Perfect Resonant Absorption of Guided Water Waves by Autler-Townes Splitting

The control of guided water wave propagation based on the Autler-Townes splitting resonance concept is demonstrated experimentally, numerically, and theoretically. Complete wave absorption is achieved using an asymmetric pointlike scatterer made of two closely spaced resonant side channels connected to a guide and designed so that its energy leakage is in perfect balance with the inherent viscous losses in the system. We demonstrate that the nature of the resonators and guide junction completely controls the positions of the wave numbers at the reflection and transmission zeros on the real axis; the asymmetry of the resonators completely controls their positions on the imaginary axis. Thus, by adjusting these two independent parameters, we obtain a zero reflection and transmission.

Edwardsiella tarda, a rare human pathogen isolated from a perihepatic abscess: Implications of transient versus long term colonization of the gastrointestinal tract

Although gastroenteritis is the most commonly described manifestation of Edwardsiella tarda infection, the pathogenesis and transient or long-term colonization of the gastrointestinal tract of this organism in human disease is not clear. We describe a rare manifestation of E. tarda infection in a perihepatic abscess in the setting of a patient with perforated cholecystitis and its successful eradication following antibiotic treatment.

A stable, unified model for resonant Faraday cages

We study some effective transmission conditions able to reproduce the effect of a periodic array of Dirichlet wires on wave propagation, in particular when the array delimits an acoustic Faraday cage able to resonate. In the study of Hewett & Hewitt (2016 Proc. R. Soc. A 472, 20160062 (doi:10.1098/rspa.2016.0062)) different transmission conditions emerge from the asymptotic analysis whose validity depends on the frequency, specifically the distance to a resonance frequency of the cage. In practice, dealing with such conditions is difficult, especially if the problem is set in the time domain. In the present study, we demonstrate the validity of a simpler unified model derived in Marigo & Maurel (2016 Proc. R. Soc. A 472, 20160068 (doi:10.1098/rspa.2016.0068)), where unified means valid whatever the distance to the resonance frequencies. The effectiveness of the model is discussed in the harmonic regime owing to explicit solutions. It is also exemplified in the time domain, where a formulation guaranteeing the stability of the numerical scheme has been implemented.

Enhanced resonance of sparse arrays of Helmholtz resonators-Application to perfect absorption

The influence of the spacing on the resonance of a periodic arrangement of Helmholtz resonators is inspected. An effective problem is used which accurately captures the properties of the resonant array within a large range of frequencies, and whose simplified version leaves an impedance condition. It is shown that the strength of the resonance is enhanced when the array becomes sparser. This degree of freedom on the radiative damping is of particular interest since it does not affect the resonance frequency nor the damping due to losses within each resonator; in addition, it does not affect the total thickness of the array. It is shown that it can be used for the design of a perfect absorbing wall.

Integrating the Epigenome to Identify Drivers of Hepatocellular Carcinoma

Disruption of epigenetic mechanisms has been intimately linked to the etiology of human cancer. Understanding how these epigenetic mechanisms (including DNA methylation [5mC], hydroxymethylation [5hmC], and histone post-translational modifications) work in concert to drive cancer initiation and progression remains unknown. Hepatocellular carcinoma (HCC) is increasing in frequency in Western countries but lacks efficacious treatments. The epigenome of HCC remains understudied. To better understand the epigenetic underpinnings of HCC, we performed a genome-wide assessment of 5mC, 5hmC, four histone modifications linked to promoter/enhancer function (H3K4me1, H3K27ac, H3K4me3, and H3K27me3), and transcription across normal, cirrhotic, and HCC liver tissue. Implementation of bioinformatic strategies integrated these epigenetic marks with each other and with transcription to provide a comprehensive epigenetic profile of how and when the liver epigenome is perturbed during progression to HCC. Our data demonstrate significant deregulation of epigenetic regulators combined with disruptions in the epigenome hallmarked by profound loss of 5hmC, locus-specific gains in 5mC and 5hmC, and markedly altered histone modification profiles, particularly remodeling of enhancers. Data integration demonstrates that these marks collaborate to influence transcription (e.g., hyper-5hmC in HCC-gained active enhancers is linked to elevated expression) of genes regulating HCC proliferation. Two such putative epigenetic driver loci identified through our integrative approach, COMT and FMO3, increase apoptosis and decrease cell viability in liver-derived cancer cell lines when ectopically re-expressed. Conclusion: Altogether, integration of multiple epigenetic parameters is a powerful tool for identifying epigenetically regulated drivers of HCC and elucidating how epigenome deregulation contributes to liver disease and HCC.

Converse Smith-Martin cell cycle kinetics by transformed B lymphocytes

Recent studies using direct live cell imaging have reported that individual B lymphocytes have correlated transit times between their G1 and S/G2/M phases. This finding is in contradiction with the influential model of Smith and Martin that assumed the bulk of the total cell cycle time variation arises in the G1 phase of the cell cycle with little contributed by the S/G2/M phase. Here we extend these studies to examine the relation between cell cycle phase lengths in two B lymphoma cell lines. We report that transformed B lymphoma cells undergo a short G1 period that displays little correlation with the time taken for the subsequent S/G2/M phase. Consequently, the bulk of the variation noted for total division times within a population is found in the S/G2/M phases and not the G1 phase. Models that reverse the expected source of variation and assume a single deterministic time in G1 followed by a lag + exponential distribution for S/G2/M fit the data well. These models can be improved further by adopting two sequential distributions or by using the stretched lognormal model developed for primary lymphocytes. We propose that shortening of G1 transit times and uncoupling from other cell cycle phases may be a hallmark of lymphocyte transformation that could serve as an observable phenotypic marker of cancer evolution.

Human genome meeting 2016 : Houston, TX, USA. 28 February - 2 March 2016

O1 The metabolomics approach to autism: identification of biomarkers for early detection of autism spectrum disorder A. K. Srivastava, Y. Wang, R. Huang, C. Skinner, T. Thompson, L. Pollard, T. Wood, F. Luo, R. Stevenson O2 Phenome-wide association study for smoking- and drinking-associated genes in 26,394 American women with African, Asian, European, and Hispanic descents R. Polimanti, J. Gelernter O3 Effects of prenatal environment, genotype and DNA methylation on birth weight and subsequent postnatal outcomes: findings from GUSTO, an Asian birth cohort X. Lin, I. Y. Lim, Y. Wu, A. L. Teh, L. Chen, I. M. Aris, S. E. Soh, M. T. Tint, J. L. MacIsaac, F. Yap, K. Kwek, S. M. Saw, M. S. Kobor, M. J. Meaney, K. M. Godfrey, Y. S. Chong, J. D. Holbrook, Y. S. Lee, P. D. Gluckman, N. Karnani, GUSTO study group O4 High-throughput identification of specific qt interval modulating enhancers at the SCN5A locus A. Kapoor, D. Lee, A. Chakravarti O5 Identification of extracellular matrix components inducing cancer cell migration in the supernatant of cultivated mesenchymal stem cells C. Maercker, F. Graf, M. Boutros O6 Single cell allele specific expression (ASE) IN T21 and common trisomies: a novel approach to understand DOWN syndrome and other aneuploidies G. Stamoulis, F. Santoni, P. Makrythanasis, A. Letourneau, M. Guipponi, N. Panousis, M. Garieri, P. Ribaux, E. Falconnet, C. Borel, S. E. Antonarakis O7 Role of microRNA in LCL to IPSC reprogramming S. Kumar, J. Curran, J. Blangero O8 Multiple enhancer variants disrupt gene regulatory network in Hirschsprung disease S. Chatterjee, A. Kapoor, J. Akiyama, D. Auer, C. Berrios, L. Pennacchio, A. Chakravarti O9 Metabolomic profiling for the diagnosis of neurometabolic disorders T. R. Donti, G. Cappuccio, M. Miller, P. Atwal, A. Kennedy, A. Cardon, C. Bacino, L. Emrick, J. Hertecant, F. Baumer, B. Porter, M. Bainbridge, P. Bonnen, B. Graham, R. Sutton, Q. Sun, S. Elsea O10 A novel causal methylation network approach to Alzheimer’s disease Z. Hu, P. Wang, Y. Zhu, J. Zhao, M. Xiong, David A Bennett O11 A microRNA signature identifies subtypes of triple-negative breast cancer and reveals MIR-342-3P as regulator of a lactate metabolic pathway A. Hidalgo-Miranda, S. Romero-Cordoba, S. Rodriguez-Cuevas, R. Rebollar-Vega, E. Tagliabue, M. Iorio, E. D’Ippolito, S. Baroni O12 Transcriptome analysis identifies genes, enhancer RNAs and repetitive elements that are recurrently deregulated across multiple cancer types B. Kaczkowski, Y. Tanaka, H. Kawaji, A. Sandelin, R. Andersson, M. Itoh, T. Lassmann, the FANTOM5 consortium, Y. Hayashizaki, P. Carninci, A. R. R. Forrest O13 Elevated mutation and widespread loss of constraint at regulatory and architectural binding sites across 11 tumour types C. A. Semple O14 Exome sequencing provides evidence of pathogenicity for genes implicated in colorectal cancer E. A. Rosenthal, B. Shirts, L. Amendola, C. Gallego, M. Horike-Pyne, A. Burt, P. Robertson, P. Beyers, C. Nefcy, D. Veenstra, F. Hisama, R. Bennett, M. Dorschner, D. Nickerson, J. Smith, K. Patterson, D. Crosslin, R. Nassir, N. Zubair, T. Harrison, U. Peters, G. Jarvik, NHLBI GO Exome Sequencing Project O15 The tandem duplicator phenotype as a distinct genomic configuration in cancer F. Menghi, K. Inaki, X. Woo, P. Kumar, K. Grzeda, A. Malhotra, H. Kim, D. Ucar, P. Shreckengast, K. Karuturi, J. Keck, J. Chuang, E. T. Liu O16 Modeling genetic interactions associated with molecular subtypes of breast cancer B. Ji, A. Tyler, G. Ananda, G. Carter O17 Recurrent somatic mutation in the MYC associated factor X in brain tumors H. Nikbakht, M. Montagne, M. Zeinieh, A. Harutyunyan, M. Mcconechy, N. Jabado, P. Lavigne, J. Majewski O18 Predictive biomarkers to metastatic pancreatic cancer treatment J. B. Goldstein, M. Overman, G. Varadhachary, R. Shroff, R. Wolff, M. Javle, A. Futreal, D. Fogelman O19 DDIT4 gene expression as a prognostic marker in several malignant tumors L. Bravo, W. Fajardo, H. Gomez, C. Castaneda, C. Rolfo, J. A. Pinto O20 Spatial organization of the genome and genomic alterations in human cancers K. C. Akdemir, L. Chin, A. Futreal, ICGC PCAWG Structural Alterations Group O21 Landscape of targeted therapies in solid tumors S. Patterson, C. Statz, S. Mockus O22 Genomic analysis reveals novel drivers and progression pathways in skin basal cell carcinoma S. N. Nikolaev, X. I. Bonilla, L. Parmentier, B. King, F. Bezrukov, G. Kaya, V. Zoete, V. Seplyarskiy, H. Sharpe, T. McKee, A. Letourneau, P. Ribaux, K. Popadin, N. Basset-Seguin, R. Ben Chaabene, F. Santoni, M. Andrianova, M. Guipponi, M. Garieri, C. Verdan, K. Grosdemange, O. Sumara, M. Eilers, I. Aifantis, O. Michielin, F. de Sauvage, S. Antonarakis O23 Identification of differential biomarkers of hepatocellular carcinoma and cholangiocarcinoma via transcriptome microarray meta-analysis S. Likhitrattanapisal O24 Clinical validity and actionability of multigene tests for hereditary cancers in a large multi-center study S. Lincoln, A. Kurian, A. Desmond, S. Yang, Y. Kobayashi, J. Ford, L. Ellisen O25 Correlation with tumor ploidy status is essential for correct determination of genome-wide copy number changes by SNP array T. L. Peters, K. R. Alvarez, E. F. Hollingsworth, D. H. Lopez-Terrada O26 Nanochannel based next-generation mapping for interrogation of clinically relevant structural variation A. Hastie, Z. Dzakula, A. W. Pang, E. T. Lam, T. Anantharaman, M. Saghbini, H. Cao, BioNano Genomics O27 Mutation spectrum in a pulmonary arterial hypertension (PAH) cohort and identification of associated truncating mutations in TBX4 C. Gonzaga-Jauregui, L. Ma, A. King, E. Berman Rosenzweig, U. Krishnan, J. G. Reid, J. D. Overton, F. Dewey, W. K. Chung O28 NORTH CAROLINA macular dystrophy (MCDR1): mutations found affecting PRDM13 K. Small, A. DeLuca, F. Cremers, R. A. Lewis, V. Puech, B. Bakall, R. Silva-Garcia, K. Rohrschneider, M. Leys, F. S. Shaya, E. Stone O29 PhenoDB and genematcher, solving unsolved whole exome sequencing data N. L. Sobreira, F. Schiettecatte, H. Ling, E. Pugh, D. Witmer, K. Hetrick, P. Zhang, K. Doheny, D. Valle, A. Hamosh O30 Baylor-Johns Hopkins Center for Mendelian genomics: a four year review S. N. Jhangiani, Z. Coban Akdemir, M. N. Bainbridge, W. Charng, W. Wiszniewski, T. Gambin, E. Karaca, Y. Bayram, M. K. Eldomery, J. Posey, H. Doddapaneni, J. Hu, V. R. Sutton, D. M. Muzny, E. A. Boerwinkle, D. Valle, J. R. Lupski, R. A. Gibbs O31 Using read overlap assembly to accurately identify structural genetic differences in an ashkenazi jewish trio S. Shekar, W. Salerno, A. English, A. Mangubat, J. Bruestle O32 Legal interoperability: a sine qua non for international data sharing A. Thorogood, B. M. Knoppers, Global Alliance for Genomics and Health - Regulatory and Ethics Working Group O33 High throughput screening platform of competent sineups: that can enhance translation activities of therapeutic target H. Takahashi, K. R. Nitta, A. Kozhuharova, A. M. Suzuki, H. Sharma, D. Cotella, C. Santoro, S. Zucchelli, S. Gustincich, P. Carninci O34 The undiagnosed diseases network international (UDNI): clinical and laboratory research to meet patient needs J. J. Mulvihill, G. Baynam, W. Gahl, S. C. Groft, K. Kosaki, P. Lasko, B. Melegh, D. Taruscio O36 Performance of computational algorithms in pathogenicity predictions for activating variants in oncogenes versus loss of function mutations in tumor suppressor genes R. Ghosh, S. Plon O37 Identification and electronic health record incorporation of clinically actionable pharmacogenomic variants using prospective targeted sequencing S. Scherer, X. Qin, R. Sanghvi, K. Walker, T. Chiang, D. Muzny, L. Wang, J. Black, E. Boerwinkle, R. Weinshilboum, R. Gibbs O38 Melanoma reprogramming state correlates with response to CTLA-4 blockade in metastatic melanoma T. Karpinets, T. Calderone, K. Wani, X. Yu, C. Creasy, C. Haymaker, M. Forget, V. Nanda, J. Roszik, J. Wargo, L. Haydu, X. Song, A. Lazar, J. Gershenwald, M. Davies, C. Bernatchez, J. Zhang, A. Futreal, S. Woodman O39 Data-driven refinement of complex disease classification from integration of heterogeneous functional genomics data in GeneWeaver E. J. Chesler, T. Reynolds, J. A. Bubier, C. Phillips, M. A. Langston, E. J. Baker O40 A general statistic framework for genome-based disease risk prediction M. Xiong, L. Ma, N. Lin, C. Amos O41 Integrative large-scale causal network analysis of imaging and genomic data and its application in schizophrenia studies N. Lin, P. Wang, Y. Zhu, J. Zhao, V. Calhoun, M. Xiong O42 Big data and NGS data analysis: the cloud to the rescue O. Dobretsberger, M. Egger, F. Leimgruber O43 Cpipe: a convergent clinical exome pipeline specialised for targeted sequencing S. Sadedin, A. Oshlack, Melbourne Genomics Health Alliance O44 A Bayesian classification of biomedical images using feature extraction from deep neural networks implemented on lung cancer data V. A. A. Antonio, N. Ono, Clark Kendrick C. Go O45 MAV-SEQ: an interactive platform for the Management, Analysis, and Visualization of sequence data Z. Ahmed, M. Bolisetty, S. Zeeshan, E. Anguiano, D. Ucar O47 Allele specific enhancer in EPAS1 intronic regions may contribute to high altitude adaptation of Tibetans C. Zeng, J. Shao O48 Nanochannel based next-generation mapping for structural variation detection and comparison in trios and populations H. Cao, A. Hastie, A. W. Pang, E. T. Lam, T. Liang, K. Pham, M. Saghbini, Z. Dzakula O49 Archaic introgression in indigenous populations of Malaysia revealed by whole genome sequencing Y. Chee-Wei, L. Dongsheng, W. Lai-Ping, D. Lian, R. O. Twee Hee, Y. Yunus, F. Aghakhanian, S. S. Mokhtar, C. V. Lok-Yung, J. Bhak, M. Phipps, X. Shuhua, T. Yik-Ying, V. Kumar, H. Boon-Peng O50 Breast and ovarian cancer prevention: is it time for population-based mutation screening of high risk genes? I. Campbell, M.-A. Young, P. James, Lifepool O53 Comprehensive coverage from low DNA input using novel NGS library preparation methods for WGS and WGBS C. Schumacher, S. Sandhu, T. Harkins, V. Makarov O54 Methods for large scale construction of robust PCR-free libraries for sequencing on Illumina HiSeqX platform H. DoddapaneniR. Glenn, Z. Momin, B. Dilrukshi, H. Chao, Q. Meng, B. Gudenkauf, R. Kshitij, J. Jayaseelan, C. Nessner, S. Lee, K. Blankenberg, L. Lewis, J. Hu, Y. Han, H. Dinh, S. Jireh, K. Walker, E. Boerwinkle, D. Muzny, R. Gibbs O55 Rapid capture methods for clinical sequencing J. Hu, K. Walker, C. Buhay, X. Liu, Q. Wang, R. Sanghvi, H. Doddapaneni, Y. Ding, N. Veeraraghavan, Y. Yang, E. Boerwinkle, A. L. Beaudet, C. M. Eng, D. M. Muzny, R. A. Gibbs O56 A diploid personal human genome model for better genomes from diverse sequence data K. C. C. Worley, Y. Liu, D. S. T. Hughes, S. C. Murali, R. A. Harris, A. C. English, X. Qin, O. A. Hampton, P. Larsen, C. Beck, Y. Han, M. Wang, H. Doddapaneni, C. L. Kovar, W. J. Salerno, A. Yoder, S. Richards, J. Rogers, J. R. Lupski, D. M. Muzny, R. A. Gibbs O57 Development of PacBio long range capture for detection of pathogenic structural variants Q. Meng, M. Bainbridge, M. Wang, H. Doddapaneni, Y. Han, D. Muzny, R. Gibbs O58 Rhesus macaques exhibit more non-synonymous variation but greater impact of purifying selection than humans R. A. Harris, M. Raveenedran, C. Xue, M. Dahdouli, L. Cox, G. Fan, B. Ferguson, J. Hovarth, Z. Johnson, S. Kanthaswamy, M. Kubisch, M. Platt, D. Smith, E. Vallender, R. Wiseman, X. Liu, J. Below, D. Muzny, R. Gibbs, F. Yu, J. Rogers O59 Assessing RNA structure disruption induced by single-nucleotide variation J. Lin, Y. Zhang, Z. Ouyang P1 A meta-analysis of genome-wide association studies of mitochondrial dna copy number A. Moore, Z. Wang, J. Hofmann, M. Purdue, R. Stolzenberg-Solomon, S. Weinstein, D. Albanes, C.-S. Liu, W.-L. Cheng, T.-T. Lin, Q. Lan, N. Rothman, S. Berndt P2 Missense polymorphic genetic combinations underlying down syndrome susceptibility E. S. Chen P4 The evaluation of alteration of ELAM-1 expression in the endometriosis patients H. Bahrami, A. Khoshzaban, S. Heidari Keshal P5 Obesity and the incidence of apolipoprotein E polymorphisms in an assorted population from Saudi Arabia population K. K. R. Alharbi P6 Genome-associated personalized antithrombotical therapy for patients with high risk of thrombosis and bleeding M. Zhalbinova, A. Akilzhanova, S. Rakhimova, M. Bekbosynova, S. Myrzakhmetova P7 Frequency of Xmn1 polymorphism among sickle cell carrier cases in UAE population M. Matar P8 Differentiating inflammatory bowel diseases by using genomic data: dimension of the problem and network organization N. Mili, R. Molinari, Y. Ma, S. Guerrier P9 Vulnerability of genetic variants to the risk of autism among Saudi children N. Elhawary, M. Tayeb, N. Bogari, N. Qotb P10 Chromatin profiles from ex vivo purified dopaminergic neurons establish a promising model to support studies of neurological function and dysfunction S. A. McClymont, P. W. Hook, L. A. Goff, A. McCallion P11 Utilization of a sensitized chemical mutagenesis screen to identify genetic modifiers of retinal dysplasia in homozygous Nr2e3^rd7 mice Y. Kong, J. R. Charette, W. L. Hicks, J. K. Naggert, L. Zhao, P. M. Nishina P12 Ion torrent next generation sequencing of recessive polycystic kidney disease in Saudi patients B. M. Edrees, M. Athar, F. A. Al-Allaf, M. M. Taher, W. Khan, A. Bouazzaoui, N. A. Harbi, R. Safar, H. Al-Edressi, A. Anazi, N. Altayeb, M. A. Ahmed, K. Alansary, Z. Abduljaleel P13 Digital expression profiling of Purkinje neurons and dendrites in different subcellular compartments A. Kratz, P. Beguin, S. Poulain, M. Kaneko, C. Takahiko, A. Matsunaga, S. Kato, A. M. Suzuki, N. Bertin, T. Lassmann, R. Vigot, P. Carninci, C. Plessy, T. Launey P14 The evolution of imperfection and imperfection of evolution: the functional and functionless fractions of the human genome D. Graur P16 Species-independent identification of known and novel recurrent genomic entities in multiple cancer patients J. Friis-Nielsen, J. M. Izarzugaza, S. Brunak P18 Discovery of active gene modules which are densely conserved across multiple cancer types reveal their prognostic power and mutually exclusive mutation patterns B. S. Soibam P19 Whole exome sequencing of dysplastic leukoplakia tissue indicates sequential accumulation of somatic mutations from oral precancer to cancer D. Das, N. Biswas, S. Das, S. Sarkar, A. Maitra, C. Panda, P. Majumder P21 Epigenetic mechanisms of carcinogensis by hereditary breast cancer genes J. J. Gruber, N. Jaeger, M. Snyder P22 RNA direct: a novel RNA enrichment strategy applied to transcripts associated with solid tumors K. Patel, S. Bowman, T. Davis, D. Kraushaar, A. Emerman, S. Russello, N. Henig, C. Hendrickson P23 RNA sequencing identifies gene mutations for neuroblastoma K. Zhang P24 Participation of SFRP1 in the modulation of TMPRSS2-ERG fusion gene in prostate cancer cell lines M. Rodriguez-Dorantes, C. D. Cruz-Hernandez, C. D. P. Garcia-Tobilla, S. Solorzano-Rosales P25 Targeted Methylation Sequencing of Prostate Cancer N. Jäger, J. Chen, R. Haile, M. Hitchins, J. D. Brooks, M. Snyder P26 Mutant TPMT alleles in children with acute lymphoblastic leukemia from México City and Yucatán, Mexico S. Jiménez-Morales, M. Ramírez, J. Nuñez, V. Bekker, Y. Leal, E. Jiménez, A. Medina, A. Hidalgo, J. Mejía P28 Genetic modifiers of Alström syndrome J. Naggert, G. B. Collin, K. DeMauro, R. Hanusek, P. M. Nishina P31 Association of genomic variants with the occurrence of angiotensin-converting-enzyme inhibitor (ACEI)-induced coughing among Filipinos E. M. Cutiongco De La Paz, R. Sy, J. Nevado, P. Reganit, L. Santos, J. D. Magno, F. E. Punzalan , D. Ona , E. Llanes, R. L. Santos-Cortes , R. Tiongco, J. Aherrera, L. Abrahan, P. Pagauitan-Alan; Philippine Cardiogenomics Study Group P32 The use of “humanized” mouse models to validate disease association of a de novo GARS variant and to test a novel gene therapy strategy for Charcot-Marie-Tooth disease type 2D K. H. Morelli, J. S. Domire, N. Pyne, S. Harper, R. Burgess P34 Molecular regulation of chondrogenic human induced pluripotent stem cells M. A. Gari, A. Dallol, H. Alsehli, A. Gari, M. Gari, A. Abuzenadah P35 Molecular profiling of hematologic malignancies: implementation of a variant assessment algorithm for next generation sequencing data analysis and clinical reporting M. Thomas, M. Sukhai, S. Garg, M. Misyura, T. Zhang, A. Schuh, T. Stockley, S. Kamel-Reid P36 Accessing genomic evidence for clinical variants at NCBI S. Sherry, C. Xiao, D. Slotta, K. Rodarmer, M. Feolo, M. Kimelman, G. Godynskiy, C. O’Sullivan, E. Yaschenko P37 NGS-SWIFT: a cloud-based variant analysis framework using control-accessed sequencing data from DBGAP/SRA C. Xiao, E. Yaschenko, S. Sherry P38 Computational assessment of drug induced hepatotoxicity through gene expression profiling C. Rangel-Escareño, H. Rueda-Zarate P40 Flowr: robust and efficient pipelines using a simple language-agnostic approach;ultraseq; fast modular pipeline for somatic variation calling using flowr S. Seth, S. Amin, X. Song, X. Mao, H. Sun, R. G. Verhaak, A. Futreal, J. Zhang P41 Applying “Big data” technologies to the rapid analysis of heterogenous large cohort data S. J. Whiite, T. Chiang, A. English, J. Farek, Z. Kahn, W. Salerno, N. Veeraraghavan, E. Boerwinkle, R. Gibbs P42 FANTOM5 web resource for the large-scale genome-wide transcription start site activity profiles of wide-range of mammalian cells T. Kasukawa, M. Lizio, J. Harshbarger, S. Hisashi, J. Severin, A. Imad, S. Sahin, T. C. Freeman, K. Baillie, A. Sandelin, P. Carninci, A. R. R. Forrest, H. Kawaji, The FANTOM Consortium P43 Rapid and scalable typing of structural variants for disease cohorts W. Salerno, A. English, S. N. Shekar, A. Mangubat, J. Bruestle, E. Boerwinkle, R. A. Gibbs P44 Polymorphism of glutathione S-transferases and sulphotransferases genes in an Arab population A. H. Salem, M. Ali, A. Ibrahim, M. Ibrahim P46 Genetic divergence of CYP3A5*3 pharmacogenomic marker for native and admixed Mexican populations J. C. Fernandez-Lopez, V. Bonifaz-Peña, C. Rangel-Escareño, A. Hidalgo-Miranda, A. V. Contreras P47 Whole exome sequence meta-analysis of 13 white blood cell, red blood cell, and platelet traits L. Polfus, CHARGE and NHLBI Exome Sequence Project Working Groups P48 Association of adipoq gene with type 2 diabetes and related phenotypes in african american men and women: The jackson heart study S. Davis, R. Xu, S. Gebeab, P Riestra, A Gaye, R. Khan, J. Wilson, A. Bidulescu P49 Common variants in casr gene are associated with serum calcium levels in koreans S. H. Jung, N. Vinayagamoorthy, S. H. Yim, Y. J. Chung P50 Inference of multiple-wave population admixture by modeling decay of linkage disequilibrium with multiple exponential functions Y. Zhou, S. Xu P51 A Bayesian framework for generalized linear mixed models in genome-wide association studies X. Wang, V. Philip, G. Carter P52 Targeted sequencing approach for the identification of the genetic causes of hereditary hearing impairment A. A. Abuzenadah, M. Gari, R. Turki, A. Dallol P53 Identification of enhancer sequences by ATAC-seq open chromatin profiling A. Uyar, A. Kaygun, S. Zaman, E. Marquez, J. George, D. Ucar P54 Direct enrichment for the rapid preparation of targeted NGS libraries C. L. Hendrickson, A. Emerman, D. Kraushaar, S. Bowman, N. Henig, T. Davis, S. Russello, K. Patel P56 Performance of the Agilent D5000 and High Sensitivity D5000 ScreenTape assays for the Agilent 4200 Tapestation System R. Nitsche, L. Prieto-Lafuente P57 ClinVar: a multi-source archive for variant interpretation M. Landrum, J. Lee, W. Rubinstein, D. Maglott P59 Association of functional variants and protein physical interactions of human MUTY homolog linked with familial adenomatous polyposis and colorectal cancer syndrome Z. Abduljaleel, W. Khan, F. A. Al-Allaf, M. Athar , M. M. Taher, N. Shahzad P60 Modification of the microbiom constitution in the gut using chicken IgY antibodies resulted in a reduction of acute graft-versus-host disease after experimental bone marrow transplantation A. Bouazzaoui, E. Huber, A. Dan, F. A. Al-Allaf, W. Herr, G. Sprotte, J. Köstler, A. Hiergeist, A. Gessner, R. Andreesen, E. Holler P61 Compound heterozygous mutation in the LDLR gene in Saudi patients suffering severe hypercholesterolemia F. Al-Allaf, A. Alashwal, Z. Abduljaleel, M. Taher, A. Bouazzaoui, H. Abalkhail, A. Al-Allaf, R. Bamardadh, M. Athar

Comprehensive development and testing of the ASIST-GBV, a screening tool for responding to gender-based violence among women in humanitarian settings

Background

Conflict affected refugees and internally displaced persons (IDPs) are at increased vulnerability to gender-based violence (GBV). Health, psychosocial, and protection services have been implemented in humanitarian settings, but GBV remains under-reported and available services under-utilized. To improve access to existing GBV services and facilitate reporting, the ASIST-GBV screening tool was developed and tested for use in humanitarian settings. This process was completed in four phases: 1) systematic literature review, 2) qualitative research that included individual interviews and focus groups with GBV survivors and service providers, respectively, 3) pilot testing of the developed screening tool, and 4) 3-month implementation testing of the screening tool. Research was conducted among female refugees, aged ≥15 years in Ethiopia, and female IDPs, aged ≥18 years in Colombia.

Results

The systematic review and meta-analysis identified a range of GBV experiences and estimated a 21.4 % prevalence of sexual violence (95 % CI:14.9-28.7) among conflict-affected populations. No existing screening tools for GBV in humanitarian settings were identified. Qualitative research with GBV survivors in Ethiopia and Colombia found multiple forms of GBV experienced by refugees and IDPs that occurred during conflict, in transit, and in displaced settings. Identified forms of violence were combined into seven key items on the screening tool: threats of violence, physical violence, forced sex, sexual exploitation, forced pregnancy, forced abortion, and early or forced marriage. Cognitive testing further refined the tool. Pilot testing in both sites demonstrated preliminary feasibility where 64.8 % of participants in Ethiopia and 44.9 % of participants in Colombia were identified with recent (last 12 months) cases of GBV. Implementation testing of the screening tool, conducted as a routine service in camp/district hospitals, allowed for identification of GBV cases and referrals to services. In this phase, 50.6 % of participants in Ethiopia and 63.4 % in Colombia screened positive for recent experiences of GBV. Psychometric testing demonstrated appropriate internal consistency of the tool (Cronbach’s α = 0.77) and item response theory demonstrated appropriate discrimination and difficulty of the tool.

Conclusion

The ASIST-GBV screening tool has demonstrated utility and validity for use in confidential identification and referral of refugees and IDPs who experience GBV.

Abstract P1-16-03: Quantitative versus semi-quantitative assessments of radiation-induced pulmonary fibrosis post adjuvant breast radiotherapy

Objective

To evaluate the quantitative versus semi-quantitative assessments of radiation induced pulmonary fibrosis (RIPF) post adjuvant breast radiotherapy (RT).

Methods

High resolution computed tomography (HRCT) assessed lung physical density changes (CTD) and physician identified HRCT visual grading scores (CTS) were analysed at the minimum of 12 months post RT at one institution. The treated side in-portal lung regions for CTD and CTS assessments were: central-axis (CA) + regions 5cm superior & inferior to CA and the corresponding mid anterolateral region respectively. Respiratory motion was accounted for by subtracting the untreated side lung density from the treated side. Mean lung densities correspond to each voxels were automatically calculated by Pinnacle software (Phillips, Eindhoven, The-Netherlands). Grading of CTS was according to the RTOG/EORTC (grade 0, 1, 2, and 3 defined as none, slight, patchy, and dense HRCT appearance respectively) and analysed by a radiologist (JL) and re-checked a radiation oncologist (PG).

Results

Total numbers of 403 patients were analysed. A substantial association was verified between CTD and CTS assessment. An increase of ∼0.01 g/ml (95% CI 0.003-0.02) in CTD with each CTS score increase of 1 was observed (Table-1a). The RIPF can be categorised quantitatively into three groups of CTS 0 vs. 1-2 vs. 3 based on the mean CTD (Table-1b).

Table-1a. Correlation between CTD and CTS method. Table-1b. Grouping of CTS based on CTD methodTable-1a. Correlation between CTD and CTS methodCTSTreated side mean CTD - LeftTreated side mean CTD - RightMean Total00.055 (119)-0.011 (136)0.020 (255)10.065 (60)0.005 (56)0.036 (116)20.083 (15)0.012 (13)0.050 (28)30.108 (4)00.108 (4)Total0.061 (198)-0.005 (205)0.028 (403)Table-1b. Grouping of CTS based on CTD methodCTSTreated side mean CTD - LeftTreated side mean CTD - RightMean Total95% Confidence interval00.055 (119)-0.011 (136)0.020 (255)0.012-0.0271-20.069 (75)0.006 (69)0.039 (144)0.029-0.04830.108 (4)00.108 (4)0.079-0.137

A cut off CTD of 0.089 g/ml exemplified the best compromise between sensitivity (100%) and specificity (88.2%) for dense HRCT appearance. However, there was no good compromise of CTD cut off for slight and patchy HRCT score possibly due to intra observer variation and the scale of the CTD measure (small increase in CTD may not be detected visually by the observer). Multivariable analysis revealed increasing age, current smoker, V20 ≥ 10% (the volume of lung that was covered by the 20Gy isodose line), central lung distance ≥ 2cm (the distance between posterior RT tangents and the chest wall), combined endocrine & chemotherapy, and treated side mean CTD to be significantly associated with development of grade ≥1 RIPF.

Conclusions

There was a good correlation between quantitative (CTD) and semi-quantitative (CTS) assessment of RIPF post adjuvant breast RT. The CTD method could be advantageous for both routine clinical practice and future clinical trials that require more detailed quantification of dense RIPF.

Citation Format: Pramana A, Browne L, Cox H, Saba A, Pham K, Trakis S, Crawford K, Hall M, Batchelor N, Lim J, Graham P. Quantitative versus semi-quantitative assessments of radiation-induced pulmonary fibrosis post adjuvant breast radiotherapy. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P1-16-03.

A rare cause of hemosuccus pancreaticus diagnosed with endoscopic ultrasound

Introduction:

Hemosuccus pancreaticus (HP), hemorrhage from the papilla of Vater through the pancreatic duct (PD), is a rare cause of upper gastrointestinal bleeding. It may be caused by chronic pancreatitis, pseudoaneurism and pancreatic tumors. Only 2% of HP involves the hepatic arteries. Endoscopic ultrasound (EUS) may not only visualize the presence of HP, previously seen on computed tomography/magnetic resonance imaging (CT/MRI), but also reveal additional pathology.

Case Report:

A 62-year-old man was admitted with severe intermittent gastrointestinal bleeding. He underwent gastroscopy, colonoscopy and capsule endoscopy without sign of bleeding. The patient had no previous history of pancreatitis or infection. On CT and MRI scan with angiography, an aneurism of the common hepatic artery (CHA) was found, with a dilatation of the main PD toward the tail of the pancreas, but no apparent source of bleeding. EUS was then performed, and could show a partial thrombosed aneurysm of a hepatica with a diameter of 5 cm. In addition, a narrow fistula between the hepatic artery and PD could be identified using power Doppler. The patient was subsequently operated, which revealed a thrombosed arteriosclerotic aneurysm in the CHA with fistula to the PD.

Conclusion:

To the best of our knowledge, this is the second reported case of a severe gastrointestinal bleeding due to a fistula between the CHA and PD. The use of EUS in diagnosing this rare condition has not been reported before, but seems feasible.

Glucocorticoids and histone deacetylase inhibitors cooperate to block the invasiveness of basal-like breast cancer cells through novel mechanisms

Aggressive cancers often express E-cadherin in cytoplasmic vesicles rather than on the plasma membrane and this may contribute to the invasive phenotype of these tumors. Therapeutic strategies are not currently available that restore the anti-invasive function of E-cadherin in cancers. MDA-MB-231 cells are a frequently used model of invasive triple-negative breast cancer, and these cells express low levels of E-cadherin that is mislocalized to cytoplasmic vesicles. MDA-MB-231 cell lines stably expressing wild-type E-cadherin or E-cadherin fused to glutathione S-transferase or green fluorescent protein were used as experimental systems to probe the mechanisms responsible for cytoplasmic E-cadherin localization in invasive cancers. Although E-cadherin expression partly reduced cell invasion in vitro, E-cadherin was largely localized to the cytoplasm and did not block the invasiveness of the corresponding orthotopic xenograft tumors. Further studies indicated that the glucocorticoid dexamethasone and the highly potent class I histone deacetylase (HDAC) inhibitor largazole cooperated to induce E-cadherin localization to the plasma membrane in triple-negative breast cancers, and to suppress cellular invasion in vitro. Dexamethasone blocked the production of the cleaved form of the CDCP1 (that is, CUB domain-containing protein 1) protein (cCDCP1) previously implicated in the pro-invasive activities of CDCP1 by upregulating the serine protease inhibitor plasminogen activator inhibitor-1. E-cadherin preferentially associated with cCDCP1 compared with the full-length form. In contrast, largazole did not influence CDCP1 cleavage, but increased the association of E-cadherin with γ-catenin. This effect on E-cadherin/γ-catenin complexes was shared with the nonisoform selective HDAC inhibitors trichostatin A (TSA) and vorinostat (suberoylanilide hydroxamic acid, SAHA), although largazole upregulated endogenous E-cadherin levels more strongly than TSA. These results demonstrate that glucocorticoids and HDAC inhibitors, both of which are currently in clinical use, cooperate to suppress the invasiveness of breast cancer cells through novel, complementary mechanisms that converge on E-cadherin.

Construction and analysis of localized responses for gradient damage models in a 1D setting

We propose a method of construction of non homogeneous solutions to the problem of traction of a bar made of an elastic-damaging material whose softening behavior is regularized by a gradient damage model. We show that, for sufficiently long bars, localization arises on sets whose length is proportional to the material internal length and with a profile which is also characteristic of the material. We point out the very sensitivity of the responses to the parameters of the damage law. All these theoretical considerations are illustrated by numerical examples.

Genetic variation in heat shock protein 70 is associated with septic shock: narrowing the association to a specific haplotype

Heat shock protein 70 (HSP70) plays a major role in immune responses. Polymorphisms within the gene have been associated with development of septic shock. This study refines the region of the HSP70 gene associated with development of septic shock and confirms its functionality. Subjects (n = 31) were grouped into one of three haplotypes based on their HSPA1B-179C>T and HSPA1B1267A>G genotypes. Mononuclear cells from these subjects were stimulated with heat-killed bacteria (10(7 )colony-forming units/mL Escherichia coli or Streptococcus pneumoniae) for 8 and 21 h. HSP70 and tumour necrosis factor (TNF) mRNA and protein levels were measured by reverse transcriptase-polymerase chain reaction and ELISA, respectively. The HSPA1B-179*C:1267*A haplotype was associated with significantly lower levels of HSPA1B mRNA and protein and higher production of TNF mRNA and protein compared to the other haplotypes. Induction of HSP70 was TNF independent. These results suggest that the HSPA1B-179C>T:1267A>G haplotype is functional and may explain the association of the HSP70 gene with development of septic shock.

Chromatin remodeling and circadian control: master regulator CLOCK is an enzyme

The molecular machinery that governs circadian rhythmicity is based on clock gene products organized in regulatory feedback loops. Recently, we have shown that CLOCK, a master circadian regulator, has histone acetyltransferase activity essential for clock gene expression. The Lys-14 residue of histone H3 is a preferential target of CLOCK-mediated acetylation. As the role of chromatin remodeling in eukaryotic transcription is well recognized, this finding identified unforeseen links between histone acetylation and cellular physiology. Indeed, we have shown that the enzymatic function of CLOCK drives circadian control. We reasoned that CLOCK's acetyltransferase activity could also target nonhistone proteins, a feature displayed by other HATs. Indeed, CLOCK also acetylates a nonhistone substrate: its own partner, BMAL1. This protein undergoes rhythmic acetylation in the mouse liver, with a timing that parallels the down-regulation of circadian transcription of clock-controlled genes. BMAL1 is specifically acetylated on a unique, highly conserved Lys-537 residue. This acetylation facilitates recruitment of the repressor CRY1 to BMAL1, indicating that CLOCK may intervene in negative circadian regulation. Our findings reveal that the enzymatic interplay between two clock core components is crucial for the circadian machinery.

Limited-dose Daclizumab versus Basiliximab: a comparison of cost and efficacy in preventing acute rejection

The purpose of this study was to compare the efficacy and cost of the limited-dose Daclizumab regimen to that of the standard-dose Basiliximab regimen. Two antibody induction regimens were compared in patients aged 18 years and older who received renal transplants from January 2002 to September 2003 and completed interleukin (IL)-2R antibody induction with standard-dose Basiliximab (20 mg x 2 doses) or limited-dose Daclizumab (1 mg/kg x 2 doses). The primary outcome measure was the incidence of acute rejection. Secondary outcomes included cost, changes in serum creatinine level, and delayed graft function. Of the 46 patients randomized, 42 patients completed the 6-month follow-up. Mean serum creatinine level at time of discharge was originally higher in the limited-dose Daclizumab group than the standard-dose Basiliximab group (1.89 vs 1.57, respectively). By 1, 3, and 6 months, mean serum creatinine values were similar between both groups, with a trend toward lower mean serum creatinine values in the limited-dose Daclizumab group. The incidence of acute rejection was also similar between the groups (6% vs 7%). The average cost difference between the 2 regimens was approximately $715. This study suggests that a limited-dose Daclizumab regimen may be an efficacious and less costly alternative to the standard-dose Basiliximab regimen for antibody induction therapy following renal transplantation.

Human growth hormone-releasing factor (hGRF)1-29-albumin bioconjugates activate the GRF receptor on the anterior pituitary in rats: identification of CJC-1295 as a long-lasting GRF analog

In vivo bioconjugation to the free thiol on Cys34 of serum albumin by a strategically placed reactive group on a bioactive peptide is a useful tool to extend plasma half-life. Three maleimido derivates of human GH-releasing factor (hGRF)(1-29) were synthesized and bioconjugated to human serum albumin ex vivo. All three human serum albumin conjugates showed enhanced in vitro stability against dipeptidylpeptidase-IV and were bioactive in a GH secretion assay in cultured rat anterior pituitary cells. When the maleimido derivatives were individually administered sc to normal male Sprague Dawley rats, an acute secretion of GH was measured in plasma. The best compound, CJC-1295, showed a 4-fold increase in GH area under the curve over a 2-h period compared with hGRF(1-29). CJC-1295, a tetrasubstituted form of hGRF(1-29) with an added N epsilon-3-maleimidopropionamide derivative of lysine at the C terminus, was selected for further pharmacokinetic evaluation, where it was found to be present in plasma beyond 72 h. A Western blot analysis of the plasma of a rat injected with CJC-1295 showed the presence of a CJC-1295 immunoreactive species on the band corresponding to serum albumin, appearing after 15 min and remaining in circulation beyond 24 h. These results led to the identification of CJC-1295 as a stable and active hGRF(1-29) analog with an extended plasma half-life.

Factors influencing the diagnosis and treatment of periodontal disease by dental practitioners in Victoria

BACKGROUND

Healthy periodontal tissues are essential to overall dental health. Therefore, the detection and management of periodontal disease is an integral part of general dental practice. The aim of this study was to investigate confidence in diagnosis and management of periodontal disease by general dental practitioners (GDPs), assess if the Dental Practice Board guidelines on periodontal record keeping are being addressed, and, if necessary, try to find ways of improving the periodontal knowledge of GDPs.

METHODS

A survey assessing practitioner confidence in diagnosing and treating periodontal disease was sent to a random selection of 550 dental care providers registered with the Dental Practice Board of Victoria.

RESULTS

Two hundred and eighty five (51.8 per cent) of questionnaires were returned completed. It was found that 79.7 per cent of the sampled population screened all new patients for periodontal disease. The majority of respondents felt confident to diagnose and treat gingivitis and initial periodontitis. However, only 61.9 per cent felt confident to diagnose aggressive/early onset periodontitis, and many were not confident in treating advanced periodontitis (36.3 per cent) or aggressive periodontitis (51.6 per cent). The majority of dentists reported that they provided most of the non surgical periodontal therapy to their patients, while most surgical treatments were referred to specialist periodontists. Factors deemed to be important in influencing the decision to provide periodontal treatment included level of training and ability to motivate patients to improve oral hygiene. Many responents requested periodontic continuing education (CE) courses be run.

CONCLUSIONS

Most of the dentists surveyed were confident to diagnose periodontal disease and to treat the more common presentations of periodontal disease. There is some evidence to suggest that some practitioners are not following the minimum requirements set by the Dental Practice Board of Victoria in relation to periodontal record keeping. The results also indicate a need for more periodontic CE courses in Victoria.

Fear learning transiently impairs hippocampal cell proliferation

We sought to determine whether contextual fear conditioning, a hippocampal-dependent task, would affect neurogenesis in the dentate gyrus of the hippocampus, and if so, to identify which aspect of the training experience accounts for the change. The immediate shock deficit paradigm was used, together with bromodeoxyuridine immunohistochemistry, to isolate the contribution of different aspects of contextual fear conditioning to neurogenesis. Contextual fear learning caused a 33% decrease in the number of proliferating cells that was anatomically restricted to the dentate gyrus with no change in cell survival or differentiation. This attenuation was not related to exposure to the conditioned stimulus alone, the footshock unconditioned stimulus alone, or the expression of fear to the context after training. Instead, the effect of context conditioning on cell proliferation appears to be specifically due to the formation of an association between the context and shock during training, an amygdala dependent function.

Wnt ligand expression in malignant melanoma: pilot study indicating correlation with histopathological features

AIMS

Secreted Wnt ligands are key proteins regulating cell-cell interactions and cell growth and differentiation. These proteins, along with other components of the Wnt signalling pathway, are involved in the malignant transformation of various human cancers, including malignant melanoma. This study defines the expression of several members of the Wnt ligand family and correlates their expression with histological characteristics.

METHODS

The expression of Wnt2, Wnt5a, Wnt5b, Wnt7b, and Wnt10b was defined by in situ, antisense RNA hybridisation of paraffin wax embedded sections of benign naevi and malignant melanoma. Immunoperoxidase based antibody staining was used to define the expression of frizzled (Fz) receptors.

RESULTS

All naevi tested strongly expressed Wnt2, Wnt5a, Wnt7b, and Wnt10b. Melanomas characterised by small, uniform cells expressed each of the Wnts in a pattern similar to that seen for benign naevi. In contrast, melanomas characterised by large, pleomorphic cells expressed Wnt10b but did not express Wnt2 and had low levels of expression of Wnt5a. Expression of Wnt7b was variable in these melanomas. Fz receptor expression was present at a low level in normal epithelium and all naevi and melanomas.

CONCLUSIONS

The expression pattern of Wnt ligands in malignant melanoma correlates with histopathological features and may provide a basis for the molecular classification of this disease.

Chronic restraint stress and chronic corticosterone treatment modulate differentially the expression of molecules related to structural plasticity in the adult rat piriform cortex

Stress and stress-related hormones induce structural changes in neurons of the adult CNS. Neurons in the hippocampus, the amygdala and the prefrontal cortex undergo neurite remodeling after chronic stress. In the hippocampus some of these effects can be mimicked with chronic administration of adrenal steroids. These changes in neuronal structure may be mediated by certain molecules related to plastic events such as the polysialylated form of the neural cell adhesion molecule (PSA-NCAM). The expression of PSA-NCAM persists in the adult hippocampus and it is up-regulated after chronic stress. The piriform cortex also displays considerable levels of PSA-NCAM during adulthood and indirect evidence suggests that it may also be the target of stress and stress related-hormones. Using immunohistochemistry we have studied the expression of PSA-NCAM and doublecortin (DCX; another protein implicated in neuronal structural plasticity) in the piriform cortex of adult rats subjected either to 21 days of chronic restraint stress or to oral corticosterone administration during the same period. Our results indicate that chronic stress and chronic corticosterone administration have differential effects on the expression of PSA-NCAM and DCX. While chronic stress increases the number of PSA-NCAM- and DCX-immunoreactive cells in the piriform cortex layer II, chronic corticosterone administration decreases these numbers. These findings indicate that stress and adrenal steroids affect the piriform cortex and suggest that in this region, as in the hippocampus, they may induce structural changes. This is a potential mechanism by which stress and corticosterone modulate functions of this limbic region, such as its participation in olfactory memory.

Aggregation of human platelets by gingipain-R from Porphyromonas gingivalis cells and membrane vesicles

The hypothesis that there is an association between periodontitis and cardiovascular disease suggests new lines of research on the mechanism whereby oral bacteria might exert systemic effects. This study was conducted to ascertain and quantitate the effect of Porphyromonas gingivalis on human platelets in vitro. A second related objective was to purify and identify the aggregating vector. Aggregation was measured by platelet turbidometry and gingipain-R was purified from P. gingivalis membrane vesicles by Sepharose 2B and hydroxyapatite chromatography. The in vitro aggregation of platelets requires that at least 1.0 x 10(4) cells be stirred with 1.35 x 10(8) platelets. The specific activity is substantially increased in the membrane vesicles that are shed by this bacterium. Aggregability was due to gingipain-R activity, a potent cysteine protease that was found to be highly concentrated in the membrane vesicle fraction. The enzyme was purified 18-fold in high yield from the membrane vesicles, and consists of two noncovalently linked proteins that migrate at 49 and 44 kDa on SDS-PAGE. Aggregation of platelets by gingipain-R was shown to be dose-dependent, and inhibited by leupeptin and arginine, but not by anti-thrombin III. This is the first report enumerating the specific number of cells and lowest concentration of membrane vesicles necessary to evoke a full human platelet response, and the first report to assign this activity to gingipain-R.

Genome-wide gene expression profiles of the developing mouse hippocampus

We have analyzed the developmental molecular programs of the mouse hippocampus, a cortical structure critical for learning and memory, by means of large-scale DNA microarray techniques. Of 11,000 genes and expressed sequence tags examined, 1,926 showed dynamic changes during hippocampal development from embryonic day 16 to postnatal day 30. Gene-cluster analysis was used to group these genes into 16 distinct clusters with striking patterns that appear to correlate with major developmental hallmarks and cellular events. These include genes involved in neuronal proliferation, differentiation, and synapse formation. A complete list of the transcriptional changes has been compiled into a comprehensive gene profile database (http://BrainGenomics.Princeton.edu), which should prove valuable in advancing our understanding of the molecular and genetic programs underlying both the development and the functions of the mammalian brain.

Effect of an essential oil-containing antiseptic mouthrinse on induction of platelet aggregation by oral bacteria in vitro

BACKGROUND

With an increasing body of data suggesting an association between periodontitis and cardiovascular disease, studies have been conducted to elucidate potential mechanisms by which oral bacteria might exert systemic effects. 2 oral bacteria, Streptococcus sanguis and Porphyromonas gingivalis, have been shown to induce platelet aggregation in vitro. This study was conducted to determine the effect of treatment with an essential oil mouthrinse (Listerine Antiseptic) on the platelet-aggregating activity of these organisms.

METHOD

Bacteria were grown under standard culture conditions. S. sanguis ATCC strain 10556 was exposed for 3 min to the essential oil mouthrinse at either full strength or a 1:1 dilution, while P. gingivalis FDC strain 381 was exposed to the essential oil mouthrinse at a 1:10 dilution. Positive control cells were treated with Hanks balanced salt solution (HBSS). Aggregation was measured using a recording platelet aggregometer. The assay of each organism in its respective mouthrinse dilution(s) or HBSS was repeated 5 times.

RESULTS

In all cases, the HBSS-treated organisms induced platelet aggregation, with mean(+/-S.E.) lag times of 12.30 (+/-1.36) min and 11.36 (+/-0.58) min for P. gingivalis and S. sanguis, respectively. In contrast, treatment with the essential oil mouthrinse completely inhibited the platelet aggregating activity of P. gingivalis and of S. sanguis exposed to the 1:1 mouthrinse dilution in all assays; the aggregating activity of S. sanguis treated with full-strength mouthrinse was completely inhibited in 4 of 5 assays, and inhibited by 75% in the 5th, for a mean inhibition of 95 +/- 1.5%.

CONCLUSION

This study provides additional evidence that the essential oil mouthrinse can interfere with bacterial cell surface-associated activities which may have clinical relevance.

On-line monitoring of radiotherapy beams: experimental results with proton beams

Proton radiotherapy is a powerful tool in the local control of cancer. The advantages of proton radiotherapy over gamma-ray therapy arise from the phenomenon known as the Bragg peak. This phenomenon enables large doses to be delivered to well-defined volumes while sparing surrounding healthy tissue. To fully realize the potential of this technique the location of the high-dose volume must be controlled very accurately. An imaging system was designed and tested to monitor the positron-emitting activity created by the beam as a means of verifying the beam's range, monitoring dose, and determining tissue composition. The prototype imaging system consists of 12 pairs of cylindrical BGO detectors shielded in lead. Each crystal was 1.9 cm in diameter, 5.0 cm long, and separated by 0.5 cm from other detectors in the row. These are arranged in two rows, 60 cm apart, with the proton beam and tissue phantoms half-way between and parallel to the detector rows. Experiments were conducted with 150 MeV continuous and macro-pulsed proton beams which had beam currents ranging from 0.14 nA to 1.75 nA. The production and decay of short-lived isotopes, 15O and 14O, was studied using 1 min irradiations with a continuous beam. These isotopes provide a significant signal on short time scales, making on-line imaging possible. Macro-pulsed beams, having a period of 10 s, were used to study on-line imaging and the production and decay of long-lived isotopes, 13N, 11C, and 18F. Decay data were acquired and on-line images were obtained between beam pulses and indicate that range verification is possible, for a 150 MeV beam, after one beam pulse, to within the 1.2 cm resolution limit of the imaging system. The dose delivered to the patient may also be monitored by observing the increase in the number of coincidence events detected between successive beam pulses. Over 80% of the initial positron-emitting activity is from 15O while the remainder is primarily 11C, 13N, 14O with traces of 18F, and 10C. Radioisotopic imaging may also be performed along the beam path by fitting decay data collected after the treatment is complete. Using this technique, it is shown that variations in elemental composition in inhomogenous treatment volumes may be identified and used to locate anatomic landmarks. Radioisotopic imaging also reveals that 14O is created well beyond the Bragg peak, apparently by secondary neutrons.

Oral feeding of renal tubular antigen abrogates interstitial nephritis and renal failure in Brown Norway rats

We have examined whether oral feeding of antigen can regulate the expression of autoimmune interstitial nephritis induced by antigen-in-adjuvant (RTA/CFA) immunization of Brown Norway rats. Male rats were divided into six experimental groups: Group I, RTA/CFA immunization alone; Groups II, III, and IV were pretreated with 1 mg (Group II), 5 mg (Group III), and 25 mg (Group IV) of oral tubular antigen every other day for ten days, followed by RTA/CFA immunization; Group V was pretreated with a control antigen, followed by RTA/CFA immunization; and Group VI was immunized with CFA alone. Renal histology, inulin clearance, DTH responses to RTA, and IgG antibody responses to RTA were monitored as endpoints of the study. Our results demonstrated that Group III and IV animals had significantly less severe renal injury, as assessed by inulin clearance and extent of renal cortical involvement by mononuclear cells. Group II and IV animals had suppressed DTH responses, and only Group IV animals had significantly depressed antigen-specific IgG serum titers. Group III animals had neither suppressed DTH responses or IgG titers. We conclude that oral administration of tubular antigen can modulate the intensity of interstitial nephritis produced by immunization, but that the regulatory mechanism is not dependent (at all doses of fed antigen) on suppressed DTH reactivity to RTA or suppressed antigen-specific IgG.

RAP-1 is an Arabidopsis MYC-like R protein homologue, that binds to G-box sequence motifs

An Arabidopsis cDNA clone encoding a DNA-binding protein, RAP-1, was isolated by southwestern screening of an Escherichia coli cDNA expression library. The protein contains a bHLH DNA-binding domain and is homologous to R proteins, regulating anthocyanin biosynthesis. RAP-1 binds to the sequence CACNTG. It is encoded by a single gene, which is expressed to high levels in root and stem and to low levels in leaf and flower. No expression could be detected in siliques. Rap-1 does not correspond to one of the known loci involved in anthocyanin biosynthesis, since it is located at a different map position. In contrast to the maize R protein Lc, RAP-1 did not induce anthocyanin biosynthesis in pea cotyledons. Thus, RAP-1 is a novel member of the bHLH class of DNA-binding proteins.

Characterization of a zinc-dependent transcriptional activator from Arabidopsis

The C2-H2 zinc-finger is a widely occurring DNA binding motif, usually present as tandem repeats. The majority of C2-H2 zinc-finger proteins that have been studied are derived from animals. Here, we characterize a member of a distinct class of plant C2-H2 zinc-finger proteins in detail. A cDNA clone encoding a DNA binding protein from Arabidopsis was isolated by SouthWestern screening. The protein, termed ZAP1 (Zinc-dependent Activator Protein-1), is encoded by a single copy gene, which is expressed to similar levels in root and flower, to a somewhat lower level in stem and to low levels in leaf and siliques. The optimal binding site was determined by random binding site selection, and the consensus sequence found is CGTTGACCGAG. The homology between ZAP1 and other DNA binding proteins is restricted to a repeated region of a stretch of 24 highly conserved amino acids followed by a zinc-finger motif (C-X4-C-X22-23-H-X1-H). The C-terminal zinc-finger region is essential for DNA binding, whereas deletion of the N-terminal one resulted in 2.5-fold reduced binding affinity. Binding of ZAP1 to DNA was abolished by metal-chelating agents. The activation domain as determined in yeast is adjacent to and possibly overlapping with the DNA binding domain. Particle bombardment experiments with plant cells showed that ZAP1 increases expression of a gusA reporter gene that is under control of ZAP1 binding sites. We conclude that ZAP1 is a plant transcriptional activator with a C2-H2 zinc-finger DNA binding domain.

The 22 bp W1 element in the pea lectin promoter is necessary and, as a multimer, sufficient for high gene expression in tobacco seeds

The pea lectin (Psl) gene encodes an abundant seed protein. Its seed-specific expression pattern is conserved in transgenic tobacco plants. Progressive 5' promoter deletions resulted in a gradual decrease of transcriptional activity in tobacco seed. A fragment of 115 bp still conferred seed-specific expression albeit at a low level. This fragment contains a 22 bp element (W1), which has been demonstrated to be important for seed-specific expression when coupled as a trimer to a heterologous TATA box (de Pater et al., Plant Cell 5:877-886, 1993). Here we show that deletion of W1 in the natural promoter context resulted in a strongly decreased level of gene expression. A 4 bp mutation of W1 reduced the expression of truncated derivatives of the Psl promoter. A single copy of W1 coupled to the TATA box of the CaMV 35S promoter directed low gene expression in seeds and leaves. Multimerization enhanced the expression in seeds up to 100-fold, to levels found with the Psl promoter, whereas the expression level in leaves remained low. These results demonstrate that the W1 element is an essential control element in the Psl promoter. When taken out of its natural context and multimerized, it is sufficient for high expression in seeds.

Binding specificity and tissue-specific expression pattern of the Arabidopsis bZIP transcription factor TGA2

The binding specificity and tissue-specific expression pattern of TGA2 (AHBP-1b), an Arabidopsis bZIP transcription factor have been determined. Filter-binding and gel-shift assays showed that TGA2 has high affinity for C-boxes (ATGACGTCAT). In this respect TGA2 is similar to other members of the Arabidopsis TGA family (such as TGA1, TGA3 and OBF4) and to tobacco TGA1a. Genomic Southern blot analysis confirmed that TGA2 is a member of the gene family. Northern blot analysis showed that the gene is expressed at similar levels in root, stem, leaf and flower t at somewhat lower levels in siliques. TGA3 was also found to be expressed at the same level throughout the plant, whereas genes encoding TGA1 and OBF4 have relatively high RNA expression levels in root. The differential expression of these genes suggests that they have distinct functions.

Dentin ablation with three infrared lasers

BACKGROUND AND OBJECTIVE

Lasers are used for caries removal in enamel and dentin, but are currently limited in their ability to remove sound tooth structure. In this study plasma interaction regimes are investigated as the principal factor determining the ablation characteristics.

STUDY DESIGN/MATERIALS AND METHODS

Three ablation parameters are considered: ablation rates (AR), surface temperatures (ST), and surface morphological characteristics. The three lasers investigated were Er:YSGG with wavelength (WL) of 2.94 mu m and pulse duration (PD) of 250 mu s, Ho:YSGG at 2.1 mu m and 250 mu s and an Nd:YAG with WL of 1.06 mu M and PD of 15ns.

RESULTS

The highest surface temperatures were observed during Er:YSGG treatment (> 300 degrees C), moderate temperatures with the Ho:YSGG (150 degrees C), and lowest with the Nd:YAG (with highest surface temperature generally lower than 80 degrees C). Ablation rates were also compared and were shown to be highest with the Er:YSGG and Ho:YSGG, and lower with the Nd:YAG (< 3 mu m). In all systems, efficient ablation was observed only in the presence of plasma. In spite of their different wavelengths, for similar spot sizes, energy, and pulse duration, ablation rates of Ho:YSGG and Er:YSGG were found to be comparable. These were an order of magnitude larger than the ablation rates observed with the nanosecond system.

CONCLUSION

Possible explanation for these observations is given in terms of plasma characteristics.

Dentin ablation with three infrared lasers

BACKGROUND AND OBJECTIVE

Lasers are used for caries removal in enamel and dentin, but are currently limited in their ability to remove sound tooth structure. In this study plasma interaction regimes are investigated as the principal factor determining the ablation characteristics.

STUDY DESIGN/MATERIALS AND METHODS

Three ablation parameters are considered: ablation rates (AR), surface temperatures (ST), and surface morphological characteristics. The three lasers investigated were Er:YSGG with wavelength (WL) of 2.94 mu m and pulse duration (PD) of 250 mu s, Ho:YSGG at 2.1 mu m and 250 mu s and an Nd:YAG with WL of 1.06 mu M and PD of 15ns.

RESULTS

The highest surface temperatures were observed during Er:YSGG treatment (> 300 degrees C), moderate temperatures with the Ho:YSGG (150 degrees C), and lowest with the Nd:YAG (with highest surface temperature generally lower than 80 degrees C). Ablation rates were also compared and were shown to be highest with the Er:YSGG and Ho:YSGG, and lower with the Nd:YAG (< 3 mu m). In all systems, efficient ablation was observed only in the presence of plasma. In spite of their different wavelengths, for similar spot sizes, energy, and pulse duration, ablation rates of Ho:YSGG and Er:YSGG were found to be comparable. These were an order of magnitude larger than the ablation rates observed with the nanosecond system.

CONCLUSION

Possible explanation for these observations is given in terms of plasma characteristics.

A 22-bp fragment of the pea lectin promoter containing essential TGAC-like motifs confers seed-specific gene expression

To elucidate the molecular mechanisms responsible for seed-specific gene expression in plants, the promoter of the pea lectin (psl) gene, encoding an abundant seed protein, was used as a model. Leaf and seed nuclear proteins bound to a region in the psl promoter containing three overlapping TGAC-like motifs, which have been shown to be a binding site for basic/leucine zipper proteins, including TGA1a. A trimer of a 22-bp region of the psl promoter, containing the TGAC-like motifs, coupled to a heterologous minimal promoter conferred low reporter gene expression in root, stem, and leaf and high expression in seed of transgenic tobacco. Expression increased during the midmaturation stage of seed development and was observed in the endosperm as well as in the embryo, where it strongly decreased within a few days after germination. This expression pattern is qualitatively identical to the expression pattern conferred by a 2000-bp fragment of the psl promoter. Nucleotides within the TGAC-like motifs important for in vitro binding are also essential for in vivo transcription activation in vegetative tissue as well as in seed. The electrophoretic mobility of a DNA-protein complex containing seed nuclear protein was different from that formed with leaf nuclear protein. Furthermore, the TGA1a steady state mRNA level in immature seed was relatively low. These results suggest that a seed-specific factor different from TGA1a, but with similar binding specificity, is responsible for gene activation in seed. We conclude that the 22-bp region contains all the information, including an essential TGAGTCATCA sequence, necessary for seed-specific expression and very likely plays an essential role in the seed-specific expression pattern of the psl gene.

The chimpanzee major histocompatibility complex class II DR subregion contains an unexpectedly high number of beta-chain genes

The major histocompatibility complex (MHC) class II DR subregion of the chimpanzee was studied by restriction fragment length polymorphism (RFLP) analysis. Genomic DNA obtained from a panel of 94 chimpanzees was digested with the restriction enzyme Taq I and hybridized with an HLA-DR beta probe specific for the 3' untranslated (UT) region. Such a screening revealed the existence of 14 distinct DRB/Taq I gene-associated fragments allowing the definition of 11 haplotypes. Segregation studies proved that the number of chimpanzee class II DRB/Taq I fragments is not constant and varies from three to six depending on the haplotype. Comparison of these data with a human reference panel manifested that some MHC DRB/Taq I fragments are shared by man and chimpanzee. Moreover, the number of HLA-DRB/Taq I gene-associated fragments detected in a panel of homozygous typing cells varies from one to three and corresponds with the number of HLA-DRB genes present for most haplotypes. However, a discrepancy is observed for the HLA-DR4, -DR7, and -DR9 haplotypes since a fourth HLA-DRB pseudogene present within these haplotypes lacks its 3' UT region and thus is not detected with the probe used. These results suggest that chimpanzees have a higher maximum number of DRB genes per haplotype than man. As a consequence, some chimpanzee haplotypes must show a dissimilar organization of the MHC DR subregion compared to their human equivalents. The implications of these findings are discussed in the context of the trans-species theory of MHC polymorphism.

Tissue-specific alterations in somatostatin mRNA accumulation in streptozocin-induced diabetes

In streptozocin-induced diabetes in rats, there is a marked increase in the content and release of immunoreactive somatostatin (SLI) from the pancreas and upper gut. To elucidate whether these SLI changes are associated with alterations in somatostatin gene transcription, we measured somatostatin mRNA (SmRNA) accumulation in these and other SLI-producing tissues. Pancreas, stomach, jejunum, hypothalamus, and cerebral cortex were removed from control rats, 6-wk-diabetic rats, and diabetic rats treated with insulin for 6 wk. Total RNA was isolated by centrifugation through CsCl and fractionated on agarose gels. A sensitive radiodensitometric hybridization assay was used to determine SmRNA levels in absolute amounts by in vitro synthesized sense-strand RNA as a quantitative standard and antisense cRNA as a specific probe. SLI was determined by radioimmunoassay. SmRNA exhibited size heterogeneity between the different control and diabetic tissues. A 2- to 3-fold increase in total SmRNA was found in pancreas and stomach of the diabetic rats that suppressed toward normal with insulin treatment. These two tissues also exhibited significant 1.6- to 2.6-fold increases in SLI, respectively. The remaining tissues showed no diabetes-related changes in SLI or SmRNA. We conclude that in insulinopenic diabetes, tissue SLI and SmRNA accumulation undergo parallel changes; are increased in pancreas and upper gut, reflecting augmented somatostatin synthesis; are reciprocally related to insulin acting directly or indirectly on somatostatin-producing cells; and are unchanged in the lower gut and brain, suggesting tissue-specific regulation of somatostatin gene transcription in diabetes.