Fusion transcript loci share many genomic features with non-fusion loci

Background Fusion transcripts are found in many tissues and have the potential to create novel functional products. Here, we investigate the genomic sequences around fusion junctions to better understand the transcriptional mechanisms mediating fusion transcription/splicing. We analyzed data from prostate (cancer) cells as previous studies have shown extensively that these cells readily undergo fusion transcription. Results We used the FusionMap program to identify high-confidence fusion transcripts from RNAseq data. The RNAseq datasets were from our (N = 8) and other (N = 14) clinical prostate tumors with adjacent non-cancer cells, and from the LNCaP prostate cancer cell line that were mock-, androgen- (DHT), and anti-androgen- (bicalutamide, enzalutamide) treated. In total, 185 fusion transcripts were identified from all RNAseq datasets. The majority (76 %) of these fusion transcripts were ‘read-through chimeras’ derived from adjacent genes in the genome. Characterization of sequences at fusion loci were carried out using a combination of the FusionMap program, custom Perl scripts, and the RNAfold program. Our computational analysis indicated that most fusion junctions (76 %) use the consensus GT-AG intron donor-acceptor splice site, and most fusion transcripts (85 %) maintained the open reading frame. We assessed whether parental genes of fusion transcripts have the potential to form complementary base pairing between parental genes which might bring them into physical proximity. Our computational analysis of sequences flanking fusion junctions at parental loci indicate that these loci have a similar propensity as non-fusion loci to hybridize. The abundance of repetitive sequences at fusion and non-fusion loci was also investigated given that SINE repeats are involved in aberrant gene transcription. We found few instances of repetitive sequences at both fusion and non-fusion junctions. Finally, RT-qPCR was performed on RNA from both clinical prostate tumors and adjacent non-cancer cells (N = 7), and LNCaP cells treated as above to validate the expression of seven fusion transcripts and their respective parental genes. We reveal that fusion transcript expression is similar to the expression of parental genes. Conclusions Fusion transcripts maintain the open reading frame, and likely use the same transcriptional machinery as non-fusion transcripts as they share many genomic features at splice/fusion junctions.

Impact of resistance on the efficacy of binary combinations of spinosad, chlorpyrifos-methyl and s-methoprene against five stored-grain beetles

Laboratory experiments were conducted to determine the efficacy of spinosad (a biopesticide), chlorpyrifos-methyl (an organophosphorus compound (OP)) and s-methoprene (a juvenile hormone analogue) applied alone and in binary combinations against five stored-grain beetles in wheat. There were three strains of Rhyzopertha dominica, and one strain each of Sitophilus oryzae, Tribolium castaneum, Oryzaephilus surinamensis and Cryptolestes ferrugineus. These strains were chosen to represent a range of possible resistant genotypes, exhibiting resistance to organophosphates, pyrethroids or methoprene. Treatments were applied at rates that are registered or likely to be registered in Australia. Adults were exposed to freshly treated wheat for 2 weeks, and the effects of treatments on mortality and reproduction were determined. No single protectant or protectant combination controlled all insect strains, based on the criterion of >99% reduction in the number of live F1 adults relative to the control. The most effective combinations were spinosad at 1 mg kg-1+chlorpyrifos-methyl at 10 mg kg-1 which controlled all strains except for OP-resistant O. surinamensis, and chlorpyrifos-methyl at 10 mg kg-1+s-methoprene at 0.6 mg kg-1 which controlled all strains except for methoprene-resistant R. dominica. The results of this study demonstrate the difficulty in Australia, and potentially other countries which use protectants, of finding protectant treatments to control a broad range of pest species in the face of resistance development.

Non-destructive assessment of Arundo donax (Poaceae) leaf quality

Leaf carbon (C) content, leaf nitrogen (N) content, and C:N ratio are especially useful for understanding plant-herbivore interactions and may be important in developing control methods for the invasive riparian plant Arundo donax L. We measured C content, N content, C:N ratio, and chlorophyll index (SPAD 502 reading) for 768 leaves from A. donax collected over a five year period at several locations in California, Nevada, and Texas. Leaf N was more variable than leaf C, and thus we developed a linear regression equation for estimating A. donax leaf N from the leaf chlorophyll index (SPAD reading). When applied to two independent data sets, the equation (leaf N content % = -0.63 + 0.08 x SPAD) produced realistic estimates that matched seasonal and spatial trends reported from a natural A. donax population. Used in conjunction with the handheld SPAD 502 meter, the equation provides a rapid, non-destructive method for estimating A. donax leaf quality.

Analysis of an internally mountable accelerometer balance system for use with non-isotropic models in shock tunnels

Knowledge of drag force is an important design parameter in aerodynamics. Measurement of aerodynamic forces at hypersonic speed is a challenge and usually ground test facilities like shock tunnels are used to carry out such tests. Accelerometer based force balances are commonly employed for measuring aerodynamic drag around bodies in hypersonic shock tunnels. In this study, we present an analysis of the effect of model material on the performance of an accelerometer balance used for measurement of drag in impulse facilities. From the experimental studies performed on models constructed out of Bakelite HYLEM and Aluminum, it is clear that the rigid body assumption does not hold good during the short testing duration available in shock tunnels. This is notwithstanding the fact that the rubber bush used for supporting the model allows unconstrained motion of the model during the short testing time available in the shock tunnel. The vibrations induced in the model on impact loading in the shock tunnel are damped out in metallic model, resulting in a smooth acceleration signal, while the signal become noisy and non-linear when we use non-isotropic materials like Bakelite HYLEM. This also implies that careful analysis and proper data reduction methodologies are necessary for measuring aerodynamic drag for non-metallic models in shock tunnels. The results from the drag measurements carried out using a 60 degrees half angle blunt cone is given in the present analysis.

Numerical studies on columnar-to-equiaxed transition in directional solidification of binary alloys

A numerical study on columnar-to-equiaxed transition (CET) during directional solidification of binary alloys is presented using a macroscopic solidification model. The position of CET is predicted numerically using a critical cooling rate criterion reported in literature. The macroscopic solidification model takes into account movement of solid phase due to buoyancy, and drag effect on the moving solid phase because of fluid motion. The model is applied to simulate the solidification process for binary alloys (Sn-Pb) and to estimate solidification parameters such as position of the liquidus, velocity of the liquidus isotherm, temperature gradient ahead of the liquidus, and cooling rate at the liquidus. Solidification phenomena under two cooling configurations are studied: one without melt convection and the other involvin thermosolutal convection. The numerically predicted positions of CET compare well with those of experiments reported in literature. Melt convection results in higher cooling rate, higher liquidus isotherm velocities, and stimulation of occurrence of CET in comparison to the nonconvecting case. The movement of solid phase aids further the process of CET. With a fixed solid phase, the occurrence of CET based on the same critical cooling rate is delayed and it occurs at a greater distance from the chill.

A dosimetric retrospective planning study comparing volumetric arc therapy (VMAT) and stereotactic body radiotherapy (SBRT) treatment plans for non-small cell lung cancer (NSCLC)

Purpose A retrospective planning study comparing volumetric arc therapy (VMAT) and stereotactic body radiotherapy (SBRT) treatment plans for non-small cell lung cancer (NSCLC). Methods and materials Five randomly selected early stage lung cancer patients were included in the study. For each patient, four plans were created: the SBRT plan and three VMAT plans using different optimisation methodologies. A total of 20 different plans were evaluated. The dose parameters of dose conformity results and the target dose constraints results were compared for these plans. Results The mean planning target volume (PTV) for all the plans (SBRT and VMAT) was 18·3 cm3, with a range from 15·6 to 20·1 cm3. The maximum dose tolerance to 1 cc of all the plans was within 140% (84 Gy) of the prescribed dose, and 95% of the PTV of all the plans received 100% of the prescribed dose (60 Gy). In all the plans, 99% of the PTV received a dose >90% of the prescribed dose, and the mean dose in all the plans ranged from 67 to 72 Gy. The planning target dose conformity for the SBRT and the VMAT (0°, 15° collimator single arc plans and dual arc) plans showed the tightness of the prescription isodose conformity to the target. Conclusions SBRT and VMAT are radiotherapy approaches that increase doses to small tumour targets without increasing doses to the organs at risk. Although VMAT offers an alternative to SBRT for NSCLC and the potential advantage of VMAT is the reduced treatment times over SBRT, the statistical results show that there was no significant difference between the SBRT and VMAT optimised plans in terms of dose conformity and organ-at-risk sparing.

Characterisation of chicken Campylobacter jejuni isolates using resolution optimised single nucleotide polymorphisms and binary gene markers

The principal objective of this study was to determine if Campylobacter jejuni genotyping methods based upon resolution optimised sets of single nucleotide polymorphisms (SNPs) and binary genetic markers were capable of identifying epidemiologically linked clusters of chicken-derived isolates. Eighty-eight C. jejuni isolates of known flaA RFLP type were included in the study. They encompassed three groups of ten isolates that were obtained at the same time and place and possessed the same flaA type. These were regarded as being epidemiologically linked. Twenty-six unlinked C. jejuni flaA type I isolates were included to test the ability of SNP and binary typing to resolve isolates that were not resolved by flaA RFLP. The remaining isolates were of different flaA types. All isolates were typed by real-time PCR interrogation of the resolution optimised sets of SNPs and binary markers. According to each typing method, the three epidemiologically linked clusters were three different clones that were well resolved from the other isolates. The 26 unlinked C. jejuni flaA type I isolates were resolved into 14 SNP-binary types, indicating that flaA typing can be unreliable for revealing epidemiological linkage. Comparison of the data with data from a fully typed set of isolates associated with human infection revealed that abundant lineages in the chicken isolates that were also found in the human isolates belonged to clonal complex (CC) -21 and CC-353, with the usually rare C-353 member ST-524 being especially abundant in the chicken collection. The chicken isolates selected to be diverse according to flaA were also diverse according to SNP and binary typing. It was observed that CC-48 was absent in the chicken isolates, despite being very common in Australian human infection isolates, indicating that this may be a major cause of human disease that is not chicken associated.

The essential and non-essential genes of Bovine herpesvirus 1

Bovine herpesvirus 1 (BoHV-1) is an economically important pathogen of cattle associated with respiratory and reproductive disease. To further develop BoHV-1 as a vaccine vector, a study was conducted to identify the essential and non-essential genes required for in vitro viability. Randominsertion mutagenesis utilizing a Tn5 transposition system and targeted gene deletion were employed to construct gene disruption and gene deletion libraries, respectively, of an infectious clone of BoHV-1. Transposon insertion position and confirmation of gene deletion were determined by direct sequencing. The essential or non-essential requirement of either transposed or deleted open reading frames (ORFs) was assessed by transfection of respective BoHV-1 DNA into host cells. Of the 73 recognized ORFs encoded by the BoHV-1 genome, 33 were determined to be essential and 36 to be non-essential for virus viability in cell culture; determining the requirement of the two dual copy ORFs was inconclusive. The majority of ORFs were shown to conform to the in vitro requirements of BoHV-1 homologues encoded by human herpesvirus 1 (HHV-1). However, ORFs encoding glycoprotein K (UL53), regulatory, membrane, tegument and capsid proteins (UL54, UL49.5, UL49, UL35, UL20, UL16 and UL7) were shown to differ in requirement when compared to HHV-1-encoded homologues.

Constitutive modeling of shape memory alloy wire with non-local rate kinetics

A constitutive modeling approach for shape memory alloy (SMA) wire by taking into account the microstructural phase inhomogeneity and the associated solid-solid phase transformation kinetics is reported in this paper. The approach is applicable to general thermomechanical loading. Characterization of various scales in the non-local rate sensitive kinetics is the main focus of this paper. Design of SMA materials and actuators not only involve an optimal exploitation of the hysteresis loops during loading-unloading, but also accounts for fatigue and training cycle identifications. For a successful design of SMA integrated actuator systems, it is essential to include the microstructural inhomogeneity effects and the loading rate dependence of the martensitic evolution, since these factors play predominant role in fatigue. In the proposed formulation, the evolution of new phase is assumed according to Weibull distribution. Fourier transformation and finite difference methods are applied to arrive at the analytical form of two important scaling parameters. The ratio of these scaling parameters is of the order of 10(6) for stress-free temperature-induced transformation and 10(4) for stress-induced transformation. These scaling parameters are used in order to study the effect of microstructural variation on the thermo-mechanical force and interface driving force. It is observed that the interface driving force is significant during the evolution. Increase in the slopes of the transformation start and end regions in the stress-strain hysteresis loop is observed for mechanical loading with higher rates.

Enzyme-catalysed non-oxidative decarboxylation of aromatic acids: I.Purification and spectroscopic properties of 2,3 dihydroxybenzoic acid decarboxylase from Image Image

In order to understand the molecular mechanism of non-oxidative decarboxylation of aromatic acids observed in microbial systems, 2,3 dihydroxybenzoic acid (DHBA) decarboxylase from Image Image was purified to homogeneity by affinity chromatography. The enzyme (Mr 120 kDa) had four identical subunits (28 kDa each) and was specific for DHBA. It had a pH optimum of 5.2 and Km was 0.34mM. The decarboxylation did not require any cofactors, nor did the enzyme had any pyruvoyl group at the active site. The carboxyl group and hydroxyl group in the Image -position were required for activity. The preliminary spectroscopic properties of the enzyme are also reported.

Non-linear resonance in strings under narrow band random excitation, part I: Planar response and stability

Non-linear planar response of a string to planar narrow band random excitation is investigated in this paper. A response equation for the mean square deflection σ2 is obtained under a single mode approximation by using the equivalent linearization technique. It is shown that the response is triple valued, as in the case of harmonic excitation, if the centre frequency of excitation Ω lies in a certain specified range. The triple valued response occurs only if the excitation bandwidth β is smaller than a critical value βcrit which is a monotonically increasing function of the intensity of excitation. An approximate method of investigating the almost sure asymptotic stability of the solution is presented and regions of instability in the Ω-σ2 plane have been charted. It is shown that planar response can become unstable either due to an unbounded growth of the in-plane component of motion or due to a spontaneous appearance of an out-of-plane component.

Cortical processing of speech and non-speech sounds in adults and newborns

Comprehension of a complex acoustic signal - speech - is vital for human communication, with numerous brain processes required to convert the acoustics into an intelligible message. In four studies in the present thesis, cortical correlates for different stages of speech processing in a mature linguistic system of adults were investigated. In two further studies, developmental aspects of cortical specialisation and its plasticity in adults were examined. In the present studies, electroencephalographic (EEG) and magnetoencephalographic (MEG) recordings of the mismatch negativity (MMN) response elicited by changes in repetitive unattended auditory events and the phonological mismatch negativity (PMN) response elicited by unexpected speech sounds in attended speech inputs served as the main indicators of cortical processes. Changes in speech sounds elicited the MMNm, the magnetic equivalent of the electric MMN, that differed in generator loci and strength from those elicited by comparable changes in non-speech sounds, suggesting intra- and interhemispheric specialisation in the processing of speech and non-speech sounds at an early automatic processing level. This neuronal specialisation for the mother tongue was also reflected in the more efficient formation of stimulus representations in auditory sensory memory for typical native-language speech sounds compared with those formed for unfamiliar, non-prototype speech sounds and simple tones. Further, adding a speech or non-speech sound context to syllable changes was found to modulate the MMNm strength differently in the left and right hemispheres. Following the acoustic-phonetic processing of speech input, phonological effort related to the selection of possible lexical (word) candidates was linked with distinct left-hemisphere neuronal populations. In summary, the results suggest functional specialisation in the neuronal substrates underlying different levels of speech processing. Subsequently, plasticity of the brain's mature linguistic system was investigated in adults, in whom representations for an aurally-mediated communication system, Morse code, were found to develop within the same hemisphere where representations for the native-language speech sounds were already located. Finally, recording and localization of the MMNm response to changes in speech sounds was successfully accomplished in newborn infants, encouraging future MEG investigations on, for example, the state of neuronal specialisation at birth.

Cortical processing of speech and non-speech sounds in autism and Asperger syndrome

Autism and Asperger syndrome (AS) are neurodevelopmental disorders characterised by deficient social and communication skills, as well as restricted, repetitive patterns of behaviour. The language development in individuals with autism is significantly delayed and deficient, whereas in individuals with AS, the structural aspects of language develop quite normally. Both groups, however, have semantic-pragmatic language deficits. The present thesis investigated auditory processing in individuals with autism and AS. In particular, the discrimination of and orienting to speech and non-speech sounds was studied, as well as the abstraction of invariant sound features from speech-sound input. Altogether five studies were conducted with auditory event-related brain potentials (ERP); two studies also included a behavioural sound-identification task. In three studies, the subjects were children with autism, in one study children with AS, and in one study adults with AS. In children with autism, even the early stages of sound encoding were deficient. In addition, these children had altered sound-discrimination processes characterised by enhanced spectral but deficient temporal discrimination. The enhanced pitch discrimination may partly explain the auditory hypersensitivity common in autism, and it may compromise the filtering of relevant auditory information from irrelevant information. Indeed, it was found that when sound discrimination required abstracting invariant features from varying input, children with autism maintained their superiority in pitch processing, but lost it in vowel processing. Finally, involuntary orienting to sound changes was deficient in children with autism in particular with respect to speech sounds. This finding is in agreement with previous studies on autism suggesting deficits in orienting to socially relevant stimuli. In contrast to children with autism, the early stages of sound encoding were fairly unimpaired in children with AS. However, sound discrimination and orienting were rather similarly altered in these children as in those with autism, suggesting correspondences in the auditory phenotype in these two disorders which belong to the same continuum. Unlike children with AS, adults with AS showed enhanced processing of duration changes, suggesting developmental changes in auditory processing in this disorder.

Modelling predicts positive and negative interactions between three Australian tropical tree species in monoculture and binary mixture

Computer modelling promises to be an important tool for analysing and predicting interactions between trees within mixed species forest plantations. This study explored the use of an individual-based mechanistic model as a predictive tool for designing mixed species plantations of Australian tropical trees. The `spatially explicit individually based-forest simulator' (SeXI-FS) modelling system was used to describe the spatial interaction of individual tree crowns within a binary mixed-species experiment. The three-dimensional model was developed and verified with field data from three forest tree species grown in tropical Australia. The model predicted the interactions within monocultures and binary mixtures of Flindersia brayleyana, Eucalyptus pellita and Elaeocarpus grandis, accounting for an average of 42% of the growth variation exhibited by species in different treatments. The model requires only structural dimensions and shade tolerance as species parameters. By modelling interactions in existing tree mixtures, the model predicted both increases and reductions in the growth of mixtures (up to +/-50% of stem volume at 7 years) compared to monocultures. This modelling approach may be useful for designing mixed tree plantations.

Electron attachment in binary mixtures of electronegative and buffer gases

The ratio of the electron attachment coefficient eta to the gas pressure p (reduced to 0 degrees C) evaluated from the Townsend current growth curves in binary mixtures of electronegative gases (SF6, CCl2F2, CO2) and buffer gases (N2, Ar, air) clearly indicate that the eta /p ratios do not scale as the partial pressure of electronegative gas in the mixture. Extensive calculations carried out using data experimentally obtained have shown that the attachment coefficient of the mixture eta mix can be expressed as eta mix= eta (1-exp- beta F/(100-F)) where eta is the attachment coefficient of the 100% electronegative gas, F is the percentage of the electronegative gas in the mixture and beta is a constant. The results of this analysis explain to a high degree of accuracy the data obtained in various mixtures and are in very good agreement with the data deduced by Itoh and co-workers (1980) using the Boltzmann equation method.