298 research outputs found
Novel stochastic and entropy-based Expectation-Maximisation algorithm for transcription factor binding site motif discovery
Get PDFThe discovery of transcription factor binding site (TFBS) motifs remains an important
and challenging problem in computational biology. This thesis presents MITSU,
a novel algorithm for TFBS motif discovery which exploits stochastic methods as a
means of both overcoming optimality limitations in current algorithms and as a framework
for incorporating relevant prior knowledge in order to improve results.
The current state of the TFBS motif discovery field is surveyed, with a focus
on probabilistic algorithms that typically take the promoter regions of coregulated
genes as input. A case is made for an approach based on the stochastic Expectation-
Maximisation (sEM) algorithm; its position amongst existing probabilistic algorithms
for motif discovery is shown. The algorithm developed in this thesis is unique amongst
existing motif discovery algorithms in that it combines the sEM algorithm with a derived
data set which leads to an improved approximation to the likelihood function.
This likelihood function is unconstrained with regard to the distribution of motif occurrences
within the input dataset. MITSU also incorporates a novel heuristic to automatically
determine TFBS motif width. This heuristic, known as MCOIN, is shown to
outperform current methods for determining motif width. MITSU is implemented in
Java and an executable is available for download.
MITSU is evaluated quantitatively using realistic synthetic data and several collections
of previously characterised prokaryotic TFBS motifs. The evaluation demonstrates
that MITSU improves on a deterministic EM-based motif discovery algorithm
and an alternative sEM-based algorithm, in terms of previously established metrics.
The ability of the sEM algorithm to escape stable fixed points of the EM algorithm,
which trap deterministic motif discovery algorithms and the ability of MITSU to discover
multiple motif occurrences within a single input sequence are also demonstrated.
MITSU is validated using previously characterised Alphaproteobacterial motifs,
before being applied to motif discovery in uncharacterised Alphaproteobacterial data.
A number of novel results from this analysis are presented and motivate two extensions
of MITSU: a strategy for the discovery of multiple different motifs within a single
dataset and a higher order Markov background model. The effects of incorporating
these extensions within MITSU are evaluated quantitatively using previously characterised
prokaryotic TFBS motifs and demonstrated using Alphaproteobacterial motifs.
Finally, an information-theoretic measure of motif palindromicity is presented and its
advantages over existing approaches for discovering palindromic motifs discussed
Relating Research and Teaching: comparing experiences and beliefs
No full textThe relationship between research and teaching has possible benefits and inherent tensions. It is a recurrent topic of discussion by faculty including engineering educators. Exploring a potentially beneficial relationship and is of interest and possible value to engineering faculty, our students, and our stakeholders. Institutions and departments have developed a range of approaches including research-led, research informed, or just plain scholarly. This paper examines the relationship between research and teaching in the undergraduate curriculum. It compares and contrasts evidence of the beliefs and experiences of the engineering faculty and the engineering student. It presents and analyses the result of surveys which gathered qualitative and qualitative data to explore the inter-relationship of research and teaching; in the curriculum; and as it is delivered and experienced in the lab, seminar room and lecture hall. This research builds on existing work developed in a preliminary study which examined ways in which synergies between research and teaching could be achieved, particularly in the ‘hard/applied’ areas of the curriculum. It analyses data from the ‘research-intensive’ and the ‘teaching-intensive’ perspective
Novel non-labile covalent binding of sulfamethoxazole reactive metabolites to cultured human lymphoid cells
No full textSulfamethoxazole (SMX) causes rare hypersensitivity syndrome reactions characterized by fever and multi-organ toxicity. Covalent binding of SMX reactive metabolites to cellular proteins has been demonstrated but the link between cytotoxicity and targets of covalent binding has not been explored. We therefore investigated the relationship between covalent binding of the reactive SMX-hydroxylamine (SMX-HA) metabolite, and its cytotoxicity to a hystiocytic lymphoma (U937) cell line. Incubation of U937 cells with 0-1 mM SMX-HA for 3 h resulted in dose-dependent cytotoxicity, as assessed by tetrazolium dye conversion at 24 h. SMX-HA caused dose-dependent covalent binding to cellular proteins as assessed by immunoblotting with SMX antisera at 3 and 24 h. Covalent binding was predominantly to proteins of approximately 45, 59 and 75 kDa, but other targets were also observed. The relative extent of binding to proteins was significantly different from the relative cytotoxicity at 24 h. Further, cells surviving at 24 h also had extensive covalent binding. Covalent binding was observed under reducing (beta-mercaptoethanol) and non-reducing conditions to plasma membrane and microsomal but not cytosolic proteins. This non-labile covalent binding has not been previously reported. These observations suggest that extensive covalent binding does not necessarily lead to cell death, allowing the accumulation of potentially immunogenic drug-protein conjugates. These observations in whole cells may be relevant to the immunopathogenesis of SMX hypersensitivity syndrome reactions.LR: 20061115; PUBM: Print; JID: 0227276; 0 (Anti-Infective Agents); 0 (Antibodies); 0 (Tetrazolium Salts); 0 (Thiazoles); 114438-33-4 (sulfamethoxazole hydroxylamine); 298-93-1 (thiazolyl blue); 723-46-6 (Sulfamethoxazole); ppublishSource type: Electronic(1
Further investigations of the role of acetylation in sulphonamide hypersensitivity reactions
No full textSulphonamide hypersensitivity reactions are believed to be mediated through reactive intermediates derived from oxidation of the para-amino group to form sulphonamide hydroxylamines. Sulphamethoxazole hydroxylamine (SMX-HA) can be acetylated by N-acetyltransferase (NAT) enzymes to form an acetoxy metabolite (acetoxySMX). In the current studies, acetoxySMX was found to be not toxic over the concentration range of 0 to 500 mu M towards a human lymphoblastoid cell line (RPMI 1788) or a human hepatoma cell line (HepG2). Further, transient expression of NAT1 in COS-1 cells or stable transfection of NAT1 and NAT2 in HepG2 cells did not alter the toxicity of SMX-HA in vitro. The activity of NAT1 in isolated mononuclear leucocytes (a reflection of systemic NAT1 activity) determined with para-aminobenzoic acid as a substrate was not different between controls (n = 11) or patients with a known hypersensitivity reaction (n = 5) (4.1 +/- 1.2 nmol min(-1) mg(-1) vs 5.7 +/- 1.4 nmol min(-1) mg(-1)). Thus, acetoxySMX is unlikely to play a significant role in mediating SMX hypersensitivity reactions and a constitutive deficiency in NAT1 activity is not a common finding in patients susceptible to SMX hypersensitivity reactions.PT: J; CR: CHAO ES, 1988, CELL BIOL TOXICOL, V4, P1 CRIBB AE, 1991, DRUG METAB DISPOS, V19, P900 CRIBB AE, 1991, J PHARMACOL EXP THER, V251, P1241 CRIBB AE, 1993, BIOCHEM PHARMACOL, V45, P1277 CRIBB AE, 1996, ADVERSE DRUG REACT T, V15, P9 CRIBB AE, 1996, CHEM RES TOXICOL, V9, P500 DUPRET JM, 1992, J BIOL CHEM, V267, P7381 KEARNS GL, 1994, J PEDIATR, V125, P805 LEE BL, 1994, CLIN PHARMACOL THER, V56, P184 NAKAMURA H, 1995, J PHARMACOL EXP THER, V274, P1099 PONSODA X, 1991, J TISSUE CULTURE MET, V13, P21 RIEDER MJ, 1989, ANN INTERN MED, V110, P286 RIEDER MJ, 1991, CLIN PHARMACOL THER, V49, P13 RILEY RJ, 1991, BIOCHEM PHARMACOL, V42, P696 SHEAR NH, 1986, ANN INTERN MED, V105, P179 SHEAR NH, 1988, J CLIN INVEST, V82, P1826 VANDERVEN AJA, 1995, BRIT J CLIN PHARMACO, V38, P147 WOLKENSTEIN P, 1995, PHARMACOGENETICS, V5, P255; NR: 18; TC: 5; J9: BIOMARKERS; PG: 6; GA: VV689Source type: Electronic(1
Calpain-induced endoplasmic reticulum stress and cell death following cytotoxic damage to renal cells
No full textCalpains and endoplasmic reticulum (ER) stress have both been implicated in renal cell death following exposure to reactive chemical toxicants (RCTs). Therefore, we explored the link between ER stress, calpain, and cell death in renal cell injury due to model RCTs (iodoacetamide, menadione, tert-butyl hydroperoxide) and ER stress inducers (tunicamycin [TUN], thapsigargin [THAPS]). The calpain inhibitor, PD150606, significantly reduced the RCT and TUN-induced cell death in the renal cell line LLC-PK1, but not death induced by THAPS. ER stress was confirmed by the significant induction of GRP78 following exposure to RCTs and ER stress inducers. While GRP94 induction was observed following RCTs and TUN, it was not statistically significant because of variability. THAPS at 5 microM significantly induced GRP94, while 20 mmicroM caused a calpain-dependent cleavage of GRP94. Caspase-12 and m-calpain were variably induced and/or cleaved following exposure to all toxicants, supporting activation of these signaling pathways. Inhibition of calpain blocked the induction of GRP78 following exposure to RCTs suggesting that calpain was contributing to the observed ER stress following RCTs. In contrast, calpain inhibition did not block ER stress protein induction following exposure to nontoxic concentrations of TUN or THAPS, indicating that calpain inhibition did not block the ER stress protein induction pathways directly. These studies demonstrate a previously unappreciated link between calpain activation and ER stress-associated cell death in renal cells. While further studies are required to clarify the molecular events involved, these results confirm that calpain activation and the ER are important related players in chemically induced renal cell damage.PUBM: Print-Electronic; DEP: 20060818; JID: 9805461; 2006/08/18 [aheadofprint]; ppublishSource type: Electronic(1
Effects of season and sample handling on measurement of plasma alpha-melanocyte-stimulating hormone concentrations in horses and ponies
No full textOBJECTIVE: To investigate effects of sample handling, storage, and collection time and season on plasma alpha-melanocyte-stimulating hormone (alpha-MSH) concentration in healthy equids. ANIMALS: 11 healthy Standardbreds and 13 healthy semiferal ponies. PROCEDURE: Plasma alpha-MSH concentration was measured by use of radioimmunoassay. Effects of delayed processing were accessed by comparing alpha-MSH concentrations in plasma immediately separated with that of plasma obtained from blood samples that were stored at 4 degrees C for 8 or 48 hours before plasma was separated. Effects of suboptimal handling were accessed by comparing alpha-MSH concentrations in plasma immediately stored at -80 degrees C with plasma that was stored at 25 degrees C for 24 hours, 4 degrees C for 48 hours or 7 days, and -20 degrees C for 30 days prior to freezing at -80 degrees C. Plasma alpha-MSH concentrations were compared among blood samples collected at 8:00 AM, 12 noon, and 4:00 PM. Plasma alpha-MSH concentrations were compared among blood samples collected in January, March, April, June, September, and November from horses and in September and May from ponies. RESULTS: Storage of blood samples at 4 degrees C for 48 hours before plasma was separated and storage of plasma samples at 4 degrees C for 7 days prior to freezing at -80 degrees C resulted in significant decreases in plasma alpha-MSH concentrations. A significantly greater plasma alpha-MSH concentration was found in September in ponies (11-fold) and horses (2-fold), compared with plasma alpha-MSH concentrations in spring. CONCLUSIONS AND CLINICAL RELEVANCE: Handling and storage conditions minimally affected plasma alpha-MSH concentrations. Seasonal variation in plasma alpha-MSH concentrations must be considered when evaluating pituitary pars intermedia dysfunction in equids.LR: 20061115; PUBM: Print; JID: 0375011; 581-05-5 (alpha-MSH); ppublishSource type: Electronic(1
Social media micro-film marketing by Chinese destinations: The case of Shaoxing
No full textMarketing destinations by micro-films via social media is becoming more popular among Chinese destinations. Little has been published about this phenomenon in the tourism literature. Using a net-nographic case study from the city of Shaoxing, this research revealed the success factors for micro-film marketing by destinations. The research results showed that during the micro-film diffusion process, destination marketers were continuously and actively engaging with followers and online and offline marketing efforts were well planned and integrated. Attractions without uniqueness were impressive to viewers by being embodied in a romantic theme. Suggestions and implications for destination marketing are given. (C) 2015 Elsevier Ltd. All rights [email protected]; [email protected]; [email protected]; [email protected]
Converging and diverging convection around axisymmetric magnetic flux tubes
Get PDFA numerical model of idealized sunspots and pores is presented, where axisymmetric cylindrical domains are used with aspect ratios (radius versus depth) up to 4. The model contains a compressible plasma with density and temperature gradients simulating the upper layer of the Sun's convection zone. Non-linear magnetohydrodynamic equations are solved numerically and time-dependent solutions are obtained where the magnetic field is pushed to the centre of the domain by convection cells. This central magnetic flux bundle is maintained by an inner convection cell, situated next to it and with a flow such that there is an inflow at the top of the numerical domain towards the flux bundle. For aspect ratio 4, a large inner cell persists in time, but for lower aspect ratios it becomes highly time dependent. For aspect ratios 2 and 3 this inner convection cell is smaller, tends to be situated towards the top of the domain next to the flux bundle, and appears and disappears with time. When it is gone, the neighbouring cell (with an opposite sense of rotation, i.e. outflow at the top) pulls the magnetic field away from the central axis. As this happens a new inner cell forms with an inflow which pushes the magnetic field towards the centre. This suggests that to maintain their form, both pores and sunspots need a neighbouring convection cell with inflow at the top towards the magnetic flux bundle. This convection cell does not have to be at the top of the convection zone and could be underneath the penumbral structure around sunspots. For an aspect ratio of 1, there is not enough space in the numerical domain for magnetic flux and convection to separate. In this case the solution oscillates between two steady states: two dominant convection cells threaded by magnetic field and one dominant cell that pushes magnetic flux towards the central axis
In-vitro formation, disposition and toxicity of n-acetoxy-sulffamethoxazole, a potential mediator of sulfamethoxazole toxicity
No full textVariation in the formation and disposition of the hydroxylamine of (SMX-HA) is thought to play an important role in the pathogenesis of sulfamethoxazole(SMX)-induced idiosyncratic adverse drug reactions. We hypothesized that, in analogy to carcinogenic arylamines, SMX-HA might be further converted to an electrophilic N-acetoxy metabolite which could play a role in mediating SMX toxicity. Accordingly, we chemically synthesized N-acetoxy-SMX, and examined the characteristics of its formation, metabolism, cytotoxicity and mutagenicity in human and bacterial test systems. The human arylamine N-acetyltransferases, (NAT)1 and NAT2, were capable of converting SMX-HA to N-acetoxy-SMX. NAT1 and NAT2 possessed similar affinities for SMX-HA (apparent K-m values of 650 and 520 mu M, respectively), but the apparent maximal velocity of the NAT1-mediated acetylation was higher than that of NAT2. (1332 vs. 37 nmol/min/U of immunoreactive NAT protein). Human peripheral blood mononuclear cells 12,000 x g supernatant fractions converted N-acetoxy-SMX mainly back to SMX-HA, and also to a lesser extent to SMX, at clinically relevant concentrations. Similar pathways were observed in human hepatic cytosolic fractions. In a cytotoxicity assay, N-acetoxy-SMX was significantly more toxic to human peripheral blood mononuclear cells than SMX-HA (16.6 vs. 11.5% dead cells at a concentration of 300 mu M). N-acetoxy-SMX was weakly mutagenic to the Salmonella typhimurium TA100 strain in the Ames test. These data suggest that the N-acetoxy metabolites of sulfonamides could potentially play a role in mediating sulfonamide idiosyncratic adverse drug reactions.PT: J; CR: BRADFORD MM, 1976, ANAL BIOCHEM, V72, P248 CRIBB AE, 1990, DRUG METAB DISPOS, V18, P784 CRIBB AE, 1990, VET RES COMMUN, V14, P241 CRIBB AE, 1991, DRUG METAB DISPOS, V19, P900 CRIBB AE, 1991, J PHARMACOL EXP THER, V259, P1241 CRIBB AE, 1991, MOL PHARMACOL, V38, P744 CRIBB AE, 1992, CLIN PHARMACOL THER, V51, P522 CRIBB AE, 1993, BIOCHEM PHARMACOL, V45, P1277 DUPRET JM, 1992, J BIOL CHEM, V267, P7381 FAMULOK M, 1989, ANGEW CHEM INT EDIT, V28, P337 GRANT DM, 1990, J CLIN INVEST, V85, P968 GRANT DM, 1991, MOL PHARMACOL, V39, P184 GRANT DM, 1992, CANCER RES, V52, P1 HANNA PE, 1985, BIOACTIVATION FOREIG, P375 HEIN DW, 1987, CARCINOGENESIS, V8, P1767 HEIN DW, 1993, CARCINOGENESIS, V14, P1633 MCMANUS ME, 1989, CLIN EXP PHARMACOL P, V16, P491 RIEDER MJ, 1987, J PHARMACOL EXP THER, V244, P724 RIEDER MJ, 1989, ANN INTERN MED, V110, P286 RIEDER MJ, 1991, CLIN PHARMACOL THER, V49, P13 RILEY RJ, 1991, BIOCHEM PHARMACOL, V42, P696 SHEAR NH, 1985, CAN J PHYSIOL PHARM, V63, P1370 SHEAR NH, 1986, ANN INTERN MED, V105, P179 SPIELBERG SP, 1980, J PHARMACOL EXP THER, V213, P395 THOMPSON DC, 1992, MUTAT RES, V279, P83; NR: 25; TC: 21; J9: J PHARMACOL EXP THER; PG: 6; GA: RV893Source type: Electronic(1
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