sRNA Profiler: A User-Focused Interface for Small RNA Mapping and Profiling

Viroids are circular, highly structured, single-stranded, non-coding RNA pathogens known to infect and cause disease in several plant species. They are known to trigger the host plant’s RNA silencing machinery. The detection of viroid-derived small RNAs (vd-sRNA) in viroid-infected host plants opened a new avenue of study in host–viroid pathogenicity. Since then, several viroid research groups have studied the vd-sRNA retrieved from different host–viroid combinations. Such studies require the segregation of 21- to 24-nucleotide long small RNAs (sRNA) from a deep-sequencing databank, followed by separating the vd-sRNA from any sRNA within this group that showed sequence similarity with either the genomic or the antigenomic strands of the viroid. Such mapped vd-sRNAs are then profiled on both the viroid’s genomic and antigenomic strands for visualization. Although several commercial interfaces are currently available for this purpose, they are all programmed for linear RNA molecules. Hence, viroid researchers must develop a computer program that accommodates the sRNAs derived from the circular viroid genome. This is a laborious process, and consequently, it often creates a bottleneck for biologists. In order to overcome this constraint, and to help the research community in general, in this study, a python-based pattern matching interface was developed so as to be able to both profile and map sRNAs on a circular genome. A “matching tolerance” feature has been included in the program, thus permitting the mapping of the sRNAs derived from the quasi-species. Additionally, the “topology” feature allows the researcher to profile sRNA derived from both linear and circular RNA molecules. The efficiency of the program was tested using previously reported deep-sequencing data obtained from two independent studies. Clearly, this novel software should be a key tool with which to both evaluate the production of sRNA and to profile them on their target RNA species, irrespective of the topology of the target RNA molecule.

Potato spindle tuber viroid infection triggers degradation of chloride channel protein CLC-b-like and Ribosomal protein S3a-like mRNAs in tomato plants

It is well established that viroid derived small RNA (vd-sRNA) induces RNA silencing of endogenous mRNA. However, it remains not clear how exactly viroid infections can lead to severe symptom induction given the fact that fewer vd-sRNAs binding the specific target mRNAs were recovered from the infected plants. To answer this question, the two least expressed (+) and (−) strand vd-sRNAs of potato spindle tuber viroid (PSTVd) binding to both the 3′ UTR and the coding region of tomato mRNAs were analyzed by infecting tomato plants with two variants of PSTVd. As products of these putative target mRNAs are involved in plant phenotype, the effect of this viroid on these genes were analyzed by infecting tomato plants with two variants of PSTVd. The direct interaction between the vd-sRNAs and putative mRNAs was validated by artificial microRNA experiments in a transient expression system and by RNA ligase-mediated rapid amplification of cDNA ends. Parallel analysis of RNA ends of viroid infected plants revealed the widespread cleavage of the target mRNAs in locations other than the vd-sRNA binding site during the viroid infection implying the viroid-infection induced vd-sRNA independent degradation of endogenous mRNAs during viroid infection.

A research model--forecasting incident rates from optimized safety program intervention strategies

INTRODUCTION/PROBLEM: Property damage incidents, workplace injuries, and safety programs designed to prevent them, are expensive aspects of doing business in contemporary industry. The National Safety Council (2002) estimated that workplace injuries cost $146.6 billion per year. Because companies are resource limited, optimizing intervention strategies to decrease incidents with less costly programs can contribute to improved productivity.

METHOD

Systematic data collection methods were employed and the forecasting ability of a time-lag relationship between interventions and incident rates was studied using various statistical methods (an intervention is not expected to have an immediate nor infinitely lasting effect on the incident rate).

RESULTS/SUMMARY

As a follow up to the initial work, researchers developed two models designed to forecast incident rates. One is based on past incident rate performance and the other on the configuration and level of effort applied to the safety and health program. Researchers compared actual incident performance to the prediction capability of each model over 18 months in the forestry operations at an electricity distribution company and found the models to allow accurate prediction of incident rates.

IMPACT ON INDUSTRY

These models potentially have powerful implications as a business-planning tool for human resource allocation and for designing an optimized safety and health intervention program to minimize incidents. Depending on the mathematical relationship, one can determine what interventions, where and how much to apply them, and when to increase or reduce human resource input as determined by the forecasted performance.

Two cases of recovery of kilocurie sources fallen from telegamma units

Recently, two incidents involving the fall of kilocurie sources from telegamma units during repairs occurred in India. In one case it was a 60Co source of activity 222 TBq (6,000 Ci) and in the other case, it was a 137Cs source of activity 75.85 TBq (2,050 Ci). The line of action planned for the recovery of the sources was to cover the sources with large quantities of lead shots sent through a sloping pipe, thereby reducing the exposure rate. Once this was arranged, the workers could go inside for further retrieval action. An aluminium container was designed and positioned over the source drawer and lead shots were poured into this container. The retrieval operation was executed as planned but with slight modifications as necessitated at the sites. The collective effective dose for the recovery of the first source was approximately 0.07 person-sievert (7 person-rem) and for the second one was < 0.01 person-sievert (1 person-rem).

Relevance of radiation penumbra in high-energy photon beam therapy

In external beam therapy, radiation penumbra is one of the factors which hinder the confinement of the dose to tumour volume and cause unnecessary irradiation of the surrounding normal tissues in the penumbral region. In the present work, the magnitudes of radiation penumbras were evaluated for various high-energy X-ray beams and cobalt-60 beams, from their respective isodose charts, at the depth of maximum ionization (dmax) and at the typical tumour centre depth of 10 cm (d10) and for field sizes of 5 x 5 cm2, 10 x 10 cm2 and 15 x 15 cm2. Although the radiation penumbra for high-energy X-ray beams up to 16 MV was found to be smaller in comparison with cobalt-60 beams, at 20 MV and beyond it tends to increase and becomes comparable to that for cobalt-60 beams. In the light of this comparison and the results of some of the cancer treatments with high-energy beams reported by various authors, the relative importance of radiation penumbra and integral dose in the treatment volume is discussed.

Application of the NSD concept in radiotherapy. Limitations due to inaccuracies in clinical dosimetry

Time dose fractionation schemes in radiotherapy have been developed on empirical lines over a period of several years. Ellis proposed the NSD formula to facilitate a meaningful comparison of clinical results from different centres and different fractionation regimes. Recent studies indicate that there is a steep tumour dose response curve which necessitates that the delivered doses must have an accuracy within +/- 5%. The ranges of the variations of the parameters in the NSD formula which still give dose estimates within this accuracy have been studied in this paper. It is concluded that because of the uncertainties involved in dose output calibration and other physical and empirical constants, extreme caution has to be exercised in routinely using the NSD concept and those of TDF, CRE, PT and BIR, which have the NSD concept as their basis.

Analysis of personnel doses from nuclear medicine procedures

With the rapid growth of the use of radiopharmaceuticals for medical diagnostic and therapeutic procedures, radiation protection of personnel has become important. In this paper, the radiation doses of 337 persons in 16 nuclear medicine centers in India are analyzed. In 1976 the average annual dose per person was 0.028 rem. The highest average dose per person per working week was 2.62 mrem. Analysis of the dose records of three major institutions for recent years reveals an increase in the average dose per worker.

Effect of field size on the radiation penumbra and integral dose for telegamma therapy units

Because of the large source size in telegamma therapy units, the boundaries of the radiation beam beyond the collimator are not well defined and a zone of falling dose and resulting penumbra are produced. In general, the collimator design is such that the geometrical penumbra is nearly equal in magnitude to the source diameter. However, the magnitude of the physical or radiation penumbra is influenced by the radiation transmitted through the edge of the collimator, the geometrical penumbra and the scatter from the source and the collimator. In the present study, the variation of radiation penumbra with field size has been investigated for two different makes of telegamma units. It is seen that the radiation penumbra can be as large as 4.8 cm for a 20 X 20 cm field. The effect of such large penumbra on the integral dose is discussed.

Californium-252 line sources: experimental verification of depth dose data using NTA films and dosage tables based on Paterson and Parker rules

Californium-252 promises to be an effective radium substitute in brachytherapy. In certain situations, such as cancer of the uterus, the dose rate near a linear source may be of interest. Paterson and Parker have tabulated the number of milligram hours for various active lengths of radium sources to give 1000 rad at different distances from the centre of the source. This paper presents similar results for Cf-252 (microgram hours to give 1000 rad neutron dose). The paper also reports the results of experimental measurements of neutron depth dose distributions for both single line sources and arrays. Kodak NTA films and a phantom were used for the study. The experimental results are found to agree well with the theoretically predicted results.

Use of tissue-to-air ratio in computation of specific absorbed fraction

This paper describes a new approach for computing specific absorbed fractions that can be used for estimating doses that result from the internal administration of radiopharmaceuticals. This approach uses the concept of the tissue-to-air ratio (TAR) which can either be calculated or experimentally determined for the radionuclides of interest. Good agreement exists between the specific absorbed fraction values obtained using measured and computed values of TAR. This implies that the measured values of TAR can be used to obtain specific absorbed fractions for all radionuclides.

Biologically effective doses from californium-252 intracavitary applications

Californium-252 which emits fission neutrons and gamma rays is being investigated for applications in brachytherapy. From available experimental results, a value of 6.2 had been arrived at as the RBE for cell killing of californium neutrons relative to radium gavva rays for intracavitary applications based on the revised Manchester system of loading. The LET distributions as well as the ratio of neutron to gamma dose-rates have been estimated and are found to remain almost constant in the volume of interest around such applications.