Base specific binding of deoxyguanylate and deoxycytidylate antibodies to double stranded DNA

Antibodies raised in rabbits against daoxyguanylate and daoxycytidylate bind to 3H-(lambda) double stranded DNA and the binding is base specific. The concentrations of antibody populations that bind to double stranded DNA are much less than those binding to denatured DNA. Due to their low concentrations, these antibodies ware not detected in earlier studies. These antibodies are expected to be useful to probe the conformational flexibilities of double stranded DNAs.

Assessment of an environmentally friendly, semi-pelagic fish trawl

Minimising catches of non-target animals in a trawl fishery reduces the impact on a marine community and may help to sustain the fishery resource in the long term. Hence the desirability for trawls that minimise impacts on non-target species while maintaining catches of target species. This study resulted from a need to further develop easily handled, semi-pelagic style trawls for Australia's Northern Fish Trawl Fishery. In November 1993 we compared catches from three differently rigged versions of a demersal wing trawl: one fished in a standard demersal configuration with its footrope on the sea bed, and two fished semi-pelagically, with their footropes raised to either 0.4-0.5 or 0.8-0.9 m above the sea bed. At two sites in the northeast Gulf of Carpentaria, each trawl type was used on the same combination of sites, grids within sites and times of day. Catches of the main target species (Lutjanus malabaricus and Lutjanus erythropterus) by the three trawl types were not significantly different. However, the mean catches of both these species and of other commercially important snappers, were highest in the semi-pelagic trawl raised 0.4-0.5 m above the sea bed. This increase could be due to a larger trawl spread or to the whole rig fishing higher in the water column. Of the 107 species of fishes analysed, 61 were caught in greater abundance in the demersal trawl. Seven species were caught more effectively in the semi-pelagic trawl with the footrope 0.4-0.5 m above the substrate; none was caught most effectively with the footrope set at 0.8-0.9 m. Epibenthic byproduct species (squid and Thenus orientalis), fish bycatch, sponges and other epibenthic invertebrates were also caught in lower numbers in the semi-pelagic trawls. The semi-pelagic trawls convincingly caught less (in both numbers and biomass) of the unwanted species which are normally discarded. Semi-pelagic fish trawls of the types tested would be suitable for Australia's Northern Fish Trawl Fishery and probably other demersal trawl fisheries that would benefit from the conservation of non-target epibenthic communities.

A towed instrument package for fisheries research in great barrier reef waters

A tethered remote instrument package (TRIP) has been developed for biological surveys over Queensland's continental shelf and slope. The present system, evolved from an earlier sled configuration, is suspended above the sea bed and towed at low speeds. Survey information is collected through video and film cameras while instrument and environmental variables are handled by a minicomputer. The operator was able to "fly" the instrument package above the substrate by using an altitude echosounder, forward-looking sonar and real-time television viewing. Unwanted movements of the viewing system were stabilized through a gyro-controlled camera-head panning system. the hydrodynamic drag of the umbilical presented a major control problem which could be overcome only by a reduction in towing speed. Despite the constraints of towing a device such as this through the coral reef environment, the package performed well during a recent biological survey where it was worked at 50% of its 350 m design depth.

Laboratory investigation on the effects of overburden pressure, water, and time on slaking induced material property degradation of coal mine spoil

In open-cut strip mining, waste material is placed in-pit to minimise operational mine costs. Slope failures in these spoil piles pose a significant safety risk to personnel, along with a financial risk from loss of equipment and scheduling delays. It has been observed that most spoil pile failures occur when the pit has been previously filled with water and then subsequently dewatered. The failures are often initiated at the base of spoil piles where the material can undergo significant slaking (disintegration) over time due to overburden pressure and water saturation. It is important to understand how the mechanical properties of base spoil material are affected by slaking when designing safe spoil pile slope angles, heights, and dewatering rates. In this study, fresh spoil material collected from a coal mine in Brown Basin Coalfield of Queensland, Australia was subjected to high overburden pressure (0 – 900 kPa) under saturated condition and maintained over a period of time (0 – 6 months) allowing the material to slake. To create the above conditions, laboratory designed pressure chambers were used. Once a spoil sample was slaked under certain overburden pressure over a period of time, it was tested for classification, permeability, and strength properties. Results of this testing program suggested that the slaking of saturated coal mine spoil increase with overburden pressure and the time duration over which the overburden pressure was maintained. Further, it was observed that shear strength and permeability of spoil decreased with increase in spoil slaking.

Base-base interactions in nucleic acids containing A-T base pairs: Structure of poly[d(A-T)]

The Watson-Crick type of base pairing is considered to be mandatory for the formation of duplex DNA. However, conformational calculations carried out in our laboratory, have shown that some combinations of backbone torsion angles and sugar pucker lead to duplexes with Hoogsteen type of base pairing also. Here we present the results of energy calculations performed on A-T containing doublet sequences in the D-form with both Hoogsteen and Watson-Crick type of base pairing and the 3 viable models for the A-T containing polynucleotide duplex poly[d(A-T)].

Base material characterisation of spoil piles at BMA coal mines

This project was an initiation to investigate slaking induced properties detrition of spoil pile materials with overburden pressure and time. The changes in the material properties over time are important parameters that control the behaviour and performance of the piles. The time dependent mechanical and hydraulic properties reported together with mineralogical changes. One chamber designed to apply slaking in the laboratory and geotechnical investigation conducted to fulfil the objective of this project.

An exploratory study on the commercialisation of heat pump-fluidised bed drying technology

Fluidised bed-heat pump drying technology offers distinctive advantages over the existing drying technology employed in the Australian food industry. However, as is the case with many other examples of innovations that have had clear relative advantages, the rates of adoption and diffusion of this technology have been very slow. "Why does this happen?" is the theme of this research study that has been undertaken with an objective to analyse a range of issues related to the market acceptance of technological innovations. The research methodology included the development of an integrated conceptual model based on an extensive review of literature in the areas of innovation diffusion, technology transfer and industrial marketing. Three major determinants associated with the market acceptance of innovations were identified as the characteristics of the innovation, adopter information processing capability and the influence of the innovation supplier on the adoption process. This was followed by a study involving more than 30 small and medium enterprises identified as potential adopters of fluidised bed-heat pump drying technology in the Australian food industry. The findings revealed that judgment was the key evaluation strategy employed by potential adopters in the particular industry sector. Further, it was evidenced that the innovations were evaluated against a predetermined criteria covering a range of aspects with emphasis on a selected set of attributes of the innovation. Implication of these findings on the commercialisation of fluidised bed-heat pump drying technology was established, and a series of recommendations was made to the innovation supplier (DPI/FT) enabling it to develop an effective commercialisation strategy.

Studies On Thermal-Decomposition Of Double-Base Propellants

The scanning thermogram of a block sample of a double-base propellant shows a shoulder around 200°C which is not observed in a powder sample of the sample propellant. The heat of decomposition was also found to be different In the two cases. Product analysis and activation energy calculations show that nitroglycerine un dergoes decomposition in the block sample, whereas it vaporizes in the powder sample.

Effect of surface-applied treatments on the above-ground performance of simulated timber joinery

We examined the effect of surface-applied treatments on the above-ground decay resistance of the tenon of mortice-and-tenon timber joints designed to simulate joinery that is exposed to the weather. Joints made from untreated radiata pine, Douglas-fir, brush box, spotted gum and copper-chrome-arsenic (CCA) treated radiata pine were exposed to the weather for 9 y on above-ground racks at five sites throughout eastern Australia. Results indicate (1) a poorly maintained external paint film generally accelerated decay, (2) a brush coat of water-repellent preservative inside the joints often extended serviceability (in some cases by a factor of up to seven times that of untreated joints) and (3) the level of protection provided by a coat of primer applied inside the joint varied and in most cases was not as effective as the water-repellent preservative treatment.

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.

Hydrodynamic pressure on a dam with a periodically corrugated reservoir bed

The problem of determining the hydrodynamic pressure, caused by earthquake forces, on a dam with a vertical upstream face and a periodically corrugated reservoir bed is solved approximately by employing a Fourier cosine transform technique to the linearised equations of inviscid and incompressible flow. A particular case of the present problem giving rise to results valid for dams with flat reservoir beds is shown to produce known results as a check of the method used.

"Ei vittu, mennään röökille" : tutkimus sitaattien tehtävistä ja tekemisestä kaunokirjallis-journalistisissa lehtijutuissa

This research deals with direct speech quotations in magazine articles through two questions: As my major research question, I study the functions of speech quotations based on a data consisting of six literary-journalistic magazine articles. My minor research question builds on the fact that there is no absolute relation between the sound waves of the spoken language and the graphemes of the written one. Hence, I study the general thoughts on how utterances should be arranged in the written form based on a large review of literature and textbooks on journalistic writing as well as interviews I have made with magazine writers and editors, and the Council of Mass Media in Finland. To support my main research questions, I also examine the reference system of the Finnish language, define the aspects of the literary-journalistic article and study vernacular cues in written speech quotations. FUNCTIONS OF QUOTATIONS. I demonstrate the results of my analysis with a six-pointed apparatus. It is a continuum which extends from the structural level of text, all the way through the explicit functions, to the implicit functions of the quotation. The explicit functions deal with the question of what is the content, whereas the implicit ones base mainly on the question how the content is presented. 1. The speech quotation is an distinctive element in the structure of the magazine article. Thereby it creates a rhythm for the text, such as episodes, paragraphs and clauses. 2. All stories are told through a plot, and in magazine articles, the speech quotations are one of the narrative elements that propel the plot forward. 3. The speech quotations create and intensify the location written in the story. This location can be a physical one but also a social one, in which case it describes the atmosphere and mood in the physical environment and of the story characters. 4. The quotations enhance the plausibility of the facts and assumptions presented in the article, and moreover, when a text is placed between quotation marks, the reader can be assured that the text has been reproduced in the authentic verbatim way. 5. Speech quotations tell about the speaker's unique way of using language and the first-hand experiences of the person quoted. 6. The sixth function of speech quotations is probably the most essential one: the quotations characterize the quoted speaker. In other words, in addition to the propositional content of the utterance, the way in which it has been said transmits a lot of the speaker's character (e.g. nature, generation, behaviour, education, attitudes etc.). It is important to notice, that these six functions of my speech quotation apparatus do not exlude one another. It means that every speech quotation basically includes all of the functions discussed above. However, in practice one or more of them have a principal role, while the others play a subsidiary role. HOW TO MAKE QUOTATIONS? It is not suprising that the field of journalism (textbooks, literature and interviews) holds heterogeneous and unestablished thoughts on how the spoken language should be arranged in written quotations, which is my minor research question. However, the most frequent and distinctive aspects can be depicted in a couple of words: serve the reader and respect the target person. Very common advice on how to arrange the quotations is − firstly, to delete such vernacular cues (e.g. repetitions and ”expletives”) that are common in spoken communication, but purposeless in the written language. − secondly, to complete the phonetic word forms of the spoken language into a more reader-friendly form (esim. punanen → punainen, 'red'), and − thirdly, to enhance the independence of clauses from the (authentic) context and to toughen reciprocal links between them. According to the knowledge of the journalistic field, utterances recorded in different points in time of an interview or a data-collecting session can be transferred as consecutive quotations or even merged together. However, if there is any temporal-spatial location written in the story, the dialogue of the story characters should also be situated in an authentic context – chronologically in the right place in the continuum of the events. To summarize, the way in which the utterances should be arranged into written speech quotations is always situationally-specific − and it is strongly based on the author's discretion.

Packed bed bioreactor for the isolation and expansion of placental-derived Mesenchymal Stromal Cells

Large numbers of Mesenchymal stem/stromal cells (MSCs) are required for clinical relevant doses to treat a number of diseases. To economically manufacture these MSCs, an automated bioreactor system will be required. Herein we describe the development of a scalable closed-system, packed bed bioreactor suitable for large-scale MSCs expansion. The packed bed was formed from fused polystyrene pellets that were air plasma treated to endow them with a surface chemistry similar to traditional tissue culture plastic. The packed bed was encased within a gas permeable shell to decouple the medium nutrient supply and gas exchange. This enabled a significant reduction in medium flow rates, thus reducing shear and even facilitating single pass medium exchange. The system was optimised in a small-scale bioreactor format (160 cm2) with murine-derived green fluorescent protein-expressing MSCs, and then scaled-up to a 2800 cm2 format. We demonstrated that placental derived MSCs could be isolated directly within the bioreactor and subsequently expanded. Our results demonstrate that the closed system large-scale packed bed bioreactor is an effective and scalable tool for large-scale isolation and expansion of MSCs.

Bed Shear from Velocity Profiles: A New Approach

A new binary law of velocity distribution has been developed to describe the velocity profile for the entire flow region. The law is a combination of logarithmic law, valid in the wall (inner) region, and parabolic law, valid in the core (outer) region of the flow. The validity of the law has been established based on earlier data on flat plates, rough and smooth pipes and experimental data obtained from rigid-walled open channels with plane sand beds. A procedure of estimating bed shear stress from the proposed law of velocity distribution using the measured velocity profile has been evolved. Bed shear estimates made according to this procedure are in agreement with the values obtained from uniform flow analysis in the case of open channel flow over a sediment bed. The proposed method of estimating the bed shear stress from the observed velocity profiles is found to be particularly useful in cases where it is difficult to determine precisely the true bed level, such as in the case of flow over sediment beds.

Stream power criterion and design of sand bed channels at incipient motion

The critical stream power criterion may be used to describe the incipient motion of cohesionless particles of plane sediment beds. The governing equation relating ``critical stream power'' to ``shear Reynolds number'' is developed by using the present experimental data as well as the data from several other sources. Simultaneously, a resistance equation, relating the ``particle Reynolds number'' to the``shear Reynolds number'' is developed for plane sediment beds in wide channels with little or no transport. By making use of these relations, a procedure is developed to design plane sediment beds such that any two of the four design variables, including particle size, energy/friction slope, flow depth, and discharge per unit width in the channel should be known to predict the remaining two variables. Finally, a straightforward design procedure using design tables/design curves and analytical methods is presented to solve six possible design problems.