Ag 3(+) DCs. This allowed the identification of a common set of phenotypic characteristics for CD8alpha-like DCs in the three mammalian species (i.e., SIRP(lo), CADM1(hi), CLEC9A(hi), CD205(hi), XCR1(hi)). Compared to CD26(-) DCs, the sheep CD26(+) DCs show 1) potent stimulation of allogeneic naive CD8(+) T cells with high selective induction of the Ifngamma and Il22 genes; 2) dominant efficacy in activating specific CD8(+) T cells against exogenous soluble Ag; and 3) selective expression of functional pathways associated with high capacity for Ag cross-presentation. Our results unravel a unifying definition of the CD8alpha(+)-like DCs across mammalian species and identify molecular candidates that could be used for the design of vaccines applying to mammals in general.

  4. A low molecular weight artificial RNA of unique size with multiple probe target regions

    NASA Technical Reports Server (NTRS)

    Pitulle, C.; Dsouza, L.; Fox, G. E.

    1997-01-01

    Artificial RNAs (aRNAs) containing novel sequence segments embedded in a deletion mutant of Vibrio proteolyticus 5S rRNA have previously been shown to be expressed from a plasmid borne growth rate regulated promoter in E. coli. These aRNAs accumulate to high levels and their detection is a promising tool for studies in molecular microbial ecology and in environmental monitoring. Herein a new construct is described which illustrates the versatility of detection that is possible with aRNAs. This 3xPen aRNA construct carries a 72 nucleotide insert with three copies of a unique 17 base probe target sequence. This aRNA is 160 nucleotides in length and again accumulates to high levels in the E. coli cytoplasm without incorporating into ribosomes. The 3xPen aRNA illustrates two improvements in detection. First, by appropriate selection of insert size, we obtained an aRNA which provides a unique and hence, easily quantifiable peak, on a high resolution gel profile of low molecular weight RNAs. Second, the existence of multiple probe targets results in a nearly commensurate increase in signal when detection is by hybridization. These aRNAs are naturally amplified and carry sequence segments that are not found in known rRNA sequences. It thus may be possible to detect them directly. An experimental step involving RT-PCR or PCR amplification of the gene could therefore be avoided.

  5. Fluorescence detection of adenosine triphosphate through an aptamer-molecular beacon multiple probe.

    PubMed

    Zeng, Xiaodan; Zhang, Xiaoling; Yang, Wen; Jia, Hongying; Li, Yamin

    2012-05-01

    An aptamer-molecular beacon (MB) multiple fluorescent probe for adenosine triphosphate (ATP) assay is proposed in this article. The ATP aptamer was used as a molecular recognition part, and an oligonucleotide (short strand, SS) partially complementary with the aptamer and an MB was used as the other part. In the presence of ATP, the aptamer bound with it, accompanied by the hybridization of MB and SS and the fluorescence recovering. Wherever there is only very weak fluorescence can be measured in the absence of ATP. Based on the relationship of recovering fluorescence and the concentration of ATP, a method for quantifying ATP has been developed. The fluorescence intensity was proportional to the concentration of ATP in the range of 10 to 500 nM with a detection limit of 0.1 nM. Moreover, this method was able to detect ATP with high selectivity in the presence of guanosine triphosphate (GTP), cytidine triphosphate (CTP), and uridine triphosphate (UTP). This method is proved to be simple with high sensitivity, selectivity, and specificity.

  6. Characterization of the molecular mechanism of the bone-anabolic activity of carfilzomib in multiple myeloma.

    PubMed

    Hu, Bo; Chen, Yu; Usmani, Saad Z; Ye, Shiqiao; Qiang, Wei; Papanikolaou, Xenofon; Heuck, Christoph J; Yaccoby, Shmuel; Williams, Bart O; Van Rhee, Frits; Barlogie, Bart; Epstein, Joshua; Qiang, Ya-Wei

    2013-01-01

    Carfilzomib, the next generation of proteasome inhibitor, may increase osteoblast-related markers in patients with multiple myeloma, but the molecular mechanism of its effect on mesenchymal stem cell differentiation to osteoblasts remains unknown. Herein, we demonstrated that carfilzomib significantly promoted mesenchymal stem cell differentiation into osteoblasts. In osteoprogenitor cells and primary mesenchymal stem cells from patients with myeloma, carfilzomib induced increases in alkaline phosphatase activity, matrix mineralization, and calcium deposition via Wnt-independent activation of β-catenin/TCF signaling. Using affinity pull-down assays with immunoblotting analysis and immunofluorescence, we found that carfilzomib induced stabilization of both free and active forms of β-catenin in a time- and dose-dependent manner that was not associated with β-catenin transcriptional regulation. Nuclear translocation of β-catenin protein was associated with TCF transcriptional activity that was independent of the effects of GSK3β-activation and of signaling induced by 19 Wnt ligands, 10 Frizzled receptors, and LRP5/6 co-receptors. Blocking activation of β-catenin/TCF signaling by dominant negative TCF1 or TCF4 attenuated carfilzomib-induced matrix mineralization. Thus, carfilzomib induced osteoblast differentiation via Wnt-independent activation of the β-catenin/TCF pathway. These results provide a novel molecular mechanism critical to understanding the anabolic role of carfilzomib on myeloma-induced bone disease.

  7. Infrared-active quadruple contrast FePt nanoparticles for multiple scale molecular imaging.

    PubMed

    Chou, Shang-Wei; Liu, Chien-Liang; Liu, Tzu-Ming; Shen, Yu-Fang; Kuo, Lun-Chang; Wu, Cheng-Ham; Hsieh, Tsung-Yuan; Wu, Pei-Chun; Tsai, Ming-Rung; Yang, Che-Chang; Chang, Kai-Yao; Lu, Meng-Hua; Li, Pai-Chi; Chen, Shi-Ping; Wang, Yu-Hsin; Lu, Chen-Wen; Chen, Yi-An; Huang, Chih-Chia; Wang, Churng-Ren Chris; Hsiao, Jong-Kai; Li, Meng-Lin; Chou, Pi-Tai

    2016-04-01

    A single nanomaterial with multiple imaging contrasts and functions is highly desired for multiscale theragnosis. Herein, we demonstrate single 1-1.9 μm infrared-active FePt alloy nanoparticles (FePt NPs) offering unprecedented four-contrast-in-one molecular imaging - computed tomography (CT), magnetic resonance imaging (MRI), photoacoustic (PA) imaging, and high-order multiphoton luminescence (HOMPL) microscopy. The PA response of FePt NPs outperforms that of infrared-active gold nanorods by 3- to 5.6-fold under identical excitation fluence and particle concentrations. HOMPL (680 nm) of an isolated FePt NP renders spatial full-width-at-half-maximum values of 432 nm and 300 nm beyond the optical diffraction limit for 1230-nm and 920-nm excitation, respectively. The in vivo targeting function was successfully visualized using HOMPL, PA imaging, CT, and MRI, thereby validating FePt as a single nanomaterial system covering up to four types (Optical/PA/CT/MRI) of molecular imaging contrast, ranging from the microscopic level to whole-body scale investigation.

  8. Coupled biophysical global ocean model and molecular genetic analyses identify multiple introductions of cryptogenic species.

    PubMed

    Dawson, Michael N; Sen Gupta, Alex; England, Matthew H

    2005-08-23

    The anthropogenic introduction of exotic species is one of the greatest modern threats to marine biodiversity. Yet exotic species introductions remain difficult to predict and are easily misunderstood because knowledge of natural dispersal patterns, species diversity, and biogeography is often insufficient to distinguish between a broadly dispersed natural population and an exotic one. Here we compare a global molecular phylogeny of a representative marine meroplanktonic taxon, the moon-jellyfish Aurelia, with natural dispersion patterns predicted by a global biophysical ocean model. Despite assumed high dispersal ability, the phylogeny reveals many cryptic species and predominantly regional structure with one notable exception: the globally distributed Aurelia sp.1, which, molecular data suggest, may occasionally traverse the Pacific unaided. This possibility is refuted by the ocean model, which shows much more limited dispersion and patterns of distribution broadly consistent with modern biogeographic zones, thus identifying multiple introductions worldwide of this cryptogenic species. This approach also supports existing evidence that (i) the occurrence in Hawaii of Aurelia sp. 4 and other native Indo-West Pacific species with similar life histories is most likely due to anthropogenic translocation, and (ii) there may be a route for rare natural colonization of northeast North America by the European marine snail Littorina littorea, whose status as endemic or exotic is unclear.

  9. Intrinsic Raman Signatures of Pristine Hybrid Perovskite CH3NH3PbI3 and its Multiple Stages of Structure Transformation

    SciTech Connect

    Chen, Qiong; Liu, Henan; Kim, Hui-Seon; Liu, Yucheng; Yang, Mengjin; Yue, Naili; Ren, Gang; Zhu, Kai; Liu, Shengzhong; Park, Nam-Gyu; Zhang, Yong

    2016-11-21

    By performing spatially resolved Raman and photoluminescence spectroscopy with different illumination conditions, we have achieved a unified understanding towards the spectroscopy signatures of the organic-inorganic hybrid perovskite, transforming from the pristine state (CH3NH3PbI3 or MAPbI3) to fully degraded state (i.e., PbI2), for samples with varying crystalline domain size from mesoscopic scale to macroscopic size, synthesized by three different techniques.

  10. Identification of molecular vulnerabilities in human multiple myeloma cells by RNA interference lethality screening of the druggable genome.

    PubMed

    Tiedemann, Rodger E; Zhu, Yuan Xao; Schmidt, Jessica; Shi, Chang Xin; Sereduk, Chris; Yin, Hongwei; Mousses, Spyro; Stewart, A Keith

    2012-02-01

    Despite recent advances in targeted treatments for multiple myeloma, optimal molecular therapeutic targets have yet to be identified. To functionally identify critical molecular targets, we conducted a genome-scale lethality study in multiple myeloma cells using siRNAs. We validated the top 160 lethal hits with four siRNAs per gene in three multiple myeloma cell lines and two non-myeloma cell lines, cataloging a total of 57 potent multiple myeloma survival genes. We identified the Bcl2 family member MCL1 and several 26S proteasome subunits among the most important and selective multiple myeloma survival genes. These results provided biologic validation of our screening strategy. Other essential targets included genes involved in RNA splicing, ubiquitination, transcription, translation, and mitosis. Several of the multiple myeloma survival genes, especially MCL1, TNK2, CDK11, and WBSCR22, exhibited differential expression in primary plasma cells compared with other human primary somatic tissues. Overall, the most striking differential functional vulnerabilities between multiple myeloma and non-multiple myeloma cells were found to occur within the 20S proteasome subunits, MCL1, RRM1, USP8, and CKAP5. We propose that these genes should be investigated further as potential therapeutic targets in multiple myeloma.

  11. Error and timing analysis of multiple time-step integration methods for molecular dynamics

    NASA Astrophysics Data System (ADS)

    Han, Guowen; Deng, Yuefan; Glimm, James; Martyna, Glenn

    2007-02-01

    Molecular dynamics simulations of biomolecules performed using multiple time-step integration methods are hampered by resonance instabilities. We analyze the properties of a simple 1D linear system integrated with the symplectic reference system propagator MTS (r-RESPA) technique following earlier work by others. A closed form expression for the time step dependent Hamiltonian which corresponds to r-RESPA integration of the model is derived. This permits us to present an analytic formula for the dependence of the integration accuracy on short-range force cutoff range. A detailed analysis of the force decomposition for the standard Ewald summation method is then given as the Ewald method is a good candidate to achieve high scaling on modern massively parallel machines. We test the new analysis on a realistic system, a protein in water. Under Langevin dynamics with a weak friction coefficient ( ζ=1 ps) to maintain temperature control and using the SHAKE algorithm to freeze out high frequency vibrations, we show that the 5 fs resonance barrier present when all degrees of freedom are unconstrained is postponed to ≈12 fs. An iso-error boundary with respect to the short-range cutoff range and multiple time step size agrees well with the analytical results which are valid due to dominance of the high frequency modes in determining integrator accuracy. Using r-RESPA to treat the long range interactions results in a 6× increase in efficiency for the decomposition described in the text.

  12. A note on the use of multiple linear regression in molecular ecology.

    PubMed

    Frasier, Timothy R

    2016-03-01

    Multiple linear regression analyses (also often referred to as generalized linear models--GLMs, or generalized linear mixed models--GLMMs) are widely used in the analysis of data in molecular ecology, often to assess the relative effects of genetic characteristics on individual fitness or traits, or how environmental characteristics influence patterns of genetic differentiation. However, the coefficients resulting from multiple regression analyses are sometimes misinterpreted, which can lead to incorrect interpretations and conclusions within individual studies, and can propagate to wider-spread errors in the general understanding of a topic. The primary issue revolves around the interpretation of coefficients for independent variables when interaction terms are also included in the analyses. In this scenario, the coefficients associated with each independent variable are often interpreted as the independent effect of each predictor variable on the predicted variable. However, this interpretation is incorrect. The correct interpretation is that these coefficients represent the effect of each predictor variable on the predicted variable when all other predictor variables are zero. This difference may sound subtle, but the ramifications cannot be overstated. Here, my goals are to raise awareness of this issue, to demonstrate and emphasize the problems that can result and to provide alternative approaches for obtaining the desired information.

  13. TRIB1 downregulates hepatic lipogenesis and glycogenesis via multiple molecular interactions.

    PubMed

    Ishizuka, Yuumi; Nakayama, Kazuhiro; Ogawa, Ayumi; Makishima, Saho; Boonvisut, Supichaya; Hirao, Atsushi; Iwasaki, Yusaku; Yada, Toshihiko; Yanagisawa, Yoshiko; Miyashita, Hiroshi; Takahashi, Masafumi; Iwamoto, Sadahiko

    2014-04-01

    Mammalian tribbles homolog 1 (TRIB1) regulates hepatic lipogenesis and is genetically associated with plasma triglyceride (TG) levels and cholesterol, but the molecular mechanisms remain obscure. We explored these mechanisms in mouse livers transfected with a TRIB1 overexpression, a shRNA template or a control (LacZ) adenovirus vector. The overexpression of TRIB1 reduced, whereas induction of the shRNA template increased, plasma glucose, TG, and cholesterol and simultaneously hepatic TG and glycogen levels. The involvement of TRIB1 in hepatic lipid accumulation was supported by the findings of a human SNP association study. A TRIB1 SNP, rs6982502, was identified in an enhancer sequence, modulated enhancer activity in reporter gene assays, and was significantly (P=9.39 × 10(-7)) associated with ultrasonographically diagnosed non-alcoholic fatty liver disease in a population of 5570 individuals. Transcriptome analyses of mouse livers revealed significant modulation of the gene sets involved in glycogenolysis and lipogenesis. Enforced TRIB1 expression abolished CCAAT/enhancer binding protein A (CEBPA), CEBPB, and MLXIPL proteins, whereas knockdown increased the protein level. Levels of TRIB1 expression simultaneously affected MKK4 (MAP2K4), MEK1 (MAP2K1), and ERK1/2 (MAPK1/3) protein levels and the phosphorylation of JNK, but not of ERK1/2. Pull-down and mammalian two-hybrid analyses revealed novel molecular interaction between TRIB1 and a hepatic lipogenic master regulator, MLXIPL. Co-expression of TRIB1 and CEBPA or MLXIPL reduced their protein levels and proteasome inhibitors attenuated the reduction. These data suggested that the modulation of TRIB1 expression affects hepatic lipogenesis and glycogenesis through multiple molecular interactions.

  14. Signature-based store checking buffer

    DOEpatents

    Sridharan, Vilas; Gurumurthi, Sudhanva

    2015-06-02

    A system and method for optimizing redundant output verification, are provided. A hardware-based store fingerprint buffer receives multiple instances of output from multiple instances of computation. The store fingerprint buffer generates a signature from the content included in the multiple instances of output. When a barrier is reached, the store fingerprint buffer uses the signature to verify the content is error-free.

  15. Molecular Signature of Biological Pathogens

    DTIC Science & Technology

    2007-11-02

    analysis. In vivo responses to initial Anthrax vaccinations and E. coli urinary tract infections were compared to in vitro responses to B. cereus and...to E. coli, respectively. E. coli urinary tract infections differed from controls, but did not group with in vitro infections, suggesting a limited

  16. Biogeography of soil organic matter molecular structure across multiple soil size fractions

    NASA Astrophysics Data System (ADS)

    Meier, C. L.; Neff, J.

    2009-12-01

    Recent work suggests that there is a common soil decomposition sequence whereby plant inputs are metabolized into a physiologically constrained set of compounds originating from microbes that may persist in soil over relatively long time-scales. Plant inputs tend to be found in coarse particulate fractions (>180 μm) with relatively fast turnover times, while microbially derived compounds tend to accrue in the finer silt + clay fractions (<53 μm) with relatively long turnover times. To investigate whether a common decomposition sequence exists, we used pyrolysis gas chromatography/mass spectrometry (py-GC/MS) to characterize the molecular structure of soil organic matter (SOM) in three size fractions (590-180 μm, 180-53 μm, and <53 μm), using soils sampled from multiple biomes (alpine tundra, sub-alpine forest, boreal forest, temperate coniferous, temperate deciduous, dry desert/savannah, and tropical forest). We hypothesized that: 1) regardless of biome, fractions >180 μm would be chemically similar, and would be characterized by lignin and other plant-derived compounds; and 2) fractions <53 μm would also be similar across biomes but would be dominated by microbially-derived compounds like polysaccharides. Across all biomes, we found that there was significantly less lignin in <53 μm fractions compared to >180 μm fractions (p<0.0001), providing some support for the idea that plant material is not incorporated into soil C pools with relatively long turnover times. However, a principal components analysis (PCA) showed that the >180 μm coarse particulate fractions also contained compounds associated with microbial origins, indicating that microbial C is not limited to <53 μm size fractions. The PCA also revealed that samples within each of the three size fractions did not cluster together (i.e. they did not share a common molecular structure), but we did note that: 1) cold alpine and sub-alpine sites were unique and chemically similar; and 2) tropical

  17. Signatures of nonthermal melting

    PubMed Central

    Zier, Tobias; Zijlstra, Eeuwe S.; Kalitsov, Alan; Theodonis, Ioannis; Garcia, Martin E.

    2015-01-01

    Intense ultrashort laser pulses can melt crystals in less than a picosecond but, in spite of over thirty years of active research, for many materials it is not known to what extent thermal and nonthermal microscopic processes cause this ultrafast phenomenon. Here, we perform ab-initio molecular-dynamics simulations of silicon on a laser-excited potential-energy surface, exclusively revealing nonthermal signatures of laser-induced melting. From our simulated atomic trajectories, we compute the decay of five structure factors and the time-dependent structure function. We demonstrate how these quantities provide criteria to distinguish predominantly nonthermal from thermal melting. PMID:26798822

  18. Molecular weight recognition in the multiple-stranded helix of a synthetic polymer without specific monomer-monomer interaction.

    PubMed

    Kumaki, Jiro; Kawauchi, Takehiro; Ute, Koichi; Kitayama, Tatsuki; Yashima, Eiji

    2008-05-21

    Stereoregular isotactic and syndiotactic poly(methyl methacrylate)s (it- and st-PMMAs) are known to form a multiple-stranded complementary helix, so-called stereocomplex (SC) through van der Waals interactions, which is a rare example of helical supramolecular structures formed by a commodity polymer. In this study, we prepared SCs by using uniform it- and st-PMMAs and those with a narrow molecular weight distribution having different molecular weights and investigated their structures in detail using high-resolution atomic force microscopy as a function of the molecular weight and molecular weight distribution of the component PMMAs. We found that complementary it- and st-PMMAs with the longer molecular length determine the total length of the SC, and molecules of the shorter component associate until they fill up or cover the longer component. These observations support a supramolecular triple-stranded helical structure of the SCs composed of a double-stranded helix of two intertwined it-PMMA chains included in a single helix of st-PMMA, and this triple-stranded helix model of the SCs appears to be applicable to the it- and st-PMMAs having a wide range of molecular weights we employed in this study. In homogeneous double-stranded helices of it-PMMA, it has been found that, in mixtures of two it-PMMAs with different molecular weights, chains of the same molecular weight selectively form a double-stranded it-PMMA helix, or recognize the molecular weights of each other ("molecular sorting"). We thus demonstrate that molecular weight recognition is possible, without any specific interaction between monomer units, through the formation of a topological multiple-stranded helical structure based upon van der Waals interaction.

  19. Deep sequencing revealed molecular signature of horizontal gene transfer of plant like transcripts in the mosquito Anopheles culicifacies: an evolutionary puzzle

    PubMed Central

    Sharma, Punita; Das De, Tanwee; Sharma, Swati; Kumar Mishra, Ashwani; Thomas, Tina; Verma, Sonia; Kumari, Vandana; Lata, Suman; Singh, Namita; Valecha, Neena; Chand Pandey, Kailash; Dixit, Rajnikant

    2015-01-01

    In prokaryotes, horizontal gene transfer (HGT) has been regarded as an important evolutionary drive to acquire and retain beneficial genes for their survival in diverse ecologies. However, in eukaryotes, the functional role of HGTs remains questionable, although current genomic tools are providing increased evidence of acquisition of novel traits within non-mating metazoan species. Here, we provide another transcriptomic evidence for the acquisition of massive plant genes in the mosquito, Anopheles culicifacies. Our multiple experimental validations including genomic PCR, RT-PCR, real-time PCR, immuno-blotting and immuno-florescence microscopy, confirmed that plant like transcripts (PLTs) are of mosquito origin and may encode functional proteins. A comprehensive molecular analysis of the PLTs and ongoing metagenomic analysis of salivary microbiome provide initial clues that mosquitoes may have survival benefits through the acquisition of nuclear as well as chloroplast encoded plant genes. Our findings of PLTs further support the similar questionable observation of HGTs in other higher organisms, which is still a controversial and debatable issue in the community of evolutionists. We believe future understanding of the underlying mechanism of the feeding associated molecular responses may shed new insights in the functional role of PLTs in the mosquito. PMID:26998230

  20. Characterization of the uncertainty of divergence time estimation under relaxed molecular clock models using multiple loci.

    PubMed

    Zhu, Tianqi; Dos Reis, Mario; Yang, Ziheng

    2015-03-01

    Genetic sequence data provide information about the distances between species or branch lengths in a phylogeny, but not about the absolute divergence times or the evolutionary rates directly. Bayesian methods for dating species divergences estimate times and rates by assigning priors on them. In particular, the prior on times (node ages on the phylogeny) incorporates information in the fossil record to calibrate the molecular tree. Because times and rates are confounded, our posterior time estimates will not approach point values even if an infinite amount of sequence data are used in the analysis. In a previous study we developed a finite-sites theory to characterize the uncertainty in Bayesian divergence time estimation in analysis of large but finite sequence data sets under a strict molecular clock. As most modern clock dating analyses use more than one locus and are conducted under relaxed clock models, here we extend the theory to the case of relaxed clock analysis of data from multiple loci (site partitions). Uncertainty in posterior time estimates is partitioned into three sources: Sampling errors in the estimates of branch lengths in the tree for each locus due to limited sequence length, variation of substitution rates among lineages and among loci, and uncertainty in fossil calibrations. Using a simple but analogous estimation problem involving the multivariate normal distribution, we predict that as the number of loci ([Formula: see text]) goes to infinity, the variance in posterior time estimates decreases and approaches the infinite-data limit at the rate of 1/[Formula: see text], and the limit is independent of the number of sites in the sequence alignment. We then confirmed the predictions by using computer simulation on phylogenies of two or three species, and by analyzing a real genomic data set for six primate species. Our results suggest that with the fossil calibrations fixed, analyzing multiple loci or site partitions is the most effective way

  1. Molecular and functional analysis of SUMF1 mutations in multiple sulfatase deficiency.

    PubMed

    Cosma, Maria Pia; Pepe, Stefano; Parenti, Giancarlo; Settembre, Carmine; Annunziata, Ida; Wade-Martins, Richard; Di Domenico, Carmela; Di Natale, Paola; Mankad, Anuj; Cox, Barbara; Uziel, Graziella; Mancini, Grazia M S; Zammarchi, Enrico; Donati, Maria Alice; Kleijer, Wim J; Filocamo, Mirella; Carrozzo, Romeo; Carella, Massimo; Ballabio, Andrea

    2004-06-01

    Multiple sulfatase deficiency (MSD) is a rare disorder characterized by impaired activity of all known sulfatases. The gene mutated in this disease is SUMF1, which encodes a protein involved in a post-translational modification at the catalytic site of all sulfatases that is necessary for their function. SUMF1 strongly enhances the activity of sulfatases when coexpressed with sulfatase in Cos-7 cells. We performed a mutational analysis of SUMF1 in 20 MSD patients of different ethnic origin. The clinical presentation of these patients was variable, ranging from severe neonatal forms to mild phenotypes showing mild neurological involvement. A total of 22 SUMF1 mutations were identified, including missense, nonsense, microdeletion, and splicing mutations. We expressed all missense mutations in culture to study their ability to enhance the activity of sulfatases. Of the predicted amino acid changes, 11 (p.R349W, p.R224W, p.L20F, p.A348P, p.S155P, p.C218Y, p.N259I, p.A279V, p.R349Q, p.C336R, p.A177P) resulted in severely impaired sulfatase-enhancing activity. Two (p.R345C and p.P266L) showed a high residual activity on some, but not all, of the nine sulfatases tested, suggesting that some SUMF1 mutations may have variable effects on the activity of each sulfatase. This study compares, for the first time, clinical, biochemical, and molecular data in MSD patients. Our results show lack of a direct correlation between the type of molecular defect and the severity of phenotype.

  2. Molecular evolution of multiple-level control of heme biosynthesis pathway in animal kingdom.

    PubMed

    Tzou, Wen-Shyong; Chu, Ying; Lin, Tzung-Yi; Hu, Chin-Hwa; Pai, Tun-Wen; Liu, Hsin-Fu; Lin, Han-Jia; Cases, Ildeofonso; Rojas, Ana; Sanchez, Mayka; You, Zong-Ye; Hsu, Ming-Wei

    2014-01-01

    Adaptation of enzymes in a metabolic pathway can occur not only through changes in amino acid sequences but also through variations in transcriptional activation, mRNA splicing and mRNA translation. The heme biosynthesis pathway, a linear pathway comprised of eight consecutive enzymes in animals, provides researchers with ample information for multiple types of evolutionary analyses performed with respect to the position of each enzyme in the pathway. Through bioinformatics analysis, we found that the protein-coding sequences of all enzymes in this pathway are under strong purifying selection, from cnidarians to mammals. However, loose evolutionary constraints are observed for enzymes in which self-catalysis occurs. Through comparative genomics, we found that in animals, the first intron of the enzyme-encoding genes has been co-opted for transcriptional activation of the genes in this pathway. Organisms sense the cellular content of iron, and through iron-responsive elements in the 5' untranslated regions of mRNAs and the intron-exon boundary regions of pathway genes, translational inhibition and exon choice in enzymes may be enabled, respectively. Pathway product (heme)-mediated negative feedback control can affect the transport of pathway enzymes into the mitochondria as well as the ubiquitin-mediated stability of enzymes. Remarkably, the positions of these controls on pathway activity are not ubiquitous but are biased towards the enzymes in the upstream portion of the pathway. We revealed that multiple-level controls on the activity of the heme biosynthesis pathway depend on the linear depth of the enzymes in the pathway, indicating a new strategy for discovering the molecular constraints that shape the evolution of a metabolic pathway.

  3. The Molecular Signature of the Stroma Response in Prostate Cancer-Induced Osteoblastic Bone Metastasis Highlights Expansion of Hematopoietic and Prostate Epithelial Stem Cell Niches

    PubMed Central

    Secondini, Chiara; Wetterwald, Antoinette; Schwaninger, Ruth; Fleischmann, Achim; Raffelsberger, Wolfgang; Poch, Olivier; Delorenzi, Mauro; Temanni, Ramzi; Mills, Ian G.; van der Pluijm, Gabri; Thalmann, George N.; Cecchini, Marco G.

    2014-01-01

    The reciprocal interaction between cancer cells and the tissue-specific stroma is critical for primary and metastatic tumor growth progression. Prostate cancer cells colonize preferentially bone (osteotropism), where they alter the physiological balance between osteoblast-mediated bone formation and osteoclast-mediated bone resorption, and elicit prevalently an osteoblastic response (osteoinduction). The molecular cues provided by osteoblasts for the survival and growth of bone metastatic prostate cancer cells are largely unknown. We exploited the sufficient divergence between human and mouse RNA sequences together with redefinition of highly species-specific gene arrays by computer-aided and experimental exclusion of cross-hybridizing oligonucleotide probes. This strategy allowed the dissection of the stroma (mouse) from the cancer cell (human) transcriptome in bone metastasis xenograft models of human osteoinductive prostate cancer cells (VCaP and C4-2B). As a result, we generated the osteoblastic bone metastasis-associated stroma transcriptome (OB-BMST). Subtraction of genes shared by inflammation, wound healing and desmoplastic responses, and by the tissue type-independent stroma responses to a variety of non-osteotropic and osteotropic primary cancers generated a curated gene signature (“Core” OB-BMST) putatively representing the bone marrow/bone-specific stroma response to prostate cancer-induced, osteoblastic bone metastasis. The expression pattern of three representative Core OB-BMST genes (PTN, EPHA3 and FSCN1) seems to confirm the bone specificity of this response. A robust induction of genes involved in osteogenesis and angiogenesis dominates both the OB-BMST and Core OB-BMST. This translates in an amplification of hematopoietic and, remarkably, prostate epithelial stem cell niche components that may function as a self-reinforcing bone metastatic niche providing a growth support specific for osteoinductive prostate cancer cells. The induction of this

  4. Molecular hydrogen (H2) combustion emissions and their isotope (D/H) signatures from domestic heaters, diesel vehicle engines, waste incinerator plants, and biomass burning

    NASA Astrophysics Data System (ADS)

    Vollmer, M. K.; Walter, S.; Mohn, J.; Steinbacher, M.; Bond, S. W.; Röckmann, T.; Reimann, S.

    2012-03-01

    Molecular hydrogen (H2), its stable isotope signature (δD), and the key combustion parameters carbon monoxide (CO), carbon dioxide (CO2), and methane (CH4) were measured from various combustion processes. H2 in the exhaust of gas and oil-fired heaters and of waste incinerator plants was generally depleted compared to ambient intake air, while CO was significantly elevated. These findings contradict the often assumed co-occurring net H2 and CO emissions in combustion processes and suggest that previous H2 emissions from combustion may have been overestimated when scaled to CO emissions. For the heater exhausts, H2 and δD generally decrease with increasing fuel-to-air ratio, from ambient values of ∼0.5 ppm and +130‰ to 0.2 ppm and -206‰, respectively. These results are interpreted as a combination of an isotopically light H2 source from fossil fuel combustion and a D/H kinetic isotope fractionation of hydrogen in the advected ambient air during its partial removal during combustion. Diesel exhaust measurements from dynamometer test stand driving cycles show elevated H2 and CO emissions during cold-start and some acceleration phases. Their molar H2/CO ratios are <0.25, significantly smaller than those for gasoline combustion. Using H2/CO emission ratios, along with CO global emission inventories, we estimate global H2 emissions for 2000, 2005, and 2010. For road transportation (gasoline and diesel), we calculate 8.6 ± 2.1 Tg, 6.3 ± 1.5 Tg, and 4.1 ± 1.0 Tg, respectively, whereas the contribution from diesel vehicles has increased from 5% to 8% over this time. Other fossil fuel emissions are believed to be negligible but H2 emissions from coal combustion are unknown. For residential (domestic) emissions, which are likely dominated by biofuel combustion, emissions for the same years are estimated at 2.7 ± 0.7 Tg, 2.8 ± 0.7 Tg, and 3.0 ± 0.8 Tg, respectively. Our wood combustion measurements are combined with results from the literature to calculate

  5. Molecular hydrogen (H2) emissions and their isotopic signatures (H/D) from a motor vehicle: implications on atmospheric H2

    NASA Astrophysics Data System (ADS)

    Vollmer, M. K.; Walter, S.; Bond, S. W.; Soltic, P.; Röckmann, T.

    2010-06-01

    Molecular hydrogen (H2), its isotopic signature (deuterium/hydrogen, δD), carbon monoxide (CO), and other compounds were studied in the exhaust of a passenger car engine fuelled with gasoline or methane and run under variable air-fuel ratios and operating modes. H2 and CO concentrations were largely reduced downstream of the three-way catalytic converter (TWC) compared to levels upstream, and showed a strong dependence on the air-fuel ratio (expressed as lambda, λ). The isotopic composition of H2 ranged from δD = -140‰ to δD = -195‰ upstream of the TWC but these values decreased to -270‰ to -370‰ after passing through the TWC. Post-TWC δD values for the fuel-rich range showed a strong dependence on TWC temperature with more negative δD for lower temperatures. These effects are attributed to a rapid temperature-dependent H-D isotope equilibration between H2 and water (H2O). In addition, post TWC δD in H2 showed a strong dependence on the fraction of removed H2, suggesting isotopic enrichment during catalytic removal of H2 with enrichment factors (ɛ) ranging from -39.8‰ to -15.5‰ depending on the operating mode. Our results imply that there may be considerable variability in real-world δD emissions from vehicle exhaust, which may mainly depend on TWC technology and exhaust temperature regime. This variability is suggestive of a δD from traffic that varies over time, by season, and by geographical location. An earlier-derived integrated pure (end-member) δD from anthropogenic activities of -270‰ (Rahn et al., 2002) can be explained as a mixture of mainly vehicle emissions from cold starts and fully functional TWCs, but enhanced δD values by >50‰ are likely for regions where TWC technology is not fully implemented. Our results also suggest that a full hydrogen isotope analysis on fuel and exhaust gas may greatly aid at understanding process-level reactions in the exhaust gas, in particular in the TWC.

  6. Molecular hydrogen (H2) emissions and their isotopic signatures (H/D) from a motor vehicle: implications on atmospheric H2

    NASA Astrophysics Data System (ADS)

    Vollmer, M. K.; Walter, S.; Bond, S. W.; Soltic, P.; Röckmann, T.

    2010-02-01

    Molecular hydrogen (H2), its isotopic signature (deuterium/hydrogen, δD), carbon monoxide (CO) and other compounds were studied in the exhaust of a passenger car engine fuelled with gasoline or methane and run under variable air-fuel ratios and operating modes. H2 and CO concentrations were largely reduced downstream of the three-way catalytic converter (TWC) compared to levels upstream, and showed a strong dependence on the air-fuel ratio (expressed as lambda, λ). The isotopic composition of H2 ranged from δD=-140‰ to δD=-195‰ upstream of the TWC but these values decreased to -270‰ to -370‰ after passing through the TWC. Post-TWC δD values for the fuel-rich range showed a strong dependence on TWC temperature with more negative δD for lower temperatures. These effects are attributed to a rapid temperature-dependent H-D isotope equilibration between H2 and water (H2O). In addition, post TWC δD in H2 showed a strong dependence on the fraction of removed H2, suggesting isotopic enrichment during catalytic removal of H2 with enrichment factors (ɛ) ranging from -39.8‰ to -15.5‰ depending on the operating mode. Our results imply that there may be considerable variability in real-world δD emissions from vehicle exhaust, which may mainly depend on TWC technology and exhaust temperature regime. This variability is suggestive of a δD from traffic that varies over time, by season, and by geographical location. An earlier-derived integrated pure (end-member) δD from anthropogenic activities of -270‰ (Rahn et al., 2002) can be explained as a mixture of mainly vehicle emissions from cold starts and fully functional TWCs, but enhanced δD values by >50‰ are likely for regions where TWC technology is not fully implemented. Our results also suggest that a full hydrogen isotope analysis on fuel and exhaust gas may greatly aid at understanding process-level reactions in the exhaust gas, in particular in the TWC.

  7. Mycophenolic Acid Inhibits Migration and Invasion of Gastric Cancer Cells via Multiple Molecular Pathways

    PubMed Central

    Dun, Boying; Sharma, Ashok; Teng, Yong; Liu, Haitao; Purohit, Sharad; Xu, Heng; Zeng, Lingwen; She, Jin-Xiong

    2013-01-01

    Mycophenolic acid (MPA) is the metabolized product and active element of mycophenolate mofetil (MMF) that has been widely used for the prevention of acute graft rejection. MPA potently inhibits inosine monophosphate dehydrogenase (IMPDH) that is up-regulated in many tumors and MPA is known to inhibit cancer cell proliferation as well as fibroblast and endothelial cell migration. In this study, we demonstrated for the first time MPA’s antimigratory and anti-invasion abilities of MPA-sensitive AGS (gastric cancer) cells. Genome-wide expression analyses using Illumina whole genome microarrays identified 50 genes with ≥2 fold changes and 15 genes with > 4 fold alterations and multiple molecular pathways implicated in cell migration. Real-time RT-PCR analyses of selected genes also confirmed the expression differences. Furthermore, targeted proteomic analyses identified several proteins altered by MPA treatment. Our results indicate that MPA modulates gastric cancer cell migration through down-regulation of a large number of genes (PRKCA, DOCK1, INF2, HSPA5, LRP8 and PDGFRA) and proteins (PRKCA, AKT, SRC, CD147 and MMP1) with promigratory functions as well as up-regulation of a number of genes with antimigratory functions (ATF3, SMAD3, CITED2 and CEAMCAM1). However, a few genes that may promote migration (CYR61 and NOS3) were up-regulated. Therefore, MPA’s overall antimigratory role on cancer cells reflects a balance between promigratory and antimigratory signals influenced by MPA treatment. PMID:24260584

  8. Molecular mechanism of action of immune-modulatory drugs thalidomide, lenalidomide and pomalidomide in multiple myeloma.

    PubMed

    Zhu, Yuan Xiao; Kortuem, K Martin; Stewart, A Keith

    2013-04-01

    Although several mechanisms have been proposed to explain the activity of thalidomide, lenalidomide and pomalidomide in multiple myeloma (MM), including demonstrable anti-angiogenic, anti-proliferative and immunomodulatory effects, the precise cellular targets and molecular mechanisms have only recently become clear. A landmark study recently identified cereblon (CRBN) as a primary target of thalidomide teratogenicity. Subsequently it was demonstrated that CRBN is also required for the anti-myeloma activity of thalidomide and related drugs, the so-called immune-modulatory drugs (IMiDs). Low CRBN expression was found to correlate with drug resistance in MM cell lines and primary MM cells. One of the downstream targets of CRBN identified is interferon regulatory factor 4 (IRF4), which is critical for myeloma cell survival and is down-regulated by IMiD treatment. CRBN is also implicated in several effects of IMiDs, such as down-regulation of tumor necrosis factor-α (TNF-α) and T cell immunomodulatory activity, demonstrating that the pleotropic actions of the IMiDs are initiated by binding to CRBN. Future dissection of CRBN downstream signaling will help to delineate the underlying mechanisms for IMiD action and eventually lead to development of new drugs with more specific anti-myeloma activities. It may also provide a biomarker to predict IMiD response and resistance.

  9. Multiple-Timestep ab Initio Molecular Dynamics Using an Atomic Basis Set Partitioning.

    PubMed

    Steele, Ryan P

    2015-12-17

    This work describes an approach to accelerate ab initio Born-Oppenheimer molecular dynamics (MD) simulations by exploiting the inherent timescale separation between contributions from different atom-centered Gaussian basis sets. Several MD steps are propagated with a cost-efficient, low-level basis set, after which a dynamical correction accounts for large basis set relaxation effects in a time-reversible fashion. This multiple-timestep scheme is shown to generate valid MD trajectories, on the basis of rigorous testing for water clusters, the methanol dimer, an alanine polypeptide, protonated hydrazine, and the oxidized water dimer. This new approach generates observables that are consistent with those of target basis set trajectories, including MD-based vibrational spectra. This protocol is shown to be valid for Hartree-Fock, density functional theory, and second-order Møller-Plesset perturbation theory approaches. Recommended pairings include 6-31G as a low-level basis set for 6-31G** or 6-311G**, as well as cc-pVDZ as the subset for accurate dynamics with aug-cc-pVTZ. Demonstrated cost savings include factors of 2.6-7.3 on the systems tested and are expected to remain valid across system sizes.

  10. Molecular mechanisms of multiple toxin–antitoxin systems are coordinated to govern the persister phenotype

    PubMed Central

    Fasani, Rick A.; Savageau, Michael A.

    2013-01-01

    Toxin–antitoxin systems are ubiquitous and have been implicated in persistence, the multidrug tolerance of bacteria, biofilms, and, by extension, most chronic infections. However, their purpose, apparent redundancy, and coordination remain topics of debate. Our model relates molecular mechanisms to population dynamics for a large class of toxin–antitoxin systems and suggests answers to several of the open questions. The generic architecture of toxin–antitoxin systems provides the potential for bistability, and even when the systems do not exhibit bistability alone, they can be coupled to create a strongly bistable, hysteretic switch between normal and toxic states. Stochastic fluctuations can spontaneously switch the system to the toxic state, creating a heterogeneous population of growing and nongrowing cells, or persisters, that exist under normal conditions, rather than as an induced response. Multiple toxin–antitoxin systems can be cooperatively marshaled for greater effect, with the dilution determined by growth rate serving as the coordinating signal. The model predicts and elucidates experimental results that show a characteristic correlation between persister frequency and the number of toxin–antitoxin systems. PMID:23781105

  11. Direct sampling of multiple single-molecular rupture dominant pathways involving a multistep transition.

    PubMed

    Jiang, Huijun; Ding, Huai; Hou, Zhonghuai

    2014-12-14

    We report a novel single-molecular rupture mechanism revealed by direct sampling of the dominant pathway using a self-optimized path sampling method. Multiple dominant pathways involving multistep transitions are identified. The rupture may take place via a direct unfolding from the native state to the unfolding state, or through a two-step pathway bypassing a distinct intermediate metastable state (IMS). This scenario facilitates us to propose a three-state kinetic model, which can produce a nonlinear dependence of the rupture time on pulling forces similar to the ones reported in the literature. In particular, molecule conformations in the IMS maintain an elongation of the tail at one terminal, by which external pulling will enhance the relative stability of IMS. Consequently, even though the overall transition rate of the multistep pathway is relatively small, the molecule still has to be ruptured via the multistep pathway rather than the direct pathway. Thus, our work demonstrates an IMS trapping effect induced rupture mechanism involving an abnormal switching from a fast dominant pathway to a slow one.

  12. Assessment of otocephalan and protacanthopterygian concepts in the light of multiple molecular phylogenies.

    PubMed

    Zaragüeta-Bagils, René; Lavoué, Sébastien; Tillier, Annie; Bonillo, Céline; Lecointre, Guillaume

    2002-12-01

    The rise of cladistics in ichthyology has dramatically improved our knowledge of teleostean basal interrelationships. However, some questions have remained open, among them the reliability of the Otocephala, a clade grouping clupeomorphs and ostariophysans, and the relationships of the Esocoidei. These two questions have been investigated in the light of new DNA sequences (from 28S and rhodopsin genes) and sequences from data banks (cytochrome b, 12-16S, 18S, MLL and RAG1). The ability of each of these markers to resolve basal teleostean interrelationships is assessed, and the cytochrome b was not found appropriate. Practical (i.e. different taxonomic samplings) and epistemological grounds led us to perform multiple separated phylogenetic analyses, in order to estimate the reliability of the above clades from their repeatability among trees from independent sequence data. The Otocephala are found monophyletic from most of the datasets; otherwise, they are not significantly contradicted from the others, which exhibit unresolved relationships. We conclude that the evidence provided here favours the sister-group relationship of clupeomorphs and ostariophysans. Morphological evidence including fossils is discussed, concluding that morphological works have not yet provided sufficient data to support this group. Salmonids and esocoids are found sister-groups from every molecular dataset in which these groups were sampled. Based on these convincing results, the Protacanthopterygii of Johnson and Patterson [1] are redefined, including the Esocoidei.

  13. New Developments in Ab Initio Multiple Spawning for Efficient Nonadiabatic Molecular Dynamics

    NASA Astrophysics Data System (ADS)

    Curchod, Basile F. E.; Sisto, Aaron; Glowacki, David R.; Martínez, Todd J.

    Ab initio multiple spawning (AIMS) describes the nonadiabatic dynamics of nuclear wavepackets by means of a linear combination of frozen Gaussians. While the Gaussian centers follow classical trajectories, the expansion coefficients are propagated according to the time-dependent Schrödinger equation. As a result of the coupling between Gaussian functions, AIMS accurately describes coherence and decoherence effects close to nonadiabatic regions. This accuracy has further been validated by the excellent agreement reported between AIMS dynamics and experimental observations. In this Contribution, we will discuss new techniques used to extend the applicability of AIMS to (i) larger molecules, (ii) long-time simulations, and (iii) dynamics involving an important number of electronic states. We will present different examples of nonadiabatic molecular dynamics in organic and atmospheric photochemistry, resulting from the interface between AIMS and the GPU-accelerated electronic structure code TeraChem. New methods improving the AIMS efficiency for larger systems will be discussed, such as the stochastic-selection AIMS. Finally, we will highlight early results on the extension of AIMS to the combined description of both internal conversion and intersystem crossing phenomena. B.F.E.C. acknowledges the Swiss National Science Foundation (fellowship P2ELP2_151927) for financial support.

  14. Significance Analysis of Prognostic Signatures

    PubMed Central

    Beck, Andrew H.; Knoblauch, Nicholas W.; Hefti, Marco M.; Kaplan, Jennifer; Schnitt, Stuart J.; Culhane, Aedin C.; Schroeder, Markus S.; Risch, Thomas; Quackenbush, John; Haibe-Kains, Benjamin

    2013-01-01

    A major goal in translational cancer research is to identify biological signatures driving cancer progression and metastasis. A common technique applied in genomics research is to cluster patients using gene expression data from a candidate prognostic gene set, and if the resulting clusters show statistically significant outcome stratification, to associate the gene set with prognosis, suggesting its biological and clinical importance. Recent work has questioned the validity of this approach by showing in several breast cancer data sets that “random” gene sets tend to cluster patients into prognostically variable subgroups. This work suggests that new rigorous statistical methods are needed to identify biologically informative prognostic gene sets. To address this problem, we developed Significance Analysis of Prognostic Signatures (SAPS) which integrates standard prognostic tests with a new prognostic significance test based on stratifying patients into prognostic subtypes with random gene sets. SAPS ensures that a significant gene set is not only able to stratify patients into prognostically variable groups, but is also enriched for genes showing strong univariate associations with patient prognosis, and performs significantly better than random gene sets. We use SAPS to perform a large meta-analysis (the largest completed to date) of prognostic pathways in breast and ovarian cancer and their molecular subtypes. Our analyses show that only a small subset of the gene sets found statistically significant using standard measures achieve significance by SAPS. We identify new prognostic signatures in breast and ovarian cancer and their corresponding molecular subtypes, and we show that prognostic signatures in ER negative breast cancer are more similar to prognostic signatures in ovarian cancer than to prognostic signatures in ER positive breast cancer. SAPS is a powerful new method for deriving robust prognostic biological signatures from clinically annotated

  15. Efficient Unrestricted Identity-Based Aggregate Signature Scheme

    PubMed Central

    Yuan, Yumin; Zhan, Qian; Huang, Hua

    2014-01-01

    An aggregate signature scheme allows anyone to compress multiple individual signatures from various users into a single compact signature. The main objective of such a scheme is to reduce the costs on storage, communication and computation. However, among existing aggregate signature schemes in the identity-based setting, some of them fail to achieve constant-length aggregate signature or require a large amount of pairing operations which grows linearly with the number of signers, while others have some limitations on the aggregated signatures. The main challenge in building efficient aggregate signature scheme is to compress signatures into a compact, constant-length signature without any restriction. To address the above drawbacks, by using the bilinear pairings, we propose an efficient unrestricted identity-based aggregate signature. Our scheme achieves both full aggregation and constant pairing computation. We prove that our scheme has existential unforgeability under the computational Diffie-Hellman assumption. PMID:25329777

  16. Efficient unrestricted identity-based aggregate signature scheme.

    PubMed

    Yuan, Yumin; Zhan, Qian; Huang, Hua

    2014-01-01

    An aggregate signature scheme allows anyone to compress multiple individual signatures from various users into a single compact signature. The main objective of such a scheme is to reduce the costs on storage, communication and computation. However, among existing aggregate signature schemes in the identity-based setting, some of them fail to achieve constant-length aggregate signature or require a large amount of pairing operations which grows linearly with the number of signers, while others have some limitations on the aggregated signatures. The main challenge in building efficient aggregate signature scheme is to compress signatures into a compact, constant-length signature without any restriction. To address the above drawbacks, by using the bilinear pairings, we propose an efficient unrestricted identity-based aggregate signature. Our scheme achieves both full aggregation and constant pairing computation. We prove that our scheme has existential unforgeability under the computational Diffie-Hellman assumption.

  17. Molecular spintronics based on single-molecule magnets composed of multiple-decker phthalocyaninato terbium(III) complex.

    PubMed

    Katoh, Keiichi; Isshiki, Hironari; Komeda, Tadahiro; Yamashita, Masahiro

    2012-06-01

    Unlike electronics, which is based on the freedom of the charge of an electron whose memory is volatile, spintronics is based on the freedom of the charge, spin, and orbital of an electron whose memory is non-volatile. Although in most GMR, TMR, and CMR systems, bulk or classical magnets that are composed of transition metals are used, this Focus Review considers the growing use of single-molecule magnets (SMMs) that are composed of multinuclear metal complexes and nanosized magnets, which exhibit slow magnetic-relaxation processes and quantum tunneling. Molecular spintronics, which combines spintronics and molecular electronics, is an emerging field of research. Using molecules is advantageous because their electronic and magnetic properties can be manipulated under specific conditions. Herein, recent developments in [LnPc]-based multiple-decker SMMs on surfaces for molecular spintronic devices are presented. First, we discuss the strategies for preparing single-molecular-memory devices by using SMMs. Next, we focus on the switching of the Kondo signal of [LnPc]-based multiple-decker SMMs that are adsorbed onto surfaces, their characterization by using STM and STS, and the relationship between the molecular structure, the electronic structure, and the Kondo resonance of [TbPc(2)]. Finally, the field-effect-transistor (FET) properties of surface-adsorbed [LnPc(2)] and [Ln(2)Pc(3)] cast films are reported, which is the first step towards controlling SMMs through their spins for applications in single-molecular memory and spintronics devices.

  18. A mixed quantum-classical molecular dynamics study of anti-tetrol and syn-tetrol dissolved in liquid chloroform: hydrogen-bond structure and its signature on the infrared absorption spectrum.

    PubMed

    Kwac, Kijeong; Geva, Eitan

    2013-12-27

    The intramolecular hydrogen-bond structure of stereoselectively synthesized syn-tetrol and anti-tetrol dissolved in deuterated chloroform is investigated via a mixed quantum-classical molecular dynamics simulation. An extensive conformational analysis is performed in order to determine the dominant conformations, the distributions among them, and their sensitivity to the method for assigning partial charges (RESP vs AM1-BCC). The signature of the conformational distribution and method of assigning partial charges on the infrared absorption spectra is analyzed in detail. The relationship between the spectra and the underlying hydrogen-bond structure is elucidated.

  19. Single and multiple molecular beacon probes for DNA hybridization studies on a silica glass surface

    NASA Astrophysics Data System (ADS)

    Fang, Xiaohong; Liu, Xiaojing; Tan, Weihong

    1999-05-01

    Surface immobilizable molecular beacons have been developed for DNA hybridization studies on a silica glass plate. Molecular beacons are a new class of oligonucleotide probes that have a loop-and-stem structure with a fluorophore and a quencher attached to the two ends of the stem. They only emit intense fluorescence when hybridize to their target molecules. This provides an excellent selectivity for the detection of DNA molecules. We have designed biotinylated molecular beacons which can be immobilized onto a solid surface. The molecular beacon is synthesized using DABCYL as the quencher and an optical stable dye, tetramethylrhodamine, as the fluorophore. Mass spectrometry is used to confirm the synthesized molecular beacon. The molecular beacons have been immobilized onto a silica surface through biotin-avidin binding. The surface immobilized molecular beacons have been used for the detection of target DNA with subnanomolar analytical sensitivity. have also immobilized two different molecular beacons on a silica surface in spatially resolved microscopic regions. The hybridization study of these two different molecular beacon probes has shown excellent selectivity for their target sequences. The newly designed molecular beacons are intended for DNA molecular interaction studies at an interface and for the development of ultrasensitive DNA sensors for a variety of applications including disease diagnosis, disease mechanism studies, new drug development, and in the investigation of molecular interactions between DNA molecules and other interesting biomolecules.

  20. The Frontier of Molecular Spintronics Based on Multiple-Decker Phthalocyaninato Tb(III) Single-Molecule Magnets.

    PubMed

    Katoh, Keiichi; Komeda, Tadahiro; Yamashita, Masahiro

    2016-04-01

    Ever since the first example of a double-decker complex (SnPc2) was discovered in 1936, MPc2 complexes with π systems and chemical and physical stabilities have been used as components in molecular electronic devices. More recently, in 2003, TbPc2 complexes were shown to be single-molecule magnets (SMMs), and researchers have utilized their quantum tunneling of the magnetization (QTM) and magnetic relaxation behavior in spintronic devices. Herein, recent developments in Ln(III)-Pc-based multiple-decker SMMs on surfaces for molecular spintronic devices are presented. In this account, we discuss how dinuclear Tb(III)-Pc multiple-decker complexes can be used to elucidate the relationship between magnetic dipole interactions and SMM properties, because these complexes contain two TbPc2 units in one molecule and their intramolecular Tb(III)-Tb(III) distances can be controlled by changing the number of stacks. Next, we focus on the switching of the Kondo signal of Tb(III)-Pc-based multiple-decker SMMs that are adsorbed onto surfaces, their characterization using STM and STS, and the relationship between the molecular structure, the electronic structure, and the Kondo resonance of Tb(III)-Pc multiple-decker complexes.

  1. Molecular signatures for Bacillus species: demarcation of the Bacillus subtilis and Bacillus cereus clades in molecular terms and proposal to limit the placement of new species into the genus Bacillus.

    PubMed

    Bhandari, Vaibhav; Ahmod, Nadia Z; Shah, Haroun N; Gupta, Radhey S

    2013-07-01

    The genus Bacillus is a phylogenetically incoherent taxon with members of the group lacking a common evolutionary history. Comprising aerobic and anaerobic spore-forming bacteria, no characteristics are known that can distinguish species of this genus from other similar endospore-forming genera. With the availability of complete genomic data from over 30 different species from this group, we have constructed detailed phylogenetic trees to determine the relationships among Bacillus and other closely related taxa. Additionally, we have performed comparative genomic analysis for the determination of molecular markers, in the form of conserved signature indels (CSIs), to assist in the understanding of relationships among species of the genus Bacillus in molecular terms. Based on the analysis, we report here the identification of 11 and 6 CSIs that clearly differentiate a 'Bacillus subtilis clade' and a 'Bacillus cereus clade', respectively, from all other species of the genus Bacillus. No molecular markers were identified that supported a larger clade within this genus. The subtilis and the cereus clades were also the largest observed monophyletic groupings among species from the genus Bacillus in the phylogenetic trees based on 16S rRNA gene sequences and those based upon concatenated sequences for 20 conserved proteins. Thus, the relationships observed among these groups of species through CSIs are independently well supported by phylogenetic analysis. The molecular markers identified in this study provide a reliable means for the reorganization of the currently polyphyletic genus Bacillus into a more evolutionarily consistent set of groups. It is recommended that the genus Bacillus sensu stricto should comprise only the monophyletic subtilis clade that is demarcated by the identified CSIs, with B. subtilis as its type species. Members of the adjoining cereus clade (referred to as the Cereus clade of bacilli), although they are distinct from the subtilis clade, will

  2. Molecular evolution of multiple forms of kisspeptins and GPR54 receptors in vertebrates.

    PubMed

    Lee, Yeo Reum; Tsunekawa, Kenta; Moon, Mi Jin; Um, Haet Nim; Hwang, Jong-Ik; Osugi, Tomohiro; Otaki, Naohito; Sunakawa, Yuya; Kim, Kyungjin; Vaudry, Hubert; Kwon, Hyuk Bang; Seong, Jae Young; Tsutsui, Kazuyoshi

    2009-06-01

    Kisspeptin and its receptor GPR54 play important roles in mammalian reproduction and cancer metastasis. Because the KiSS and GPR54 genes have been identified in a limited number of vertebrate species, mainly in mammals, the evolutionary history of these genes is poorly understood. In the present study, we have cloned multiple forms of kisspeptin and GPR54 cDNAs from a variety of vertebrate species. We found that fish have two forms of kisspeptin genes, KiSS-1 and KiSS-2, whereas Xenopus possesses three forms of kisspeptin genes, KiSS-1a, KiSS-1b, and KiSS-2. The nonmammalian KiSS-1 gene was found to be the ortholog of the mammalian KiSS-1 gene, whereas the KiSS-2 gene is a novel form, encoding a C-terminally amidated dodecapeptide in the Xenopus brain. This study is the first to identify a mature form of KiSS-2 product in the brain of any vertebrate. Likewise, fish possess two receptors, GPR54-1 and GPR54-2, whereas Xenopus carry three receptors, GPR54-1a, GPR54-1b, and GPR54-2. Sequence identity and genome synteny analyses indicate that Xenopus GPR54-1a is a human GPR54 ortholog, whereas Xenopus GPR54-1b is a fish GPR54-1 ortholog. Both kisspeptins and GPR54s were abundantly expressed in the Xenopus brain, notably in the hypothalamus, suggesting that these ligand-receptor pairs have neuroendocrine and neuromodulatory roles. Synthetic KiSS-1 and KiSS-2 peptides activated GPR54s expressed in CV-1 cells with different potencies, indicating differential ligand selectivity. These data shed new light on the molecular evolution of the kisspeptin-GPR54 system in vertebrates.

  3. Cytogenetic and molecular evidence suggest multiple origins and geographical parthenogenesis in Nothoscordum gracile (Alliaceae)

    PubMed Central

    Souza, Luiz Gustavo Rodrigues; Crosa, Orfeo; Speranza, Pablo; Guerra, Marcelo

    2012-01-01

    Background and Aims Nothoscordum gracile is an apomitic tetraploid widely distributed throughout the Americas and naturalized in many temperate regions of other continents. It has been suggested to form a species complex with sexual and apomictic N. nudicaule and N. macrostemon. Tetraploids of these species also share a structurally heterozygous chromosome complement 2n = 19 (13M + 6A). In this work, the origin of N. gracile and its relationships with its related species was investigated based on cytological and molecular data. Methods Cytogenetic analyses were based on meiotic behaviour, CMA bands, localization of 5S and 45S rDNA sites, and genomic in situ hybridization (GISH). Nuclear ITS and plastidial trnL-trnF sequences were also obtained for most individuals. Key Results Proximal CMA bands were observed in the long arms of all acrocentrics of 2x and 4x N. macrostemon but not in diploid and some tetraploid cytotypes of N. nudicaule. Samples of N. gracile showed a variable number of CMA bands in the long arms of acrocentrics. Analysis of ITS sequences, dot-blot, GISH, and 5S and 45S rDNA sites, revealed no differentiation among the three species. The trnL-trnF cpDNA fragment showed variation with a trend to geographical structuring irrespective of morphospecies and fully congruent with karyotype variation. Conclusions The 2n = 19 karyotype was probably formed by a centric fusion event occurring in N. nudicaule and later transmitted to tetraploid cytotypes of N. macrostemon. Diploids of N. nudicaule and N. macrostemon appeared as consistent recently diverged species, whereas tetraploid apomicts seem to constitute an assemblage of polyploid hybrids originating from multiple independent hybridization events between them, part of which are morphologically recognizable as N. gracile. PMID:22362660

  4. Molecular hydrogen (H2) combustion emissions and their isotope (D/H) signatures from domestic heaters, diesel vehicle engines, waste incinerator plants, and biomass burning

    NASA Astrophysics Data System (ADS)

    Vollmer, M. K.; Walter, S.; Mohn, J.; Steinbacher, M.; Bond, S. W.; Röckmann, T.; Reimann, S.

    2012-07-01

    Molecular hydrogen (H2), its stable isotope signature (δD), and the key combustion parameters carbon monoxide (CO), carbon dioxide (CO2), and methane (CH4) were measured from various combustion processes. H2 in the exhaust of gas and oil-fired heaters and of waste incinerator plants was generally depleted compared to ambient intake air, while CO was significantly elevated. These findings contradict the often assumed co-occurring net H2 and CO emissions in combustion processes and suggest that previous H2 emissions from combustion may have been overestimated when scaled to CO emissions. For the gas and oil-fired heater exhausts, H2 and δD generally decrease with increasing CO2, from ambient values of ~0.5 ppm and +130‰ to 0.2 ppm and -206‰, respectively. These results are interpreted as a combination of an isotopically light H2 source from fossil fuel combustion and a D/H kinetic isotope fractionation of hydrogen in the advected ambient air during its partial removal during combustion. Diesel exhaust measurements from dynamometer test stand driving cycles show elevated H2 and CO emissions during cold-start and some acceleration phases. While H2 and CO emissions from diesel vehicles are known to be significantly less than those from gasoline vehicles (on a fuel-energy base), we find that their molar H2/CO ratios (median 0.026, interpercentile range 0.12) are also significantly less compared to gasoline vehicle exhaust. Using H2/CO emission ratios, along with CO global emission inventories, we estimate global H2 emissions for 2000, 2005, and 2010. For road transportation (gasoline and diesel), we calculate 8.3 ± 2.2 Tg, 6.0 ± 1.5 Tg, and 3.8 ± 0.94 Tg, respectively, whereas the contribution from diesel vehicles is low (0.9-1.4%). Other fossil fuel emissions are believed to be negligible but H2 emissions from coal combustion are unknown. For residential (domestic) emissions, which are likely dominated by biofuel combustion, emissions for the same years are

  5. Observation of ambipolar switching in a silver nanoparticle single-electron transistor with multiple molecular floating gates

    NASA Astrophysics Data System (ADS)

    Yamamoto, Makoto; Shinohara, Shuhei; Tamada, Kaoru; Ishii, Hisao; Noguchi, Yutaka

    2016-03-01

    Ambipolar switching behavior was observed in a silver nanoparticle (AgNP)-based single-electron transistor (SET) with tetra-tert-butyl copper phthalocyanine (ttbCuPc) as a molecular floating gate. Depending on the wavelength of the incident light, the stability diagram shifted to the negative and positive directions along the gate voltage axis. These results were explained by the photoinduced charging of ttbCuPc molecules in the vicinity of AgNPs. Moreover, multiple device states were induced by the light irradiation at a wavelength of 600 nm, suggesting that multiple ttbCuPc molecules individually worked as a floating gate.

  6. An integrative and comparative study of pan-cancer transcriptomes reveals distinct cancer common and specific signatures

    PubMed Central

    Cao, Zhen; Zhang, Shihua

    2016-01-01

    To investigate the commonalities and specificities across tumor lineages, we perform a systematic pan-cancer transcriptomic study across 6744 specimens. We find six pan-cancer subnetwork signatures which relate to cell cycle, immune response, Sp1 regulation, collagen, muscle system and angiogenesis. Moreover, four pan-cancer subnetwork signatures demonstrate strong prognostic potential. We also characterize 16 cancer type-specific subnetwork signatures which show diverse implications to somatic mutations, somatic copy number aberrations, DNA methylation alterations and clinical outcomes. Furthermore, some of them are strongly correlated with histological or molecular subtypes, indicating their implications with tumor heterogeneity. In summary, we systematically explore the pan-cancer common and cancer type-specific gene subnetwork signatures across multiple cancers, and reveal distinct commonalities and specificities among cancers at transcriptomic level. PMID:27633916

  7. Signature Tracking for Optimized Nutrition and Training (STRONG)

    DTIC Science & Technology

    2014-08-01

    ii   AFRL-RH-WP-TP-2014-0038 SIGNATURE TRACKING FOR OPTIMIZED NUTRITION AND TRAINING (STRONG) Joshua Hagen Human Signatures Branch...Signature TRacking for Optimized Nutrition and TraininG (STRONG) 5a. CONTRACT NUMBER In-House 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 62202F 6...human performance augmentation led by multiple researchers at AFRL. Research areas include Physical Training, Nutrition /Supplementation, Signatures, and

  8. Revolutionizing our View of Protostellar Multiplicity and Disks: The VLA Nascent Disk and Multiplicity (VANDAM) Survey of the Perseus Molecular Cloud

    NASA Astrophysics Data System (ADS)

    Tobin, J. J.; Looney, L. W.; Li, Z.-Y.; Chandler, C. J.; Dunham, M. M.; Segura-Cox, D.; Cox, E. G.; Harris, R. J.; Melis, C.; Sadavoy, S. I.; Pérez, L.; Kratter, K.

    2016-05-01

    There is substantial evidence for disk formation taking place during the early stages of star formation and for most stars being born in multiple systems; however, protostellar multiplicity and disk searches have been hampered by low resolution, sample bias, and variable sensitivity. We have conducted an unbiased, high-sensitivity Karl G. Jansky Very Large Array (VLA) survey toward all known protostars (n = 94) in the Perseus molecular cloud (d ˜ 230 pc), with a resolution of ˜ 15 AU (0.06'') at λ = 8 mm. We have detected candidate protostellar disks toward 17 sources (with 12 of those in the Class 0 stage) and we have found substructure on < 50 AU scales for three Class 0 disk candidates, possibly evidence for disk fragmentation. We have discovered 16 new multiple systems (or new components) in this survey; the new systems have separations < 500 AU and 3 by < 30 AU. We also found a bi-modal distribution of separations, with peaks at ˜ 75 AU and ˜ 3000 AU, suggestive of formation through two distinct mechanisms: disk and turbulent fragmentation. The results from this survey demonstrate the necessity and utility of uniform, unbiased surveys of protostellar systems at millimeter and centimeter wavelengths.

  9. Signature extension through the application of cluster matching algorithms to determine appropriate signature transformations

    NASA Technical Reports Server (NTRS)

    Lambeck, P. F.; Rice, D. P.

    1976-01-01

    Signature extension is intended to increase the space-time range over which a set of training statistics can be used to classify data without significant loss of recognition accuracy. A first cluster matching algorithm MASC (Multiplicative and Additive Signature Correction) was developed at the Environmental Research Institute of Michigan to test the concept of using associations between training and recognition area cluster statistics to define an average signature transformation. A more recent signature extension module CROP-A (Cluster Regression Ordered on Principal Axis) has shown evidence of making significant associations between training and recognition area cluster statistics, with the clusters to be matched being selected automatically by the algorithm.

  10. Condensed Matter: Electronic Structure, Electrical, Magnetic, and Optical Properties Entanglement Entropy Signature of Quantum Phase Transitions in a Multiple Spin Interactions Model

    NASA Astrophysics Data System (ADS)

    Huang, Hai-Lin

    2011-02-01

    Through the Jordan—Wigner transformation, the entanglement entropy and ground state phase diagrams of exactly solvable spin model with alternating and multiple spin exchange interactions are investigated by means of Green's function theory. In the absence of four-spin interactions, the ground state presents plentiful quantum phases due to the multiple spin interactions and magnetic fields. It is shown that the two-site entanglement entropy is a good indicator of quantum phase transition (QPT). In addition, the alternating interactions can destroy the magnetization plateau and wash out the spin-gap of low-lying excitations. However, in the presence of four-spin interactions, apart from the second order QPTs, the system manifests the first order QPT at the tricritical point and an additional new phase called “spin waves”, which is due to the collapse of the continuous tower-like low-lying excitations modulated by the four-spin interactions for large three-spin couplings.

  11. Signatures support program

    NASA Astrophysics Data System (ADS)

    Hawley, Chadwick T.

    2009-05-01

    The Signatures Support Program (SSP) leverages the full spectrum of signature-related activities (collections, processing, development, storage, maintenance, and dissemination) within the Department of Defense (DOD), the intelligence community (IC), other Federal agencies, and civil institutions. The Enterprise encompasses acoustic, seismic, radio frequency, infrared, radar, nuclear radiation, and electro-optical signatures. The SSP serves the war fighter, the IC, and civil institutions by supporting military operations, intelligence operations, homeland defense, disaster relief, acquisitions, and research and development. Data centers host and maintain signature holdings, collectively forming the national signatures pool. The geographically distributed organizations are the authoritative sources and repositories for signature data; the centers are responsible for data content and quality. The SSP proactively engages DOD, IC, other Federal entities, academia, and industry to locate signatures for inclusion in the distributed national signatures pool and provides world-wide 24/7 access via the SSP application.

  12. Molecular evidence for multiple paternity in a population of the Viviparous Tule Perch Hysterocarpus traski.

    PubMed

    Liu, Jin-Xian; Tatarenkov, Andrey; O'Rear, Teejay A; Moyle, Peter B; Avise, John C

    2013-03-01

    Population density might be an important variable in determining the degree of multiple paternity. In a previous study, a high level of multiple paternity was detected in the shiner perch Cymatogaster aggregata, a species with high population density and a high mate encounter rate. The tule perch Hysterocarpus traski is phylogenetically closely related to C. aggregata, but it has relatively lower population density, which may result in distinct patterns of multiple paternity in these 2 species. To test the hypothesis that mate encounter rate may affect the rate of successful mating, we used polymorphic microsatellite markers to identify multiple paternity in the progeny arrays of 12 pregnant females from a natural population of tule perch. Multiple paternity was detected in 11 (92%) of the 12 broods. The number of sires per brood ranged from 1 to 4 (mean 2.5) but with no correlation between sire number and brood size. Although the brood size of tule perch is considerably larger than that of shiner perch (40.7 vs. 12.9, respectively), the average number of sires per brood in tule perch is much lower than that in shiner perch (2.5 vs. 4.6, respectively). These results are consistent with the hypothesis that mate encounter rate is an important factor affecting multiple mating.

  13. Determination of 3D molecular orientation by concurrent polarization analysis of multiple Raman modes in broadband CARS spectroscopy

    PubMed Central

    2016-01-01

    A theoretical description is presented about a new analysis method to determine three-dimensional (3D) molecular orientation by concurrently analyzing multiple Raman polarization profiles. Conventional approaches to polarization Raman spectroscopy are based on single peaks, and their 2D-projected polarization profiles are limited in providing 3D orientational information. Our new method analyzes multiple Raman profiles acquired by a single polarization scanning measurement of broadband coherent anti-Stokes Raman scattering (BCARS). Because the analysis uses only dimensionless quantities, such as intensity ratios and phase difference between multiple profiles, the results are not affected by sample concentration and the system response function. We describe how to determine the 3D molecular orientation with the dimensionless observables by using two simplified model cases. In addition, we discuss the effect of orientational broadening on the polarization profiles in the two model cases. We find that in the presence of broadening we can still determine the mean 3D orientation angles and, furthermore, the degree of orientational broadening. PMID:26561197

  14. Diabatic Population Matrix Formalism for Performing Molecular Mechanics Style Simulations with Multiple Electronic States.

    PubMed

    Park, Jae Woo; Rhee, Young Min

    2014-12-09

    An accurate description of nonbonded interactions is important in investigating dynamics of molecular systems. In many situations, fixed point charge models are successfully applied to explaining various chemical phenomena. However, these models with conventional formulations will not be appropriate in elucidating the detailed dynamics during nonadiabatic events. This is mainly because the chemical properties of any molecule, especially its electronic populations, significantly change with respect to molecular distortions in the vicinity of the surface crossing. To overcome this issue in molecular simulations yet within the framework of the fixed point charge model, we define a diabatic electronic population matrix and substitute it for the conventional adiabatic partial charges. We show that this matrix can be readily utilized toward attaining more reliable descriptions of Coulombic interactions, in combination with the interpolation formalism for obtaining the intramolecular interaction potential. We demonstrate how the mixed formalism with the diabatic charges and the interpolation can be applied to molecular simulations by conducting adiabatic and nonadiabatic molecular dynamics trajectory calculations of the green fluorescent protein chromophore anion in aqueous environment.

  15. Using Multiple Approaches, including δ18O Signatures of Phosphate to Investigate Potential Phosphorus Limitation and Cycling under Changing Climate Conditions

    NASA Astrophysics Data System (ADS)

    Roberts, K.; Paytan, A.; Field, C. B.; Honn, E.; Edwards, E.; Gottlieb, R.

    2012-12-01

    Phosphorus (P) is often a limiting or co-limiting nutrient in terrestrial systems. It has been proposed that it will play an even greater role in ecosystems experiencing some of the many predicted effects of climate change, in particular release from nitrogen limitation. Recent work in 2007 by Menge et al. suggests that this is indeed a possibility. To investigate the potential for P limitation, and P cycling under multiple controlled conditions we collected samples from the Jasper Ridge Global Change Experiment (JRGCE) in May 2011. For over a decade the JRGCE has been manipulating four key parameters predicted to change in the future in a native Californian grassland system. Elevated Nitrogen deposition, increased precipitation, increased pCO2, and increased temperature are applied and monitored in a split plot design at the Jasper Ridge Biological Preserve in the eastern foothills of the Santa Cruz Mountains, California. Work done previously at the site using a suite of indicators of the potential P limitation suggest P limitation in some of the manipulated plots in the JRGCE. In this study we replicate a subset of the prior analyses to compare inter-annual signals of P limitation, and further attempt to utilize the oxygen isotopes of phosphate to investigate P cycling in soils at JRGCE. A fractional soil extraction process for phosphate enables separation of several operationally defined P pools, and provides auxiliary information regarding the relative concentrations of bio-available P, and relevant minerals in this grassland system under the varied conditions.

  16. Molecular investigation of a dicentric 13;17 chromosome found in a 21-week gestation fetus with multiple congenital abnormalities.

    PubMed

    Cockwell, A E; Maloney, V K; Thomas, N S; Smith, E L; Gonda, P; Bass, P; Crolla, J A

    2006-01-01

    We report a 21-week gestation fetus terminated because of multiple congenital abnormalities seen on ultrasound scan, including ventriculomegaly, possible clefting of the hard palate, cervical hemivertebrae, micrognathia, abnormal heart, horseshoe kidney and a 2-vessel umbilical cord. On cytogenetic examination, the fetus was found to have a male karyotype with 45 chromosomes with a dicentric chromosome, which appeared to consist of the long arms of chromosomes 13 and 17. Molecular genetic investigations and fluorescence in situ hybridization (FISH) unexpectedly showed that the derivative chromosome contained two interstitial blocks of chromosome 17 short arm sequences, totalling approximately 7 Mb, between the two centromeres. This effectively made the fetus monosomic for approximately 15 Mb of 17p without the concurrent trisomy for another chromosome normally seen following malsegregation of reciprocal translocations. It also illustrates the complexity involved in the formation of some structurally abnormal chromosomes, which can only be resolved by detailed molecular investigations.

  17. Multiple Simulated Annealing-Molecular Dynamics (MSA-MD) for Conformational Space Search of Peptide and Miniprotein.

    PubMed

    Hao, Ge-Fei; Xu, Wei-Fang; Yang, Sheng-Gang; Yang, Guang-Fu

    2015-10-23

    Protein and peptide structure predictions are of paramount importance for understanding their functions, as well as the interactions with other molecules. However, the use of molecular simulation techniques to directly predict the peptide structure from the primary amino acid sequence is always hindered by the rough topology of the conformational space and the limited simulation time scale. We developed here a new strategy, named Multiple Simulated Annealing-Molecular Dynamics (MSA-MD) to identify the native states of a peptide and miniprotein. A cluster of near native structures could be obtained by using the MSA-MD method, which turned out to be significantly more efficient in reaching the native structure compared to continuous MD and conventional SA-MD simulation.

  18. Molecular basis for multiple sulfatase deficiency and mechanism for formylglycine generation of the human formylglycine-generating enzyme.

    PubMed

    Dierks, Thomas; Dickmanns, Achim; Preusser-Kunze, Andrea; Schmidt, Bernhard; Mariappan, Malaiyalam; von Figura, Kurt; Ficner, Ralf; Rudolph, Markus Georg

    2005-05-20

    Sulfatases are enzymes essential for degradation and remodeling of sulfate esters. Formylglycine (FGly), the key catalytic residue in the active site, is unique to sulfatases. In higher eukaryotes, FGly is generated from a cysteine precursor by the FGly-generating enzyme (FGE). Inactivity of FGE results in multiple sulfatase deficiency (MSD), a fatal autosomal recessive syndrome. Based on the crystal structure, we report that FGE is a single-domain monomer with a surprising paucity of secondary structure and adopts a unique fold. The effect of all 18 missense mutations found in MSD patients is explained by the FGE structure, providing a molecular basis of MSD. The catalytic mechanism of FGly generation was elucidated by six high-resolution structures of FGE in different redox environments. The structures allow formulation of a novel oxygenase mechanism whereby FGE utilizes molecular oxygen to generate FGly via a cysteine sulfenic acid intermediate.

  19. Vibrational Signatures of Isomeric Lithiated N-acetyl-D-hexosamines by Gas-Phase Infrared Multiple-Photon Dissociation (IRMPD) Spectroscopy

    NASA Astrophysics Data System (ADS)

    Tan, Yanglan; Zhao, Ning; Liu, Jinfeng; Li, Pengfei; Stedwell, Corey N.; Yu, Long; Polfer, Nicolas C.

    2017-03-01

    Three lithiated N-acetyl-D-hexosamine (HexNAc) isomers, N-acetyl-D-glucosamine (GlcNAc), N-acetyl-D-galactosamine (GalNAc), and N-acetyl-D-mannosamine (ManNAc) are investigated as model monosaccharide derivatives by gas-phase infrared multiple-photon dissociation (IRMPD) spectroscopy. The hydrogen stretching region, which is attributed to OH and NH stretching modes, reveals some distinguishing spectral features of the lithium-adducted complexes that are useful in terms of differentiating these isomers. In order to understand the effect of lithium coordination on saccharide structure, and therefore anomericity, chair configuration, and hydrogen bonding networks, the conformational preferences of lithiated GlcNAc, GalNAc, and ManNAc are studied by comparing the experimental measurements with density functional theory (DFT) calculations. The experimental results of lithiated GlcNAc and GalNAc show a good match to the theoretical spectra of low-energy structures adopting a 4 C 1 chair conformation, consistent with this motif being the dominant conformation in condensed-phase monosaccharides. The epimerization effect upon going to lithiated ManNAc is significant, as in this case the 1 C 4 chair conformers give a more compelling match with the experimental results, consistent with their lower calculated energies. A contrasting computational study of these monosaccharides in their neutral form suggests that the lithium cation coordination with Lewis base oxygens can play a key role in favoring particular structural motifs (e.g., a 4 C 1 versus 1 C 4 ) and disrupting hydrogen bond networks, thus exhibiting specific IR spectral features between these closely related lithium-chelated complexes.

  20. Vibrational Signatures of Isomeric Lithiated N-acetyl-D-hexosamines by Gas-Phase Infrared Multiple-Photon Dissociation (IRMPD) Spectroscopy

    NASA Astrophysics Data System (ADS)

    Tan, Yanglan; Zhao, Ning; Liu, Jinfeng; Li, Pengfei; Stedwell, Corey N.; Yu, Long; Polfer, Nicolas C.

    2017-01-01

    Three lithiated N-acetyl-D-hexosamine (HexNAc) isomers, N-acetyl-D-glucosamine (GlcNAc), N-acetyl-D-galactosamine (GalNAc), and N-acetyl-D-mannosamine (ManNAc) are investigated as model monosaccharide derivatives by gas-phase infrared multiple-photon dissociation (IRMPD) spectroscopy. The hydrogen stretching region, which is attributed to OH and NH stretching modes, reveals some distinguishing spectral features of the lithium-adducted complexes that are useful in terms of differentiating these isomers. In order to understand the effect of lithium coordination on saccharide structure, and therefore anomericity, chair configuration, and hydrogen bonding networks, the conformational preferences of lithiated GlcNAc, GalNAc, and ManNAc are studied by comparing the experimental measurements with density functional theory (DFT) calculations. The experimental results of lithiated GlcNAc and GalNAc show a good match to the theoretical spectra of low-energy structures adopting a 4 C 1 chair conformation, consistent with this motif being the dominant conformation in condensed-phase monosaccharides. The epimerization effect upon going to lithiated ManNAc is significant, as in this case the 1 C 4 chair conformers give a more compelling match with the experimental results, consistent with their lower calculated energies. A contrasting computational study of these monosaccharides in their neutral form suggests that the lithium cation coordination with Lewis base oxygens can play a key role in favoring particular structural motifs (e.g., a 4 C 1 versus 1 C 4 ) and disrupting hydrogen bond networks, thus exhibiting specific IR spectral features between these closely related lithium-chelated complexes.

  1. Molecular signatures for the phylum Aquificae and its different clades: proposal for division of the phylum Aquificae into the emended order Aquificales, containing the families Aquificaceae and Hydrogenothermaceae, and a new order Desulfurobacteriales ord. nov., containing the family Desulfurobacteriaceae.

    PubMed

    Gupta, Radhey S; Lali, Ricky

    2013-09-01

    We report here detailed phylogenetic and comparative analyses on 11 sequenced genomes from the phylum Aquificae to identify molecular markers that are specific for the species from this phylum or its different families (viz. Aquificaceae, Hydrogenothermaceae and Desulfurobacteriaceae). In phylogenetic trees based on 16S rRNA gene or concatenated sequences for 32 conserved proteins, species from the three Aquificae families formed distinct clades. These trees also supported a strong relationship between the Aquificaceae and Hydrogenothermaceae families. In parallel, comparative analyses on protein sequences from Aquificae genomes have identified 46 conserved signature indels (CSIs) in broadly distributed proteins that are either exclusively or mainly found in members of the phylum Aquificae or its different families and subclades. Four of these CSIs, which are found in all sequenced Aquificae species, provide potential molecular markers for this phylum. Twelve, six and thirteen other CSIs that respectively are specific for the sequenced Aquificaceae, Hydrogenothermaceae and Desulfurobacteriaceae species provide molecular markers and novel tools for the identification of members of these families and for genetic and biochemical studies on them. Lastly, these studies have identified 11 CSIs in divergent proteins that are uniquely shared by members of the Aquificaceae and Hydrogenothermaceae families providing strong evidence that these two groups of bacteria shared a common ancestor exclusive of all other Aquificae (bacteria). The species from these two families are also very similar in their metabolic and physiological properties and they consist of aerobic or microaerophilic bacteria, which generally obtain energy by oxidation of hydrogen or reduced sulfur compounds by molecular oxygen. Based upon their strong association in phylogenetic trees, unique shared presence of large numbers of CSIs in different proteins, and similarities in their metabolic and

  2. Molecular approach to find target(s) for oligoclonal bands in multiple sclerosis

    PubMed Central

    Rand, K.; Houck, H.; Denslow, N.; Heilman, K.

    1998-01-01

    OBJECTIVES—Oligoclonal bands are a characteristic finding in the CSF of patients with multiple sclerosis, yet their target antigen(s) remain unknown. The objective was to determine whether a filamentous phage peptide library could be employed to allow the oligoclonal bands to select their own target epitopes.
METHODS—CSF IgG antibody from 14 patients with multiple sclerosis and 14 controls was used to select individual phage clones from a bacteriophage library containing≈4 × 107 different hexamers expressed on its surface pIII protein. The amino acid sequence selected was deduced by sequencing the DNA of the genetically engineered insert.
RESULTS—In general, after three rounds of selection, CSF from both patients with multiple sclerosis and controls selected one to two consistent peptide motifs. Five out of 14 patients with multiple sclerosis, and one control, selected the amino acid sequence motif, RRPFF. Given 20 possible amino acids per position, the likelihood of five patients selecting the same linear five amino acid sequence is at most 1.6 × 10-13, corrected for the number of clones sequenced. A GenBank computer search showed that this sequence is found in the Epstein-Barr Virus nuclear antigen (EBNA-1), and a heat shock protein αB crystallin. Human serum antibodies to a synthetic peptide containing RRPFF were virtually exclusively found in patients with prior infection by Epstein-Barr virus. Other studies have suggested a relation between Epstein-Barr virus infection and multiple sclerosis, including nearly 100% Epstein-Barr virus seropositivity among patients with multiple sclerosis and increased concentrations of antibody to EBNA in CSF of patients with multiple sclerosis. By antigen specific immunoblotting, antibodies to the RRPFF motif in the CSF were shown to correspond to a subset of oligoclonal bands in the CSF from the same patient.
CONCLUSION—This study shows that phage epitope display libraries may be used to select amino acid

  3. Multiple hydrogen bonds tuning guest/host excited-state proton transfer reaction: its application in molecular recognition.

    PubMed

    Chou, He-Chun; Hsu, Chin-Hao; Cheng, Yi-Ming; Cheng, Chung-Chih; Liu, Hsiao-Wei; Pu, Shih-Chieh; Chou, Pi-Tai

    2004-02-18

    A molecular recognition concept exploiting multiple-hydrogen-bond fine-tuned excited-state proton-transfer (ESPT) was conveyed using 3,4,5,6-tetrahydrobis(pyrido[3,2-g]indolo)[2,3-a:3',2'-j]acridine (1a). The catalytic type 1a/carboxylic acids hydrogen-bonding (HB) complexes undergo ultrafast ESPT, resulting in an anomalously large Stokes shifted tautomer emission (lambdamax approximately 600 nm). Albeit forming a quadruple HB complex, ESPT is prohibited in the noncatalytic-type 1a/urea complexes (lambdamax approximately 430 nm). The HB configuration tuning ESPT properties lead to a feasible design for sensing multiple-HB-site analytes of biological interest.

  4. Molecular phylogenies support homoplasy of multiple morphological characters used in the taxonomy of Heteroscleromorpha (Porifera: Demospongiae).

    PubMed

    Morrow, Christine C; Redmond, Niamh E; Picton, Bernard E; Thacker, Robert W; Collins, Allen G; Maggs, Christine A; Sigwart, Julia D; Allcock, A Louise

    2013-09-01

    Sponge classification has long been based mainly on morphocladistic analyses but is now being greatly challenged by more than 12 years of accumulated analyses of molecular data analyses. The current study used phylogenetic hypotheses based on sequence data from 18S rRNA, 28S rRNA, and the CO1 barcoding fragment, combined with morphology to justify the resurrection of the order Axinellida Lévi, 1953. Axinellida occupies a key position in different morphologically derived topologies. The abandonment of Axinellida and the establishment of Halichondrida Vosmaer, 1887 sensu lato to contain Halichondriidae Gray, 1867, Axinellidae Carter, 1875, Bubaridae Topsent, 1894, Heteroxyidae Dendy, 1905, and a new family Dictyonellidae van Soest et al., 1990 was based on the conclusion that an axially condensed skeleton evolved independently in separate lineages in preference to the less parsimonious assumption that asters (star-shaped spicules), acanthostyles (club-shaped spicules with spines), and sigmata (C-shaped spicules) each evolved more than once. Our new molecular trees are congruent and contrast with the earlier, morphologically based, trees. The results show that axially condensed skeletons, asters, acanthostyles, and sigmata are all homoplasious characters. The unrecognized homoplasious nature of these characters explains much of the incongruence between molecular-based and morphology-based phylogenies. We use the molecular trees presented here as a basis for re-interpreting the morphological characters within Heteroscleromorpha. The implications for the classification of Heteroscleromorpha are discussed and a new order Biemnida ord. nov. is erected.

  5. Improved detection of nasopharyngeal cocolonization by multiple pneumococcal serotypes by use of latex agglutination or molecular serotyping by microarray.

    PubMed

    Turner, Paul; Hinds, Jason; Turner, Claudia; Jankhot, Auscharee; Gould, Katherine; Bentley, Stephen D; Nosten, François; Goldblatt, David

    2011-05-01

    Identification of Streptococcus pneumoniae in the nasopharynx is critical for an understanding of transmission, estimates of vaccine efficacy, and possible replacement disease. Conventional nasopharyngeal swab (NPS) culture and serotyping (the WHO protocol) is likely to underestimate multiple-serotype carriage. We compared the WHO protocol with methods aimed at improving cocolonization detection. One hundred twenty-five NPSs from an infant pneumococcal-carriage study, containing ≥ 1 serotype by WHO culture, were recultured in duplicate. A sweep of colonies from one plate culture was serotyped by latex agglutination. DNA extracted from the second plate was analyzed by S. pneumoniae molecular-serotyping microarray. Multiple serotypes were detected in 11.2% of the swabs by WHO culture, 43.2% by sweep serotyping, and 48.8% by microarray. Sweep and microarray were more likely to detect multiple serotypes than WHO culture (P < 0.0001). Cocolonization detection rates were similar between microarray and sweep, but the microarray identified the greatest number of serotypes. A common serogroup type was identified in 95.2% of swabs by all methods. WHO methodology significantly underestimates multiple-serotype carriage compared to these alternate methods. Sweep serotyping is cost-effective and field deployable but may fail to detect serotypes at low abundance, whereas microarray serotyping is more costly and technology dependent but may detect these additional minor carried serotypes.

  6. A Targeted “Capture” and “Removal” Scavenger toward Multiple Pollutants for Water Remediation based on Molecular Recognition

    PubMed Central

    Wang, Jie; Shen, Haijing; Hu, Xiaoxia; Li, Yan; Li, Zhihao; Xu, Jinfan; Song, Xiufeng; Zeng, Haibo

    2015-01-01

    For the water remediation techniques based on adsorption, the long‐standing contradictories between selectivity and multiple adsorbability, as well as between affinity and recyclability, have put it on weak defense amid more and more severe environment crisis. Here, a pollutant‐targeting hydrogel scavenger is reported for water remediation with both high selectivity and multiple adsorbability for several pollutants, and with strong affinity and good recyclability through rationally integrating the advantages of multiple functional materials. In the scavenger, aptamers fold into binding pockets to accommodate the molecular structure of pollutants to afford perfect selectivity, and Janus nanoparticles with antibacterial function as well as anisotropic surfaces to immobilize multiple aptamers allow for simultaneously handling different kinds of pollutants. The scavenger exhibits high efficiencies in removing pollutants from water and it can be easily recycled for many times without significant loss of loading capacities. Moreover, the residual concentrations of each contaminant are well below the drinking water standards. Thermodynamic behavior of the adsorption process is investigated and the rate‐controlling process is determined. Furthermore, a point of use device is constructed and it displays high efficiency in removing pollutants from environmental water. The scavenger exhibits great promise to be applied in the next generation of water purification systems. PMID:27774394

  7. A Molecular Analysis of Training Multiple versus Single Manipulations to Establish a Generalized Manipulative Imitation Repertoire

    ERIC Educational Resources Information Center

    Hartley, Breanne K.

    2009-01-01

    This study evaluates the necessity of training multiple versus single manipulative-imitations per object in order to establish generalized manipulative-imitation. Training took place in Croyden Avenue School's Early Childhood Developmental Delay preschool classroom in Kalamazoo, MI. Two groups of 3 children each were trained to imitate in order to…

  8. Molecular Markers for Prostate Cancer Risk Stratification from Multiple Ultrasound-Guided Biopsies

    DTIC Science & Technology

    2014-12-01

    that this line of investigation should be extended to deeper DNA sequencing on a clinically relevant number of cases in order to establish prognostic...molecular biomarkers for PCa. 15. SUBJECT TERMS Prostate cancer, prognosis, diagnosis, CNV, genomics, DNA sequence, biopsy 16. SECURITY...begun our work on Objective 2. 2. KEYWORDS Prostate; cancer; biopsy; DNA copy number; DNA sequencing; biomarkers; lineage; single-cell DNA

  9. Molecular Detection of Multiple Emerging Pathogens in Sputa from Cystic Fibrosis Patients

    PubMed Central

    Bittar, Fadi; Richet, Hervé; Dubus, Jean-Christophe; Reynaud-Gaubert, Martine; Stremler, Nathalie; Sarles, Jacques; Raoult, Didier; Rolain, Jean-Marc

    2008-01-01

    Background There is strong evidence that culture-based methods detect only a small proportion of bacteria present in the respiratory tracts of cystic fibrosis (CF) patients. Methodology/Principal Findings Standard microbiological culture and phenotypic identification of bacteria in sputa from CF patients have been compared to molecular methods by the use of 16S rDNA amplification, cloning and sequencing. Twenty-five sputa from CF patients were cultured that yield 33 isolates (13 species) known to be pathogens during CF. For molecular cloning, 760 clones were sequenced (7.2±3.9 species/sputum), and 53 different bacterial species were identified including 16 species of anaerobes (30%). Discrepancies between culture and molecular data were numerous and demonstrate that accurate identification remains challenging. New or emerging bacteria not or rarely reported in CF patients were detected including Dolosigranulum pigrum, Dialister pneumosintes, and Inquilinus limosus. Conclusions/Significance Our results demonstrate the complex microbial community in sputa from CF patients, especially anaerobic bacteria that are probably an underestimated cause of CF lung pathology. Metagenomic analysis is urgently needed to better understand those complex communities in CF pulmonary infections. PMID:18682840

  10. Multiple templates-based homology modeling enhances structure quality of AT1 receptor: validation by molecular dynamics and antagonist docking.

    PubMed

    Sokkar, Pandian; Mohandass, Shylajanaciyar; Ramachandran, Murugesan

    2011-07-01

    We present a comparative account on 3D-structures of human type-1 receptor (AT1) for angiotensin II (AngII), modeled using three different methodologies. AngII activates a wide spectrum of signaling responses via the AT1 receptor that mediates physiological control of blood pressure and diverse pathological actions in cardiovascular, renal, and other cell types. Availability of 3D-model of AT1 receptor would significantly enhance the development of new drugs for cardiovascular diseases. However, templates of AT1 receptor with low sequence similarity increase the complexity in straightforward homology modeling, and hence there is a need to evaluate different modeling methodologies in order to use the models for sensitive applications such as rational drug design. Three models were generated for AT1 receptor by, (1) homology modeling with bovine rhodopsin as template, (2) homology modeling with multiple templates and (3) threading using I-TASSER web server. Molecular dynamics (MD) simulation (15 ns) of models in explicit membrane-water system, Ramachandran plot analysis and molecular docking with antagonists led to the conclusion that multiple template-based homology modeling outweighs other methodologies for AT1 modeling.

  11. Multiple large clusters of tuberculosis in London: a cross-sectional analysis of molecular and spatial data.

    PubMed

    Smith, Catherine M; Maguire, Helen; Anderson, Charlotte; Macdonald, Neil; Hayward, Andrew C

    2017-01-01

    Large outbreaks of tuberculosis (TB) represent a particular threat to disease control because they reflect multiple instances of active transmission. The extent to which long chains of transmission contribute to high TB incidence in London is unknown. We aimed to estimate the contribution of large clusters to the burden of TB in London and identify risk factors. We identified TB patients resident in London notified between 2010 and 2014, and used 24-locus mycobacterial interspersed repetitive units-variable number tandem repeat strain typing data to classify cases according to molecular cluster size. We used spatial scan statistics to test for spatial clustering and analysed risk factors through multinomial logistic regression. TB isolates from 7458 patients were included in the analysis. There were 20 large molecular clusters (with n>20 cases), comprising 795 (11%) of all cases; 18 (90%) large clusters exhibited significant spatial clustering. Cases in large clusters were more likely to be UK born (adjusted odds ratio 2.93, 95% CI 2.28-3.77), of black-Caribbean ethnicity (adjusted odds ratio 3.64, 95% CI 2.23-5.94) and have multiple social risk factors (adjusted odds ratio 3.75, 95% CI 1.96-7.16). Large clusters of cases contribute substantially to the burden of TB in London. Targeting interventions such as screening in deprived areas and social risk groups, including those of black ethnicities and born in the UK, should be a priority for reducing transmission.

  12. Multiple large clusters of tuberculosis in London: a cross-sectional analysis of molecular and spatial data

    PubMed Central

    Maguire, Helen; Anderson, Charlotte; Macdonald, Neil; Hayward, Andrew C.

    2017-01-01

    Large outbreaks of tuberculosis (TB) represent a particular threat to disease control because they reflect multiple instances of active transmission. The extent to which long chains of transmission contribute to high TB incidence in London is unknown. We aimed to estimate the contribution of large clusters to the burden of TB in London and identify risk factors. We identified TB patients resident in London notified between 2010 and 2014, and used 24-locus mycobacterial interspersed repetitive units–variable number tandem repeat strain typing data to classify cases according to molecular cluster size. We used spatial scan statistics to test for spatial clustering and analysed risk factors through multinomial logistic regression. TB isolates from 7458 patients were included in the analysis. There were 20 large molecular clusters (with n>20 cases), comprising 795 (11%) of all cases; 18 (90%) large clusters exhibited significant spatial clustering. Cases in large clusters were more likely to be UK born (adjusted odds ratio 2.93, 95% CI 2.28–3.77), of black-Caribbean ethnicity (adjusted odds ratio 3.64, 95% CI 2.23–5.94) and have multiple social risk factors (adjusted odds ratio 3.75, 95% CI 1.96–7.16). Large clusters of cases contribute substantially to the burden of TB in London. Targeting interventions such as screening in deprived areas and social risk groups, including those of black ethnicities and born in the UK, should be a priority for reducing transmission. PMID:28149918

  13. Uncertainty in hydrological signatures

    NASA Astrophysics Data System (ADS)

    Westerberg, I. K.; McMillan, H. K.

    2015-09-01

    Information about rainfall-runoff processes is essential for hydrological analyses, modelling and water-management applications. A hydrological, or diagnostic, signature quantifies such information from observed data as an index value. Signatures are widely used, e.g. for catchment classification, model calibration and change detection. Uncertainties in the observed data - including measurement inaccuracy and representativeness as well as errors relating to data management - propagate to the signature values and reduce their information content. Subjective choices in the calculation method are a further source of uncertainty. We review the uncertainties relevant to different signatures based on rainfall and flow data. We propose a generally applicable method to calculate these uncertainties based on Monte Carlo sampling and demonstrate it in two catchments for common signatures including rainfall-runoff thresholds, recession analysis and basic descriptive signatures of flow distribution and dynamics. Our intention is to contribute to awareness and knowledge of signature uncertainty, including typical sources, magnitude and methods for its assessment. We found that the uncertainties were often large (i.e. typical intervals of ±10-40 % relative uncertainty) and highly variable between signatures. There was greater uncertainty in signatures that use high-frequency responses, small data subsets, or subsets prone to measurement errors. There was lower uncertainty in signatures that use spatial or temporal averages. Some signatures were sensitive to particular uncertainty types such as rating-curve form. We found that signatures can be designed to be robust to some uncertainty sources. Signature uncertainties of the magnitudes we found have the potential to change the conclusions of hydrological and ecohydrological analyses, such as cross-catchment comparisons or inferences about dominant processes.

  14. Molecular and isotopic signatures in sediments and gas hydrate of the central/southwestern Ulleung Basin: high alkalinity escape fuelled by biogenically sourced methane

    NASA Astrophysics Data System (ADS)

    Kim, Ji-Hoon; Park, Myong-Ho; Chun, Jong-Hwa; Lee, Joo Yong

    2011-02-01

    Natural marine gas hydrate was discovered in Korean territorial waters during a 2007 KIGAM cruise to the central/southwestern Ulleung Basin, East Sea. The first data on the geochemical characterization of hydrate-bound water and gas are presented here for cold seep site 07GHP-10 in the central basin sector, together with analogous data for four sites (07GHP-01, 07GHP-02, 07GHP-03, and 07GHP-14) where no hydrates were detected in other cores from the central/southwestern sectors. Hydrate-bound water displayed very low concentrations of major ions (Cl-, SO{4/2-}, Na+, Mg2+, K+, and Ca2+), and more positive δD (15.5‰) and δ18O (2.3‰) signatures compared to seawater. Cl- freshening and more positive isotopic values were also observed in the pore water at gas hydrate site 07GHP-10. The inferred sulfate-methane interface (SMI) was very shallow (<5 mbsf) at least at four sites, suggesting the widespread occurrence of anaerobic oxidation of methane (AOM) at shallow sediment depths, and possibly high methane flux. Around the SMI, pore water alkalinity was very high (>40 mM), but the carbon isotopic ratios of dissolved inorganic carbon (δ13CDIC) did not show minimum values typical of AOM. Moreover, macroscopic authigenic carbonates were not observed at any of the core sites. This can plausibly be explained by carbon with high δ13C values diffusing upward from below the SMI, increasing alkalinity via deep methanogenesis and eventually escaping as alkalinity into the water column, with minor precipitation as solid phase. This contrasts, but is not inconsistent with recent reports of methane-fuelled carbonate formation at other sites in the southwestern basin sector. Methane was the main hydrocarbon component (>99.85%) of headspace, void, and hydrate-bound gases, C1/C2+ ratios were at least 1,000, and δ13CCH4 and δDCH4 values were in the typical range of methane generated by microbial reduction of CO2. This is supported by the δ13CC2H6 signatures of void and hydrate

  15. Signatures of topological Josephson junctions

    NASA Astrophysics Data System (ADS)

    Peng, Yang; Pientka, Falko; Berg, Erez; Oreg, Yuval; von Oppen, Felix

    2016-08-01

    Quasiparticle poisoning and diabatic transitions may significantly narrow the window for the experimental observation of the 4 π -periodic dc Josephson effect predicted for topological Josephson junctions. Here, we show that switching-current measurements provide accessible and robust signatures for topological superconductivity which persist in the presence of quasiparticle poisoning processes. Such measurements provide access to the phase-dependent subgap spectrum and Josephson currents of the topological junction when incorporating it into an asymmetric SQUID together with a conventional Josephson junction with large critical current. We also argue that pump-probe experiments with multiple current pulses can be used to measure the quasiparticle poisoning rates of the topological junction. The proposed signatures are particularly robust, even in the presence of Zeeman fields and spin-orbit coupling, when focusing on short Josephson junctions. Finally, we also consider microwave excitations of short topological Josephson junctions which may complement switching-current measurements.

  16. Shared and unique responses of plants to multiple individual stresses and stress combinations: physiological and molecular mechanisms

    PubMed Central

    Pandey, Prachi; Ramegowda, Venkategowda; Senthil-Kumar, Muthappa

    2015-01-01

    In field conditions, plants are often simultaneously exposed to multiple biotic and abiotic stresses resulting in substantial yield loss. Plants have evolved various physiological and molecular adaptations to protect themselves under stress combinations. Emerging evidences suggest that plant responses to a combination of stresses are unique from individual stress responses. In addition, plants exhibit shared responses which are common to individual stresses and stress combination. In this review, we provide an update on the current understanding of both unique and shared responses. Specific focus of this review is on heat–drought stress as a major abiotic stress combination and, drought–pathogen and heat–pathogen as examples of abiotic–biotic stress combinations. We also comprehend the current understanding of molecular mechanisms of cross talk in relation to shared and unique molecular responses for plant survival under stress combinations. Thus, the knowledge of shared responses of plants from individual stress studies and stress combinations can be utilized to develop varieties with broad spectrum stress tolerance. PMID:26442037

  17. Plasma proteomic profiles from disease-discordant monozygotic twins suggest that molecular pathways are shared in multiple systemic autoimmune diseases*

    PubMed Central

    2011-01-01

    Introduction Although systemic autoimmune diseases (SAID) share many clinical and laboratory features, whether they also share some common features of pathogenesis remains unclear. We assessed plasma proteomic profiles among different SAID for evidence of common molecular pathways that could provide insights into pathogenic mechanisms shared by these diseases. Methods Differential quantitative proteomic analyses (one-dimensional reverse-phase liquid chromatography-mass spectrometry) were performed to assess patterns of plasma protein expression. Monozygotic twins (four pairs discordant for systemic lupus erythematosus, four pairs discordant for juvenile idiopathic arthritis and two pairs discordant for juvenile dermatomyositis) were studied to minimize polymorphic gene effects. Comparisons were also made to 10 unrelated, matched controls. Results Multiple plasma proteins, including acute phase reactants, structural proteins, immune response proteins, coagulation and transcriptional factors, were differentially expressed similarly among the different SAID studied. Multivariate Random Forest modeling identified seven proteins whose combined altered expression levels effectively segregated affected vs. unaffected twins. Among these seven proteins, four were also identified in univariate analyses of proteomic data (syntaxin 17, α-glucosidase, paraoxonase 1, and the sixth component of complement). Molecular pathway modeling indicated that these factors may be integrated through interactions with a candidate plasma biomarker, PON1 and the pro-inflammatory cytokine IL-6. Conclusions Together, these data suggest that different SAID may share common alterations of plasma protein expression and molecular pathways. An understanding of the mechanisms leading to the altered plasma proteomes common among these SAID may provide useful insights into their pathogeneses. PMID:22044644

  18. Detection of molecular signatures of selection at microsatellite loci in the South African abalone (Haliotis midae) using a population genomic approach.

    PubMed

    Rhode, Clint; Vervalle, Jessica; Bester-van der Merwe, Aletta E; Roodt-Wilding, Rouvay

    2013-06-01

    Identifying genomic regions that may be under selection is important for elucidating the genetic architecture of complex phenotypes underlying adaptation to heterogeneous environments. A population genomic approach, using a classical neutrality test and various Fst-outlier detection methods was employed to evaluate genome-wide polymorphism data in order to identify loci that may be candidates for selection amongst six populations (three cultured and three wild) of the South African abalone, Haliotis midae. Approximately 9% of the genome-wide microsatellite markers were putatively subject to directional selection, whilst 6-18% of the genome is thought to be influenced by balancing selection. Genetic diversity estimates for candidate loci under directional selection was significantly reduced in comparison to candidate neutral loci, whilst candidate balancing selection loci demonstrated significantly higher levels of genetic diversity (Kruskal-Wallis test, P<0.05). Pairwise Fst estimates based on candidate directional selection loci also demonstrated increased levels of differentiation between study populations. Various candidate loci under selection showed significant inter-chromosomal linkage disequilibrium, suggesting possible gene-networks underling adaptive phenotypes. Furthermore, several loci had significant hits to known genes when performing BLAST searches to NCBI's non-redundant databases, whilst others are known to be derived from expressed sequences even though homology to a known gene could not be established. A number of loci also demonstrated relatively high similarity to transposable elements. The association of these loci to functional and genomically active sequences could in part explain the observed signatures of selection.

  19. Multiple Ionization of Free Ubiquitin Molecular Ions in Extreme Ultraviolet Free-Electron Laser Pulses.

    PubMed

    Schlathölter, Thomas; Reitsma, Geert; Egorov, Dmitrii; Gonzalez-Magaña, Olmo; Bari, Sadia; Boschman, Leon; Bodewits, Erwin; Schnorr, Kirsten; Schmid, Georg; Schröter, Claus Dieter; Moshammer, Robert; Hoekstra, Ronnie

    2016-08-26

    The fragmentation of free tenfold protonated ubiquitin in intense 70 femtosecond pulses of 90 eV photons from the FLASH facility was investigated. Mass spectrometric investigation of the fragment cations produced after removal of many electrons revealed fragmentation predominantly into immonium ions and related ions, with yields increasing linearly with intensity. Ionization clearly triggers a localized molecular response that occurs before the excitation energy equilibrates. Consistent with this interpretation, the effect is almost unaffected by the charge state, as fragmentation of sixfold deprotonated ubiquitin leads to a very similar fragmentation pattern. Ubiquitin responds to EUV multiphoton ionization as an ensemble of small peptides.

  20. Molecular etiology of arthrogryposis in multiple families of mostly Turkish origin

    PubMed Central

    Bayram, Yavuz; Karaca, Ender; Coban Akdemir, Zeynep; Yilmaz, Elif Ozdamar; Tayfun, Gulsen Akay; Aydin, Hatip; Torun, Deniz; Bozdogan, Sevcan Tug; Gezdirici, Alper; Isikay, Sedat; Atik, Mehmed M.; Gambin, Tomasz; Harel, Tamar; El-Hattab, Ayman W.; Charng, Wu-Lin; Pehlivan, Davut; Jhangiani, Shalini N.; Muzny, Donna M.; Karaman, Ali; Celik, Tamer; Yuregir, Ozge Ozalp; Yildirim, Timur; Bayhan, Ilhan A.; Boerwinkle, Eric; Gibbs, Richard A.; Elcioglu, Nursel; Tuysuz, Beyhan; Lupski, James R.

    2016-01-01

    BACKGROUND. Arthrogryposis, defined as congenital joint contractures in 2 or more body areas, is a clinical sign rather than a specific disease diagnosis. To date, more than 400 different disorders have been described that present with arthrogryposis, and variants of more than 220 genes have been associated with these disorders; however, the underlying molecular etiology remains unknown in the considerable majority of these cases. METHODS. We performed whole exome sequencing (WES) of 52 patients with clinical presentation of arthrogryposis from 48 different families. RESULTS. Affected individuals from 17 families (35.4%) had variants in known arthrogryposis-associated genes, including homozygous variants of cholinergic γ nicotinic receptor (CHRNG, 6 subjects) and endothelin converting enzyme–like 1 (ECEL1, 4 subjects). Deleterious variants in candidate arthrogryposis-causing genes (fibrillin 3 [FBN3], myosin IXA [MYO9A], and pleckstrin and Sec7 domain containing 3 [PSD3]) were identified in 3 families (6.2%). Moreover, in 8 families with a homozygous mutation in an arthrogryposis-associated gene, we identified a second locus with either a homozygous or compound heterozygous variant in a candidate gene (myosin binding protein C, fast type [MYBPC2] and vacuolar protein sorting 8 [VPS8], 2 families, 4.2%) or in another disease-associated genes (6 families, 12.5%), indicating a potential mutational burden contributing to disease expression. CONCLUSION. In 58.3% of families, the arthrogryposis manifestation could be explained by a molecular diagnosis; however, the molecular etiology in subjects from 20 families remained unsolved by WES. Only 5 of these 20 unrelated subjects had a clinical presentation consistent with amyoplasia; a phenotype not thought to be of genetic origin. Our results indicate that increased use of genome-wide technologies will provide opportunities to better understand genetic models for diseases and molecular mechanisms of genetically

  1. Molecular image-directed biopsies: improving clinical biopsy selection in patients with multiple tumors

    NASA Astrophysics Data System (ADS)

    Harmon, Stephanie A.; Tuite, Michael J.; Jeraj, Robert

    2016-10-01

    Site selection for image-guided biopsies in patients with multiple lesions is typically based on clinical feasibility and physician preference. This study outlines the development of a selection algorithm that, in addition to clinical requirements, incorporates quantitative imaging data for automatic identification of candidate lesions for biopsy. The algorithm is designed to rank potential targets by maximizing a lesion-specific score, incorporating various criteria separated into two categories: (1) physician-feasibility category including physician-preferred lesion location and absolute volume scores, and (2) imaging-based category including various modality and application-specific metrics. This platform was benchmarked in two clinical scenarios, a pre-treatment setting and response-based setting using imaging from metastatic prostate cancer patients with high disease burden (multiple lesions) undergoing conventional treatment and receiving whole-body [18F]NaF PET/CT scans pre- and mid-treatment. Targeting of metastatic lesions was robust to different weighting ratios and candidacy for biopsy was physician confirmed. Lesion ranked as top targets for biopsy remained so for all patients in pre-treatment and post-treatment biopsy selection after sensitivity testing was completed for physician-biased or imaging-biased scenarios. After identifying candidates, biopsy feasibility was evaluated by a physician and confirmed for 90% (32/36) of high-ranking lesions, of which all top choices were confirmed. The remaining cases represented lesions with high anatomical difficulty for targeting, such as proximity to sciatic nerve. This newly developed selection method was successfully used to quantitatively identify candidate lesions for biopsies in patients with multiple lesions. In a prospective study, we were able to successfully plan, develop, and implement this technique for the selection of a pre-treatment biopsy location.

  2. Molecular image-directed biopsies: improving clinical biopsy selection in patients with multiple tumors.

    PubMed

    Harmon, Stephanie A; Tuite, Michael J; Jeraj, Robert

    2016-10-21

    Site selection for image-guided biopsies in patients with multiple lesions is typically based on clinical feasibility and physician preference. This study outlines the development of a selection algorithm that, in addition to clinical requirements, incorporates quantitative imaging data for automatic identification of candidate lesions for biopsy. The algorithm is designed to rank potential targets by maximizing a lesion-specific score, incorporating various criteria separated into two categories: (1) physician-feasibility category including physician-preferred lesion location and absolute volume scores, and (2) imaging-based category including various modality and application-specific metrics. This platform was benchmarked in two clinical scenarios, a pre-treatment setting and response-based setting using imaging from metastatic prostate cancer patients with high disease burden (multiple lesions) undergoing conventional treatment and receiving whole-body [(18)F]NaF PET/CT scans pre- and mid-treatment. Targeting of metastatic lesions was robust to different weighting ratios and candidacy for biopsy was physician confirmed. Lesion ranked as top targets for biopsy remained so for all patients in pre-treatment and post-treatment biopsy selection after sensitivity testing was completed for physician-biased or imaging-biased scenarios. After identifying candidates, biopsy feasibility was evaluated by a physician and confirmed for 90% (32/36) of high-ranking lesions, of which all top choices were confirmed. The remaining cases represented lesions with high anatomical difficulty for targeting, such as proximity to sciatic nerve. This newly developed selection method was successfully used to quantitatively identify candidate lesions for biopsies in patients with multiple lesions. In a prospective study, we were able to successfully plan, develop, and implement this technique for the selection of a pre-treatment biopsy location.

  3. CytoSolve: A Scalable Computational Method for Dynamic Integration of Multiple Molecular Pathway Models.

    PubMed

    Ayyadurai, V A Shiva; Dewey, C Forbes

    2011-03-01

    A grand challenge of computational systems biology is to create a molecular pathway model of the whole cell. Current approaches involve merging smaller molecular pathway models' source codes to create a large monolithic model (computer program) that runs on a single computer. Such a larger model is difficult, if not impossible, to maintain given ongoing updates to the source codes of the smaller models. This paper describes a new system called CytoSolve that dynamically integrates computations of smaller models that can run in parallel across different machines without the need to merge the source codes of the individual models. This approach is demonstrated on the classic Epidermal Growth Factor Receptor (EGFR) model of Kholodenko. The EGFR model is split into four smaller models and each smaller model is distributed on a different machine. Results from four smaller models are dynamically integrated to generate identical results to the monolithic EGFR model running on a single machine. The overhead for parallel and dynamic computation is approximately twice that of a monolithic model running on a single machine. The CytoSolve approach provides a scalable method since smaller models may reside on any computer worldwide, where the source code of each model can be independently maintained and updated.

  4. Multiple Molecular and Cellular Mechanisms of Action of Lycopene in Cancer Inhibition

    PubMed Central

    Trejo-Solís, Cristina; Pedraza-Chaverrí, Jose; Torres-Ramos, Mónica; Jiménez-Farfán, Dolores; Cruz Salgado, Arturo; Serrano-García, Norma; Osorio-Rico, Laura; Sotelo, Julio

    2013-01-01

    Epidemiological studies suggest that including fruits, vegetables, and whole grains in regular dietary intake might prevent and reverse cellular carcinogenesis, reducing the incidence of primary tumours. Bioactive components present in food can simultaneously modulate more than one carcinogenic process, including cancer metabolism, hormonal balance, transcriptional activity, cell-cycle control, apoptosis, inflammation, angiogenesis and metastasis. Some studies have shown an inverse correlation between a diet rich in fruits, vegetables, and carotenoids and a low incidence of different types of cancer. Lycopene, the predominant carotenoid found in tomatoes, exhibits a high antioxidant capacity and has been shown to prevent cancer, as evidenced by clinical trials and studies in cell culture and animal models. In vitro studies have shown that lycopene treatment can selectively arrest cell growth and induce apoptosis in cancer cells without affecting normal cells. In vivo studies have revealed that lycopene treatment inhibits tumour growth in the liver, lung, prostate, breast, and colon. Clinical studies have shown that lycopene protects against prostate cancer. One of the main challenges in cancer prevention is the integration of new molecular findings into clinical practice. Thus, the identification of molecular biomarkers associated with lycopene levels is essential for improving our understanding of the mechanisms underlying its antineoplastic activity. PMID:23970935

  5. Statistical clumped isotope signatures

    PubMed Central

    Röckmann, T.; Popa, M. E.; Krol, M. C.; Hofmann, M. E. G.

    2016-01-01

    High precision measurements of molecules containing more than one heavy isotope may provide novel constraints on element cycles in nature. These so-called clumped isotope signatures are reported relative to the random (stochastic) distribution of heavy isotopes over all available isotopocules of a molecule, which is the conventional reference. When multiple indistinguishable atoms of the same element are present in a molecule, this reference is calculated from the bulk (≈average) isotopic composition of the involved atoms. We show here that this referencing convention leads to apparent negative clumped isotope anomalies (anti-clumping) when the indistinguishable atoms originate from isotopically different populations. Such statistical clumped isotope anomalies must occur in any system where two or more indistinguishable atoms of the same element, but with different isotopic composition, combine in a molecule. The size of the anti-clumping signal is closely related to the difference of the initial isotope ratios of the indistinguishable atoms that have combined. Therefore, a measured statistical clumped isotope anomaly, relative to an expected (e.g. thermodynamical) clumped isotope composition, may allow assessment of the heterogeneity of the isotopic pools of atoms that are the substrate for formation of molecules. PMID:27535168

  6. HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales

    DOE PAGES

    Riccardi, Demian M.; Parks, Jerry M.; Johs, Alexander; ...

    2015-03-20

    HackaMol is an open source, object-oriented toolkit written in Modern Perl that organizes atoms within molecules and provides chemically intuitive attributes and methods. The library consists of two components: HackaMol, the core that contains classes for storing and manipulating molecular information, and HackaMol::X, the extensions that use the core. We tested the core; it is well-documented and easy to install across computational platforms. Our goal for the extensions is to provide a more flexible space for researchers to develop and share new methods. In this application note, we provide a description of the core classes and two extensions: HackaMol::X::Calculator, anmore » abstract calculator that uses code references to generalize interfaces with external programs, and HackaMol::X::Vina, a structured class that provides an interface with the AutoDock Vina docking program.« less

  7. HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales

    SciTech Connect

    Riccardi, Demian M.; Parks, Jerry M.; Johs, Alexander; Smith, Jeremy C.

    2015-03-20

    HackaMol is an open source, object-oriented toolkit written in Modern Perl that organizes atoms within molecules and provides chemically intuitive attributes and methods. The library consists of two components: HackaMol, the core that contains classes for storing and manipulating molecular information, and HackaMol::X, the extensions that use the core. We tested the core; it is well-documented and easy to install across computational platforms. Our goal for the extensions is to provide a more flexible space for researchers to develop and share new methods. In this application note, we provide a description of the core classes and two extensions: HackaMol::X::Calculator, an abstract calculator that uses code references to generalize interfaces with external programs, and HackaMol::X::Vina, a structured class that provides an interface with the AutoDock Vina docking program.

  8. Efficient and extendible class scheme for the combined reaction-diffusion of multiple molecular species

    NASA Astrophysics Data System (ADS)

    Stella, Sabrina; Chignola, Roberto; Milotti, Edoardo

    2014-03-01

    When dealing with large numbers of cells in biophysical simulations, it is important to properly manage the different substances that diffuse and react in and around cells. Although in an object-oriented programming environment it seems more natural to define cells as the basic objects, it turns out that individual substances are better suited to take this role. Here we describe the biophysical problem and our computational solution, and display the results obtained with a toy model. We find that the new implementation does not decrease performance and yet it leads to a much better structured and modular code. This will make more realistic programs with many molecular pathways much more modular and readily extendible.

  9. HackaMol: An Object-Oriented Modern Perl Library for Molecular Hacking on Multiple Scales.

    PubMed

    Riccardi, Demian; Parks, Jerry M; Johs, Alexander; Smith, Jeremy C

    2015-04-27

    HackaMol is an open source, object-oriented toolkit written in Modern Perl that organizes atoms within molecules and provides chemically intuitive attributes and methods. The library consists of two components: HackaMol, the core that contains classes for storing and manipulating molecular information, and HackaMol::X, the extensions that use the core. The core is well-tested, well-documented, and easy to install across computational platforms. The goal of the extensions is to provide a more flexible space for researchers to develop and share new methods. In this application note, we provide a description of the core classes and two extensions: HackaMol::X::Calculator, an abstract calculator that uses code references to generalize interfaces with external programs, and HackaMol::X::Vina, a structured class that provides an interface with the AutoDock Vina docking program.

  10. MILLIMETER MULTIPLICITY IN DR21(OH): OUTFLOWS, MOLECULAR CORES, AND ENVELOPES

    SciTech Connect

    Zapata, Luis A.; Loinard, Laurent; Rodriguez, Luis F.; Galvan-Madrid, R.; Su, Y.-N.; Menten, Karl M.; Patel, Nimesh

    2012-01-10

    We present sensitive high angular resolution ({approx}1'') millimeter continuum and line observations from the massive star-forming region DR21(OH) located in the Cygnus X molecular cloud. Within the well-known dusty MM1-2 molecular cores, we report the detection of a new cluster of about 10 compact continuum millimeter sources with masses between 5 and 24 M{sub Sun }, and sizes of a few thousands of astronomical units. These objects are likely to be large dusty envelopes surrounding massive protostars, some of them most probably driving several of the outflows that emanate from this region. Additionally, we report the detection of strong millimeter emission of formaldehyde (H{sub 2}CO) and methanol (CH{sub 3}OH) near 218 GHz as well as compact emission from the typical outflow tracers carbon monoxide and silicon monoxide (CO and SiO) toward this massive star-forming region. The H{sub 2}CO and CH{sub 3}OH emission is luminous ({approx}10{sup -4} L{sub Sun }), well resolved, and found along the collimated methanol maser outflow first identified at centimeter wavelengths and in the sources SMA6 and SMA7. Our observations suggest that this maser outflow might be energized by a millimeter source called SMA4 located in the MM2 dusty core. The CO and SiO emission traces some other collimated outflows that emanate from MM1-2 cores, and are not related with the low-velocity maser outflow.

  11. The endogenous and reactive depression subtypes revisited: integrative animal and human studies implicate multiple distinct molecular mechanisms underlying major depressive disorder

    PubMed Central

    2014-01-01

    that ‘endogenous’ and ‘reactive’ subtypes of depression are associated with largely distinct changes in gene-expression. However, they also suggest that the molecular signature of ‘reactive’ depression caused by early stressors differs considerably from that of ‘reactive’ depression caused by late stressors. A small set of genes was consistently dysregulated across each paradigm and in post-mortem brain tissue of depressed patients suggesting a final common pathway to the disorder. These genes included the VAMP-2 gene, which has previously been associated with Axis-I disorders including MDD, bipolar depression, schizophrenia and with antidepressant treatment response. We also discuss the implications of our findings for disease classification, personalized medicine and case-control studies of MDD. PMID:24886127

  12. Molecular Mechanisms of p53 Deregulation in Cancer: An Overview in Multiple Myeloma

    PubMed Central

    Herrero, Ana B.; Rojas, Elizabeta A.; Misiewicz-Krzeminska, Irena; Krzeminski, Patryk; Gutiérrez, Norma C.

    2016-01-01

    The p53 pathway is inactivated in the majority of human cancers. Although this perturbation frequently occurs through the mutation or deletion of p53 itself, there are other mechanisms that can attenuate the pathway and contribute to tumorigenesis. For example, overexpression of important p53 negative regulators, such as murine double minute 2 (MDM2) or murine double minute 4 (MDM4), epigenetic deregulation, or even alterations in TP53 mRNA splicing. In this work, we will review the different mechanisms of p53 pathway inhibition in cancer with special focus on multiple myeloma (MM), the second most common hematological malignancy, with low incidence of p53 mutations/deletions but growing evidence of indirect p53 pathway deregulation. Translational implications for MM and cancer prognosis and treatment are also reviewed. PMID:27916892

  13. Molecular Mechanisms of p53 Deregulation in Cancer: An Overview in Multiple Myeloma.

    PubMed

    Herrero, Ana B; Rojas, Elizabeta A; Misiewicz-Krzeminska, Irena; Krzeminski, Patryk; Gutiérrez, Norma C

    2016-11-30

    The p53 pathway is inactivated in the majority of human cancers. Although this perturbation frequently occurs through the mutation or deletion of p53 itself, there are other mechanisms that can attenuate the pathway and contribute to tumorigenesis. For example, overexpression of important p53 negative regulators, such as murine double minute 2 (MDM2) or murine double minute 4 (MDM4), epigenetic deregulation, or even alterations in TP53 mRNA splicing. In this work, we will review the different mechanisms of p53 pathway inhibition in cancer with special focus on multiple myeloma (MM), the second most common hematological malignancy, with low incidence of p53 mutations/deletions but growing evidence of indirect p53 pathway deregulation. Translational implications for MM and cancer prognosis and treatment are also reviewed.

  14. Reusable nanostencils for creating multiple biofunctional molecular nanopatterns on polymer substrate.

    PubMed

    Huang, Min; Galarreta, Betty C; Artar, Alp; Adato, Ronen; Aksu, Serap; Altug, Hatice

    2012-09-12

    In this paper, we demonstrate a novel method for high throughput patterning of bioprobes with nanoscale features on biocompatible polymer substrate. Our technique, based on nanostencil lithography, employs high resolution and robust masks integrated with array of reservoirs. We show that the smallest pattern size can reach down to 100 nm. We also show that different types of biomolecules can be patterned on the same substrate simultaneously. Furthermore, the stencil can be reused multiple times to generate a series of identical patterns at low cost. Finally, we demonstrate that biomolecules can be covalently patterned on the surface while retaining their biofunctionalities. By offering the flexibility on the nanopattern design and enabling the reusability of the stencil, our approach significantly simplifies the bionanopatterning process and therefore could have profound implications in diverse biological and medical applications.

  15. Multiple time step molecular dynamics in the optimized isokinetic ensemble steered with the molecular theory of solvation: Accelerating with advanced extrapolation of effective solvation forces

    SciTech Connect

    Omelyan, Igor E-mail: omelyan@icmp.lviv.ua; Kovalenko, Andriy

    2013-12-28

    We develop efficient handling of solvation forces in the multiscale method of multiple time step molecular dynamics (MTS-MD) of a biomolecule steered by the solvation free energy (effective solvation forces) obtained from the 3D-RISM-KH molecular theory of solvation (three-dimensional reference interaction site model complemented with the Kovalenko-Hirata closure approximation). To reduce the computational expenses, we calculate the effective solvation forces acting on the biomolecule by using advanced solvation force extrapolation (ASFE) at inner time steps while converging the 3D-RISM-KH integral equations only at large outer time steps. The idea of ASFE consists in developing a discrete non-Eckart rotational transformation of atomic coordinates that minimizes the distances between the atomic positions of the biomolecule at different time moments. The effective solvation forces for the biomolecule in a current conformation at an inner time step are then extrapolated in the transformed subspace of those at outer time steps by using a modified least square fit approach applied to a relatively small number of the best force-coordinate pairs. The latter are selected from an extended set collecting the effective solvation forces obtained from 3D-RISM-KH at outer time steps over a broad time interval. The MTS-MD integration with effective solvation forces obtained by converging 3D-RISM-KH at outer time steps and applying ASFE at inner time steps is stabilized by employing the optimized isokinetic Nosé-Hoover chain (OIN) ensemble. Compared to the previous extrapolation schemes used in combination with the Langevin thermostat, the ASFE approach substantially improves the accuracy of evaluation of effective solvation forces and in combination with the OIN thermostat enables a dramatic increase of outer time steps. We demonstrate on a fully flexible model of alanine dipeptide in aqueous solution that the MTS-MD/OIN/ASFE/3D-RISM-KH multiscale method of molecular dynamics

  16. Multiple time step molecular dynamics in the optimized isokinetic ensemble steered with the molecular theory of solvation: Accelerating with advanced extrapolation of effective solvation forces

    NASA Astrophysics Data System (ADS)

    Omelyan, Igor; Kovalenko, Andriy

    2013-12-01

    We develop efficient handling of solvation forces in the multiscale method of multiple time step molecular dynamics (MTS-MD) of a biomolecule steered by the solvation free energy (effective solvation forces) obtained from the 3D-RISM-KH molecular theory of solvation (three-dimensional reference interaction site model complemented with the Kovalenko-Hirata closure approximation). To reduce the computational expenses, we calculate the effective solvation forces acting on the biomolecule by using advanced solvation force extrapolation (ASFE) at inner time steps while converging the 3D-RISM-KH integral equations only at large outer time steps. The idea of ASFE consists in developing a discrete non-Eckart rotational transformation of atomic coordinates that minimizes the distances between the atomic positions of the biomolecule at different time moments. The effective solvation forces for the biomolecule in a current conformation at an inner time step are then extrapolated in the transformed subspace of those at outer time steps by using a modified least square fit approach applied to a relatively small number of the best force-coordinate pairs. The latter are selected from an extended set collecting the effective solvation forces obtained from 3D-RISM-KH at outer time steps over a broad time interval. The MTS-MD integration with effective solvation forces obtained by converging 3D-RISM-KH at outer time steps and applying ASFE at inner time steps is stabilized by employing the optimized isokinetic Nosé-Hoover chain (OIN) ensemble. Compared to the previous extrapolation schemes used in combination with the Langevin thermostat, the ASFE approach substantially improves the accuracy of evaluation of effective solvation forces and in combination with the OIN thermostat enables a dramatic increase of outer time steps. We demonstrate on a fully flexible model of alanine dipeptide in aqueous solution that the MTS-MD/OIN/ASFE/3D-RISM-KH multiscale method of molecular dynamics

  17. Differentially Expressed Genes and Signature Pathways of Human Prostate Cancer

    PubMed Central

    Myers, Jennifer S.; von Lersner, Ariana K.; Robbins, Charles J.; Sang, Qing-Xiang Amy

    2015-01-01

    Genomic technologies including microarrays and next-generation sequencing have enabled the generation of molecular signatures of prostate cancer. Lists of differentially expressed genes between malignant and non-malignant states are thought to be fertile sources of putative prostate cancer biomarkers. However such lists of differentially expressed genes can be highly variable for multiple reasons. As such, looking at differential expression in the context of gene sets and pathways has been more robust. Using next-generation genome sequencing data from The Cancer Genome Atlas, differential gene expression between age- and stage- matched human prostate tumors and non-malignant samples was assessed and used to craft a pathway signature of prostate cancer. Up- and down-regulated genes were assigned to pathways composed of curated groups of related genes from multiple databases. The significance of these pathways was then evaluated according to the number of differentially expressed genes found in the pathway and their position within the pathway using Gene Set Enrichment Analysis and Signaling Pathway Impact Analysis. The “transforming growth factor-beta signaling” and “Ran regulation of mitotic spindle formation” pathways were strongly associated with prostate cancer. Several other significant pathways confirm reported findings from microarray data that suggest actin cytoskeleton regulation, cell cycle, mitogen-activated protein kinase signaling, and calcium signaling are also altered in prostate cancer. Thus we have demonstrated feasibility of pathway analysis and identified an underexplored area (Ran) for investigation in prostate cancer pathogenesis. PMID:26683658

  18. Multiple reaction monitoring-based determination of bovine α-lactalbumin in infant formulas and whey protein concentrates by ultra-high performance liquid chromatography-tandem mass spectrometry using tryptic signature peptides and synthetic peptide standards.

    PubMed

    Zhang, Jingshun; Lai, Shiyun; Zhang, Yu; Huang, Baifen; Li, Duo; Ren, Yiping

    2012-05-21

    The determination of α-lactalbumin in various dairy products attracts wide attention in multidiscipline fields because of its nutritional and biological functions. In the present study, we quantified the bovine α-lactalbumin in various infant formulas and whey protein concentrates using ultra-high performance liquid chromatography coupled to tandem mass spectrometer in multiple reaction monitoring mode. Bovine α-lactalbumin was quantified by employing the synthetic internal standard based on the molar equivalent relationship among the internal standard, bovine α-lactalbumin and their signature peptides. This study especially focused on the recovery rates of the sample preparation procedure and robust quantification of total bovine α-lactalbumin in its native and thermally denatured form with a synthetic internal standard KILDKVGINNYWLAHKALCSE. The observed recovery rates of bovine α-lactalbumin ranged from 95.8 to 100.6% and the reproducibility was excellent (RSD<6%) at different spiking levels. The limit of quantitation is 10 mg/100 g for infant formulas and whey protein concentrates. In order to validate the applicability of the method, 21 brands of infant formulas were analyzed. The acquired contents of bovine α-lactalbumin were 0.67-1.84 g/100g in these infant formulas in agreement with their label claimed values. The experiment of heat treatment time showed that the loss of native α-lactalbumin enhanced with an increasing intensity of heat treatment. Comparing with Ren's previous method by analysis of only native bovine α-lactalbumin, the present method at the peptide level proved to be highly suitable for measuring bovine α-lactalbumin in infant formulas and whey protein concentrates, avoiding forgoing the thermally induced denatured α-lactalbumin caused by the technological processing.

  19. Molecular Evidence for Multiple Origins of the European Spined Loaches (Teleostei, Cobitidae)

    PubMed Central

    Perdices, Anabel; Bohlen, Joerg; Šlechtová, Vendula; Doadrio, Ignacio

    2016-01-01

    We present a phylogenetic investigation of the Northern Clade, the major monophyletic clade within the freshwater fish family Cobitidae, one of the most prominent families of freshwater fishes found in Asian and European waters. Phylogenetic reconstructions based on the cytochrome b and RAG-1 genes show the genera Microcobitis, Sabanejewia, Koreocobitis and Kichulchoia as monophyletic groups. These reconstructions also show a Cobitis sensu lato and a Misgurnus sensu lato group. The Cobitis sensu lato group includes all species of Cobitis, Iksookimia, Niwaella and Kichulchoia, while the Misgurnus sensu lato group includes Misgurnus, Paramisgurnus and Koreocobitis. Although the monophyly of both the Cobitis sensu lato and Misgurnus sensu lato groups is supported, relationships within the groups are incongruent with current generic definitions. The absence of monophyly of most genera included in the Cobitis sensu lato group (Cobitis, Iksookimia and Niwaella) or their low genetic differentiation (Kichuchoia) supports their consideration as synonyms of Cobitis. Molecular phylogenies indicate that the Asian species of Misgurnus experienced a mitochondrial introgression from a lineage of Cobitis. We also find two nuclear haplotypes in the same Cobitis species from the Adriatic area that, in the absence of morphological differentiation, may indicate molecular introgression. Most lineages within the Northern Clade consist of species found in East Asia. However, some lineages also contain species from Europe and Asia Minor. The phylogenetic relationships presented here are consistent with previous studies suggesting an East Asian origin of the Northern Clade. According to the current distributions and phylogenetic relationships of the Misgurnus sensu lato and Cobitis clade lineages, particularly of M. fossilis and C. melanoleuca, the range expansion of East Asian species into Europe was most likely via Siberia into Northern and Central Europe. Phylogenetic analyses also show

  20. Molecular diagnostics of a single drug-resistant multiple myeloma case using targeted next-generation sequencing

    PubMed Central

    Ikeda, Hiroshi; Ishiguro, Kazuya; Igarashi, Tetsuyuki; Aoki, Yuka; Hayashi, Toshiaki; Ishida, Tadao; Sasaki, Yasushi; Tokino, Takashi; Shinomura, Yasuhisa

    2015-01-01

    A 69-year-old man was diagnosed with IgG λ-type multiple myeloma (MM), Stage II in October 2010. He was treated with one cycle of high-dose dexamethasone. After three cycles of bortezomib, the patient exhibited slow elevations in the free light-chain levels and developed a significant new increase of serum M protein. Bone marrow cytogenetic analysis revealed a complex karyotype characteristic of malignant plasma cells. To better understand the molecular pathogenesis of this patient, we sequenced for mutations in the entire coding regions of 409 cancer-related genes using a semiconductor-based sequencing platform. Sequencing analysis revealed eight nonsynonymous somatic mutations in addition to several copy number variants, including CCND1 and RB1. These alterations may play roles in the pathobiology of this disease. This targeted next-generation sequencing can allow for the prediction of drug resistance and facilitate improvements in the treatment of MM patients. PMID:26491355

  1. Molecular genetic analysis and ecological evidence reveals multiple cryptic species among thynnine wasp pollinators of sexually deceptive orchids.

    PubMed

    Griffiths, Kate E; Trueman, John W H; Brown, Graham R; Peakall, Rod

    2011-04-01

    Sexually deceptive Chiloglottis orchids lure their male thynnine wasp pollinators to the flower by emitting semiochemicals that mimic the specific sex pheromone of the wasp. Sexual deception is possible because chemical rather than visual cues play the key role in wasp mate search, suggesting that cryptic wasp species may be frequent. We investigated this prospect among Neozeleboria wasp pollinators of Chiloglottis orchids, drawing on evidence from molecular phylogenetic analysis at three genes (CO1, rhodopsin and wingless), population genetic and statistical parsimony analysis at CO1, orchid associations and their semiochemicals, and geographic ranges. We found a compelling relationship between genetically defined wasp groups, orchid associations, semiochemicals and geographic range, despite a frequent lack of detectable morphological differences. Our findings reveal multiple cryptic species among orchid pollinators and indicate that chemical changes are important for wasp reproductive isolation and speciation. The diversity of Neozeleboria may have enabled, rather than constrained, pollinator-driven speciation in these orchids.

  2. Digital Signature Management.

    ERIC Educational Resources Information Center

    Hassler, Vesna; Biely, Helmut

    1999-01-01

    Describes the Digital Signature Project that was developed in Austria to establish an infrastructure for applying smart card-based digital signatures in banking and electronic-commerce applications. Discusses the need to conform to international standards, an international certification infrastructure, and security features for a public directory…

  3. Multiple elements controlling the expression of wheat high molecular weight glutenin paralogs.

    PubMed

    Makai, Szabolcs; Éva, Csaba; Tamás, László; Juhász, Angéla

    2015-11-01

    Analysis of gene expression data generated by high-throughput microarray transcript profiling experiments coupled with cis-regulatory elements enrichment study and cluster analysis can be used to define modular gene programs and regulatory networks. Unfortunately, the high molecular weight glutenin subunits of wheat (Triticum aestivum) are more similar than microarray data alone would allow to distinguish between the three homoeologous gene pairs. However, combining complementary DNA (cDNA) expression libraries with microarray data, a co-expressional network was built that highlighted the hidden differences between these highly similar genes. Duplex clusters of cis-regulatory elements were used to focus the co-expressional network of transcription factors to the putative regulatory network of Glu-1 genes. The focused network helped to identify several transcriptional gene programs in the endosperm. Many of these programs demonstrated a conserved temporal pattern across the studied genotypes; however, few others showed variance. Based on this network, transient gene expression assays were performed with mutated promoters to inspect the control of tissue specificity. Results indicated that the interactions of the ABRE│CBF cluster with distal promoter regions may have a dual role in regulation by both recruiting the transcription complex as well as suppressing it in non-endosperm tissue. A putative model of regulation is discussed.

  4. Relationships among pest flour beetles of the genus Tribolium (Tenebrionidae) inferred from multiple molecular markers

    PubMed Central

    Angelini, David R.; Jockusch, Elizabeth L.

    2008-01-01

    Model species often provide initial hypotheses and tools for studies of development, genetics, and molecular evolution in closely related species. Flour beetles of the genus Tribolium MacLeay (1825) are one group with potential for such comparative studies. Tribolium castaneum (Herbst 1797) is an increasingly useful developmental genetic system. The convenience with which congeneric and other species of tenebrionid flour beetles can be reared in the laboratory makes this group attractive for comparative studies on a small phylogenetic scale. Here we present the results of phylogenetic analyses of relationships among the major pest species of Tribolium based on two mitochondrial and three nuclear markers (cytochrome oxidase 1, 16S ribosomal DNA, wingless, 28S ribosomal DNA, histone H3). The utility of partitioning the dataset in a manner informed by biological structure and function is demonstrated by comparing various partitioning strategies. In parsimony and partitioned Bayesian analyses of the combined dataset, the castaneum and confusum species groups are supported as monophyletic and as each other’s closest relatives. However, a sister group relationship between this clade and Tribolium brevicornis (Leconte 1859) is not supported. Therefore, we suggest transferring brevicornis group species to the genus Aphanotus Leconte (1862). The inferred phylogeny provides an evolutionary framework for comparative studies using flour beetles. PMID:18024090

  5. Molecular analysis of BRAF V600E mutation in multiple nodules of pulmonary Langerhans cell histiocytosis.

    PubMed

    Dimmler, Arno; Geddert, Helene; Werner, Martin; Faller, Gerhard

    2017-02-20

    Pulmonary Langerhans cell histiocytosis (PLCH) is a rare, smoking-related histiocytic disorder with variable clinical symptoms. Like in other non-pulmonary Langerhans cell proliferations, PLCH has recently been shown to harbour BRAF V600E mutations in a significant subset of cases, thus challenging the concept of PLCH being a reactive disorder. Here, we analysed 38 formalin-fixed and paraffin-embedded PLCH nodules of nine patients for BRAF mutation using two different molecular methods. Using pyrosequencing and allele-specific quantitative PCR (AS-PCR), BRAF V600E mutations were found in 16/38 (42%) and 31/37 (84%) nodules, respectively. Analysing different nodules of the same patients with pyrosequencing 3/6 patients showed a concordant BRAF mutation status. When allele-specific quantitative PCR was used, condordant results were found in 5/6 patients. Our findings clearly indicate that (a) the sensitivity of the method used is crucial in analysing BRAF mutation status, (b) AS-PCR is more sensitive in detecting BRAF V600E mutations than pyrosequencing,

  6. Preclinical anatomical, molecular, and functional imaging of the lung with multiple modalities.

    PubMed

    Gammon, Seth T; Foje, Nathan; Brewer, Elizabeth M; Owers, Elizabeth; Downs, Charles A; Budde, Matthew D; Leevy, W Matthew; Helms, My N

    2014-05-15

    In vivo imaging is an important tool for preclinical studies of lung function and disease. The widespread availability of multimodal animal imaging systems and the rapid rate of diagnostic contrast agent development have empowered researchers to noninvasively study lung function and pulmonary disorders. Investigators can identify, track, and quantify biological processes over time. In this review, we highlight the fundamental principles of bioluminescence, fluorescence, planar X-ray, X-ray computed tomography, magnetic resonance imaging, and nuclear imaging modalities (such as positron emission tomography and single photon emission computed tomography) that have been successfully employed for the study of lung function and pulmonary disorders in a preclinical setting. The major principles, benefits, and applications of each imaging modality and technology are reviewed. Limitations and the future prospective of multimodal imaging in pulmonary physiology are also discussed. In vivo imaging bridges molecular biological studies, drug design and discovery, and the imaging field with modern medical practice, and, as such, will continue to be a mainstay in biomedical research.

  7. Development of a model community to evaluate efficient removal of genetic signatures from spacecraft surfaces: issues pertaining to sampling, sample processing, and molecular analyses

    NASA Astrophysics Data System (ADS)

    La Duc, Myron; Kwan, Kelly; Cooper, Moogega; Stam, Christina; Vaishampayan, Parag; Benardini, James Nick; Moissl-Eichinger, Christine; Andersen, Gary; Spry, James A.; Venkateswaran, Kasthuri

    Despite advances in the specificity and sensitivity of molecular biological technologies, the ef-ficient recovery of DNA from low-biomass samples remains extremely challenging. Optimal methods to extract these biomolecules should 1) achieve the greatest total yield; 2) reflect comprehensive microbial diversity of the sampled environment; and 3) assert reproducible re-sults. For an in-depth assessment of the wide spectrum of microorganisms present in the low-biomass spacecraft assembly clean room environment, technologies facilitating efficient col-lection, sample processing, and analysis are needed. To this end, a homogenous mixture of equal concentrations of 11 distinct microbial lineages having significant relevance to planetary protection (bacteria, archaea, and fungi; aerobes and anaerobes; cells and spores; rods and cocci) was prepared. Suitable aliquots of this "model" community were then characterized us-ing a parallel set of downstream molecular analyses which revealed the level of microbial DNA, extracellular DNA, dissolved organic matter, and particulate non-microbial substances present in the community. Appropriate subsamples of this model community were dried on stainless steel metal surfaces, and procedures targeting the efficient removal and recovery of community member DNAs were evaluated. The collection and release of genetic materials from cotton and flocked nylon swabs were compared. Several automated nucleic acid extraction methods were assessed for both total DNA yield and conservation of microbial community structure. Uni-versal small subunit rrn Q-PCR, species-specific Q-PCR, and DNA microarray methodologies were used in concert to estimate the recovery of both individual members, and the community as a whole. Results of this study will enable consideration of future planetary protection policy amendments based on modern molecular methods.

  8. Satellite signatures in SLR observations

    NASA Technical Reports Server (NTRS)

    Appleby, G. M.

    1993-01-01

    We examine the evidence for the detection of satellite-dependent signatures in the laser range observations obtained by the UK single-photon Satellite Laser Ranging (SLR) System models of the expected observation distributions from Ajisai and Lageos are developed from the published satellite spread functions and from the characteristics of the SLR System and compared with the observations. The effects of varying return strengths are discussed using the models and by experimental observations of Ajisai, during which a range of return levels from single to multiple photons is achieved. The implications of these results for system-dependent center for mass corrections are discussed.

  9. A MOLECULAR EXAMINATION OF RELATEDNESS, MULTIPLE PATERNITY, AND COHABITATION OF THE SOUTHERN PLAINS WOODRAT (NEOTOMA MICROPUS)

    PubMed Central

    Baxter, B. Dnate’; Mendez-Harclerode, Francisca M.; Fulhorst, Charles F.; Bradley, Robert D.

    2009-01-01

    Two hundred twenty-two individuals of the southern plains woodrat (Neotoma micropus) were captured from 198 excavated middens at 10 discrete collecting sites from a single population in south-central Texas. Field data, mitochondrial D-loop haplotypes, and polymorphic microsatellite loci (5–7) were used to determine genetic patterns in parentage, relatedness, and mating strategy. Microsatellite loci were highly polymorphic (average observed heterozygosity = 0.859) and were used to construct genotypes that were unique for each individual (probability of identical genotypes: 1 in 2,104,567). Results indicated a high frequency of multiple paternity (6 of 9 litters), evidence of repeat mating between the same 2 individuals, and no indication of male dominance at any collection site. Examination of these data suggested a promiscuous mating system. Within a site, average relatedness between adult females was similar to that between adult males. A higher level of cohabitation from that previously documented was recorded and finer-scale analyses revealed high levels of relatedness between most cohabiting individuals. Taken with results from other studies of mating behaviors of N. micropus, our results suggest that mating and social behavior of this species are likely influenced by population density. PMID:20011670

  10. Molecular Epidemiology and Characterization of Multiple-Drug Resistant (MDR) Clinical Isolates of Acinetobacter baumannii

    PubMed Central

    El-Shazly, Sherief; Dashti, Ali; Vali, Leila; Bolaris, Michael; Ibrahim, Ashraf S.

    2015-01-01

    Objectives We aimed to identify the genetic relatedness of multiple-drug resistance (MDR) in Acinetobacter baumannii clinical isolates recovered from a hospital in Los Angeles. Methods Twenty one MDR A. baumannii isolates were collected and their antibiotic susceptibility were determined according to the CLSI guidelines. Genes coding for antibiotic resistance were identified by PCR and their identities were confirmed by DNA sequencing. Clonal relationships were studied by pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST). Results MDR consistently correlated with the presence of oxacillinases, mostly in the form of plasmid-mediated OXA-23 enzyme which were detected in 12 (57.1%) isolates. GES-type carbapenemases were found in 20 (95.2%) strains, AAC in all 21 (100%) strains, PER in 7 (33.3%) strains and ISAba1 has been detected in 16 (76.2%) isolates. The association between ISAba1 and resistant genes confirms insertion elements as a source of β-lactamase production. Of the 21 clinical isolates, 5 were found to be related to sequence type-1 (ST1) and 16 to ST2 as analyzed by MLST. PFGE demonstrated that the majority of clinical isolates are highly related (>85%). Conclusions This study supports a more complete understanding of genotyping of antibiotic resistance for better assessment of MDR strains transmission. PMID:26518066

  11. Molecular Diversity Within Melanomys caliginosus (Rodentia: Oryzomyini): Evidence for Multiple Species

    PubMed Central

    Hanson, J. Delton; Bradley, Robert D.

    2010-01-01

    Nucleotide sequences from the mitochondrial DNA cytochrome-b gene were used to infer phylogenetic relationships and estimate genetic distances from 10 individuals of Melanomys caliginosus and to explore the hypothesis that this taxon is comprised of multiple species. Individuals of four geographic populations of M. caliginosus from Central America (Nicaragua and Costa Rica), Panama, Venezuela, and Ecuador, respectively, were included in this analysis. Topologies obtained from maximum parsimony and Bayesian inference analyses were identical and produced clades referable to each of the geographic populations. Genetic distances between any pair-wise comparisons of the four groups (except between Panamanian and Venezuelan samples) were comparable to values estimated from comparisons of sister species in the closely related genus Nectomys. Distances between samples from Panama and Venezuela were greater than those of samples within the Ecuadorian and Central American clades, but less than that between species of Nectomys. Based on results from the sequence data, it appears that all four of the populations should be elevated to species level; however, additional data are needed to resolve the nomenclature of the Panamanian and Venezuelan populations. PMID:21614136

  12. Addressing Different Active Neutron Interrogation Signatures from Fissionable Material

    SciTech Connect

    D. L. Chichester; E. H. Seabury

    2009-10-01

    In a continuing effort to examine portable methods for implementing active neutron interrogation for detecting shielded fissionable material research is underway to investigate the utility of analyzing multiple time-correlated signatures. Time correlation refers here to the existence of unique characteristics of the fission interrogation signature related to the start and end of an irradiation, as well as signatures present in between individual pulses of an irradiating source. Traditional measurement approaches in this area have typically worked to detect die-away neutrons after the end of each pulse, neutrons in between pulses related to the decay of neutron emitting fission products, or neutrons or gamma rays related to the decay of neutron emitting fission products after the end of an irradiation exposure. In this paper we discus the potential weaknesses of assessing only one signature versus multiple signatures and make the assertion that multiple complimentary and orthogonal measurements should be used to bolster the performance of active interrogation systems, helping to minimize susceptibility to the weaknesses of individual signatures on their own. Recognizing that the problem of detection is a problem of low count rates, we are exploring methods to integrate commonly used signatures with rarely used signatures to improve detection capabilities for these measurements. In this paper we will discuss initial activity in this area with this approach together with observations of some of the strengths and weaknesses of using these different signatures.

  13. Molecularly Engineered Organic-Inorganic Hybrid Perovskite with Multiple Quantum Well Structure for Multicolored Light-Emitting Diodes

    PubMed Central

    Hu, Hongwei; Salim, Teddy; Chen, Bingbing; Lam, Yeng Ming

    2016-01-01

    Organic-inorganic hybrid perovskites have the potential to be used as a new class of emitters with tunable emission, high color purity and good ease of fabrication. Recent studies have so far been focused on three-dimensional (3D) perovskites, such as CH3NH3PbBr3 and CH3NH3PbI3 for green and infrared emission. Here, we explore a new series of hybrid perovskite emitters with a general formula of (C4H9NH3)2(CH3NH3)n−1PbnI3n+1 (where n = 1, 2, 3), which possesses a multiple quantum well structure. The quantum well thickness of these materials is adjustable through simple molecular engineering which results in a continuously tunable bandgap and emission spectra. Deep saturated red emission was obtained with a peak external quantum efficiency of 2.29% and a maximum luminance of 214 cd/m2. Green and blue LEDs were also demonstrated through halogen substitutions in these hybrid perovskites. We expect these results to open up the way towards high performance perovskite LEDs through molecular-structure engineering of these perovskite emitters. PMID:27633084

  14. Investigation of the interaction between quercetin and human serum albumin by multiple spectra, electrochemical impedance spectra and molecular modeling.

    PubMed

    Dai, Jie; Zou, Ting; Wang, Li; Zhang, Yezhong; Liu, Yi

    2014-12-01

    Quercetin (Qu), a flavonoid compound, exists widely in the human diet and exhibits a variety of pharmacological activities. This work is aimed at studying the effect of Qu on the bioactive protein, human serum albumin (HSA) under simulated biophysical conditions. Multiple spectroscopic methods (including fluorescence and circular dichroism), electrochemical impedance spectra (EIS) and molecular modeling were employed to investigate the interaction between Qu and HSA. The fluorescence quenching and EIS experimental results showed that the fluorescence quenching of HSA was caused by formation of a Qu-HSA complex in the ground state, which belonged to the static quenching mechanism. Based on the calculated thermodynamic parameters, it concluded that the interaction was a spontaneous process and hydrogen bonds combined with van der Waal's forces played a major role in stabilizing the Qu-HSA complex. Molecular modeling results demonstrated that several amino acids participated in the binding process and the formed Qu-HSA complex was stabilized by H-bonding network at site I in sub-domain IIA, which was further confirmed by the site marker competitive experiments. The evidence from circular dichroism (CD) indicated that the secondary structure and microenvironment of HSA were changed. Alterations in the conformation of HSA were observed with a reduction in the amount of α helix from 59.9% (free HSA) to 56% (Qu-HSA complex), indicating a slight unfolding of the protein polypeptides.

  15. Molecular cytogenetic identification of a wheat-rye 1R addition line with multiple spikelets and resistance to powdery mildew.

    PubMed

    Yang, Wujuan; Wang, Changyou; Chen, Chunhuan; Wang, Yajuan; Zhang, Hong; Liu, Xinlun; Ji, Wanquan

    2016-04-01

    Alien addition lines are important for transferring useful genes from alien species into common wheat. Rye is an important and valuable gene resource for improving wheat disease resistance, yield, and environment adaptation. A new wheat-rye addition line, N9436B, was developed from the progeny of the cross of common wheat (Triticum aestivum L., 2n = 6x = 42, AABBDD) cultivar Shaanmai 611 and rye (Secale cereal L., 2n = 2x = 14, RR) accession Austrian rye. We characterized this new line by cytology, genomic in situ hybridization (GISH), fluorescence in situ hybridization (FISH), molecular markers, and disease resistance screening. N9436B was stable in morphology and cytology, with a chromosome composition of 2n = 42 + 2t = 22II. GISH investigations showed that this line contained two rye chromosomes. GISH, FISH, and molecular maker identification suggested that the introduced R chromosome and the missing wheat chromosome arms were 1R chromosome and 2DL chromosome arm, respectively. N9436B exhibited 30-37 spikelets per spike and a high level of resistance to powdery mildew (Blumeria graminis f. sp. tritici, Bgt) isolate E09 at the seedling stage. N9436B was cytologically stable, had the trait of multiple spikelets, and was resistant to powdery mildew; this line should thus be useful in wheat improvement.

  16. International Myeloma Working Group molecular classification of multiple myeloma: spotlight review.

    PubMed

    Fonseca, R; Bergsagel, P L; Drach, J; Shaughnessy, J; Gutierrez, N; Stewart, A K; Morgan, G; Van Ness, B; Chesi, M; Minvielle, S; Neri, A; Barlogie, B; Kuehl, W M; Liebisch, P; Davies, F; Chen-Kiang, S; Durie, B G M; Carrasco, R; Sezer, Orhan; Reiman, Tony; Pilarski, Linda; Avet-Loiseau, H

    2009-12-01

    Myeloma is a malignant proliferation of monoclonal plasma cells. Although morphologically similar, several subtypes of the disease have been identified at the genetic and molecular level. These genetic subtypes are associated with unique clinicopathological features and dissimilar outcome. At the top hierarchical level, myeloma can be divided into hyperdiploid and non-hyperdiploid subtypes. The latter is mainly composed of cases harboring IgH translocations, generally associated with more aggressive clinical features and shorter survival. The three main IgH translocations in myeloma are the t(11;14)(q13;q32), t(4;14)(p16;q32) and t(14;16)(q32;q23). Trisomies and a more indolent form of the disease characterize hyperdiploid myeloma. A number of genetic progression factors have been identified including deletions of chromosomes 13 and 17 and abnormalities of chromosome 1 (1p deletion and 1q amplification). Other key drivers of cell survival and proliferation have also been identified such as nuclear factor- B-activating mutations and other deregulation factors for the cyclin-dependent pathways regulators. Further understanding of the biological subtypes of the disease has come from the application of novel techniques such as gene expression profiling and array-based comparative genomic hybridization. The combination of data arising from these studies and that previously elucidated through other mechanisms allows for most myeloma cases to be classified under one of several genetic subtypes. This paper proposes a framework for the classification of myeloma subtypes and provides recommendations for genetic testing. This group proposes that genetic testing needs to be incorporated into daily clinical practice and also as an essential component of all ongoing and future clinical trials.

  17. International Myeloma Working Group molecular classification of multiple myeloma: spotlight review

    PubMed Central

    Fonseca, R; Bergsagel, PL; Drach, J; Shaughnessy, J.; Gutierrez, N; Stewart, AK; Morgan, G; Van Ness, B; Chesi, M; Minvielle, S; Neri, A; Barlogie, B; Kuehl, WM; Liebisch, P; Davies, F; Chen-Kiang, S; Durie, BGM; Carrasco, R; Sezer, Orhan; Reiman, Tony; Pilarski, Linda; Avet-Loiseau, H

    2010-01-01

    Myeloma is a malignant proliferation of monoclonal plasma cells. Although morphologically similar, several subtypes of the disease have been identified at the genetic and molecular level. These genetic subtypes are associated with unique clinico-pathological features and dissimilar outcome. At the top hierarchical level, myeloma can be divided into hyperdiploid and non-hyperdiploid subtypes. The latter is mainly composed of cases harboring IgH translocations, generally associated with more aggressive clinical features and shorter survival. The three main IgH translocations in myeloma are the t(11;14)(q13;q32), t(4;14)(p16;q32) and t(14;16)(q32;q23). Trisomies and a more indolent form of the disease characterize hyperdiploid myeloma. A number of genetic progression factors have been identified including deletions of chromosomes 13 and 17 and abnormalities of chromosome 1 (1p deletion and 1q amplification). Other key drivers of cell survival and proliferation have also been identified such as nuclear factor- B-activating mutations and other deregulation factors for the cyclin-dependent pathways regulators. Further understanding of the biological subtypes of the disease has come from the application of novel techniques such as gene expression profiling and array-based comparative genomic hybridization. The combination of data arising from these studies and that previously elucidated through other mechanisms allows for most myeloma cases to be classified under one of several genetic subtypes. This paper proposes a framework for the classification of myeloma subtypes and provides recommendations for genetic testing. This group proposes that genetic testing needs to be incorporated into daily clinical practice and also as an essential component of all ongoing and future clinical trials. PMID:19798094

  18. Molecular phylogenetics of moray eels (Muraenidae) demonstrates multiple origins of a shell-crushing jaw (Gymnomuraena, Echidna) and multiple colonizations of the Atlantic Ocean.

    PubMed

    Reece, Joshua S; Bowen, Brian W; Smith, David G; Larson, Allan

    2010-11-01

    Moray eels (Muraenidae) are apex predators on coral reefs around the world, but they are not well studied because their cryptic habitats and occasionally aggressive behaviors make them difficult to collect. We provide a molecular phylogeny of moray eels including 44 species representing two subfamilies, eight genera, and