Oligo-Not Only for Silencing: Overlooked Potential for Multidirectional Action in Plants.

Oligo technology is a low-cost and easy-to-implement method for direct manipulation of gene activity. The major advantage of this method is that gene expression can be changed without requiring stable transformation. Oligo technology is mainly used for animal cells. However, the use of oligos in plants seems to be even easier. The oligo effect could be similar to that induced by endogenous miRNAs. In general, the action of exogenously introduced nucleic acids (Oligo) can be divided into a direct interaction with nucleic acids (genomic DNA, hnRNA, transcript) and an indirect interaction via the induction of processes regulating gene expression (at the transcriptional and translational levels) involving regulatory proteins using endogenous cellular mechanisms. Presumed mechanisms of oligonucleotides' action in plant cells (including differences from animal cells) are described in this review. Basic principles of oligo action in plants that allow bidirectional changes in gene activity and even those that lead to heritable epigenetic changes in gene expression are presented. The effect of oligos is related to the target sequence at which they are directed. This paper also compares different delivery methods and provides a quick guide to using IT tools to help design oligonucleotides.

Influence of Basalt Aggregate Crushing Technology on Its Geometrical Properties-Preliminary Studies.

The use of mineral aggregates is related to the increasing demand in construction, railway and road infrastructures. However, mineral aggregates can appear to be of variable quality, directly affecting their suitability for respective earthwork applications. Since the production of mineral aggregates should ensure the standardized, high-quality requirements of the final product, rock-crushing mechanisms should be investigated in a detailed manner. In this context, the aim of the present study is to evaluate and analyze the geometric parameters of basalt aggregates as a result of several rock comminution processes. Basalt aggregates from two deposits in Poland were used in the study. The samples are differentiated regarding both lithological variances, mineral composition as well as the host rock's tuff content. The rock comminution processes were conducted using two types of crushers, namely the laboratory-scale jaw and cone crushers. The feed for crushing was designed based on the original geometric grain composition and the separated feed in the form of flaky and non-flaky particles. The crushability test results demonstrated that the interparticle compression in the jaw crusher resulted in finer products compared to the one in the cone crusher. It was also observed that the flakiness and shape indexes decreased after crushing, both in the feed with the original geometric composition of the grains and those with flaky and non-flaky particles. Nevertheless, a higher flakiness index was obtained after the crushing of non-flaky particles and a lower one after the crushing of flaky particles. The flakiness index for grains below 16 mm after the crushing process was less than 10%, which indicates a more favorable result compared to the original feed. In addition, it was shown that flaky and non-cubical particles were accumulated in the finest (below 8 mm) and coarsest (above 20 mm) fractions in jaw and cone crushing processes, receiving flakiness and shape indexes ranging up to 80-100%. Finally, it was also observed that the lithological variances of the feed material have a significant impact on the particle size distribution of the product. More profoundly, basalt aggregates with a higher tuff content and weathering degree have a higher degree of crushing. The present study, in this context, provides accurate and satisfying information on understanding the crushing mechanisms of two important crushing equipment as well as their rock-crusher interactions.

Evaluation of the Structure and Geometric Properties of Crushed Igneous Rock Aggregates.

The aim of this publication is to analyze the influence of rock mineral composition and rock geometric properties on the quality of crushed aggregates, from the perspective of selecting an adequate aggregate production technology. This research is based on samples of crushed aggregates from plants processing igneous rocks from four different igneous deposits. In the case of the geometric properties, shape and flakiness indexes were identified and subsequently analyzed along with particle size distribution. The performed tests allowed a conclusion that the shape of the particle is influenced by the mineral composition and size distribution. The grain size analysis demonstrated that flaky and non-cubical particles concentrate in the finest grain fractions, and the least variable shape index is observed for basalt aggregate. Some problems were also observed to exist in relation to the classification of grain shape. In the literature, the notions of regular and irregular grains seem to be used interchangeably with the notions of flaky and non-flaky grains. The performed tests show that flaky grains do not necessarily have to be non-cubical and vice versa. Therefore, this article proposes an approach in which the applied technique is precisely explained and the shape of grains is described with four notions: cubical, non-cubical, flaky, and non-flaky. The article also finally concludes that the next step in the research on selecting an optimal production technology of high-quality aggregates should be to analyze the selection of the fragmentation process while also characterizing the geometric properties of the aggregates.

Wear and Fragmentation Resistance of Mineral Aggregates-A Review of Micro-Deval and Los Angeles Tests.

The aim of this article is to present the current knowledge and experiences related to wear and fragmentation resistance tests and to indicate those of their aspects that require further research. For this purpose, a review of the literature was performed. Results show that tests of resistance to wear (the MDE/DS test) and fragmentation (the LA test) are performed worldwide according to different standards (and thus following different test methods), which prevents a comparison of the obtained results. Comparative research into the MDE/DS and LA tests indicates that the MDE/DS test is more effective. The disadvantage of both tests lies in the dimension range of the aggregate. In addition, the use of steel balls in the LA test may not reflect the actual influence that the internal properties of the material have on the fragmentation process. A final review of the available knowledge allowed the formulation of proposals regarding further research directions, such as proposed changes of test methods, extensive analysis, and selection of optimal dimensions for tested aggregates, analysis of short-term and long-term tests, as well as extensive research into and an analysis of the impact of crushing on the physical, mechanical, and geometric properties of aggregates.

Small is beautiful: low activity alpha and gamma sources for small-scale radiation protection research experiments.

PURPOSE: Uncertainties regarding the magnitude of health effects following exposure to low doses of ionizing radiation remain a matter of concern both for professionals and for the public. There is consensus within the international radiation research community that more research is required on biological effects of radiation doses below 100 mGy applied at low dose rates. Moreover, there is a demand for increasing education and training of future radiation researchers and regulators. Research, education and training is primarily carried out at universities but university-based radiation research is often hampered by limited access to radiation sources. The aim of the present report is to describe small and cost-effective low activity gamma and alpha sources that can easily be installed and used in university laboratories. METHODS AND RESULTS: A gamma radiation source was made from an euxenite-(Y) rock (Y,Ca,Ce,U,Th)(Nb,Ta,Ti)2O6) that was found in an abandoned mine in Sweden. It allows exposing cells grown in culture dishes to radiation at a dose rate of 50 µGy/h and lower. Three alpha sources were custom-made and yield a dose rate of 1 mGy/h each. The construction, dosimetry and cellular effects of the sources are described. CONCLUSIONS: We hope that the report will stimulate research and training activities in the low dose field by facilitating access to radiation sources.

Joint inhibition of mitochondrial complex IV and alternative oxidase by genetic or chemical means represses chloroplast transcription in Arabidopsis.

Changes in the functional state of mitochondria have profound effects on other cellular compartments. Genome-wide expression analysis of Arabidopsisrps10 mutants with an RNAi-silenced expression of mitoribosomal S10 protein has revealed extensive transcriptional reprogramming. A meta-analysis comparing expression datasets of 25 mitochondrial perturbations showed a high similarity of the aox1a:rpoTmp mutant, which is defective in the alternative oxidase (AOX1a) and dual-targeted mitochondrial and plastid RNA polymerase (RPOTmp), to rps10. Both rps10 and aox1a:rpoTmp showed a significantly decreased electron flux through both the cytochrome and the alternative respiratory pathways, and a markedly decreased the expression of nuclear-encoded components of the chloroplast transcription machinery. In line with this, a decreased level of plastid transcripts was observed in rps10 and aox1a:rpoTmp, which was reflected in a reduced rate of chloroplast transcription. Chemical treatment of wild-type seedlings with respiratory inhibitors showed that only simultaneous and direct inhibition of complex IV and AOX activity decreased the level of plastid transcripts. Taken together, both chemical and genetic studies show that the limitation of the activity of two mitochondrial terminal oxidases, complex IV and AOX, negatively impacts chloroplast transcription. Salicylic acid and oxygen are discussed as putative mediators of the signalling pathway between mitochondria, nucleus and chloroplasts. This article is part of the theme issue 'Retrograde signalling from endosymbiotic organelles'.

Deficiency of mitoribosomal S10 protein affects translation and splicing in Arabidopsis mitochondria.

The ribosome is not only a protein-making machine, but also a regulatory element in protein synthesis. This view is supported by our earlier data showing that Arabidopsis mitoribosomes altered due to the silencing of the nuclear RPS10 gene encoding mitochondrial ribosomal protein S10 differentially translate mitochondrial transcripts compared with the wild-type. Here, we used ribosome profiling to determine the contribution of transcriptional and translational control in the regulation of protein synthesis in rps10 mitochondria compared with the wild-type ones. Oxidative phosphorylation system proteins are preferentially synthesized in wild-type mitochondria but this feature is lost in the mutant. The rps10 mitoribosomes show slightly reduced translation efficiency of most respiration-related proteins and at the same time markedly more efficiently synthesize ribosomal proteins and MatR and TatC proteins. The mitoribosomes deficient in S10 protein protect shorter transcript fragments which exhibit a weaker 3-nt periodicity compared with the wild-type. The decrease in the triplet periodicity is particularly drastic for genes containing introns. Notably, splicing is considerably less effective in the mutant, indicating an unexpected link between the deficiency of S10 and mitochondrial splicing. Thus, a shortage of the mitoribosomal S10 protein has wide-ranging consequences on mitochondrial gene expression.

[Ribosome profiling as an innovative tool to study the process of protein synthesis]. / Profilowanie rybosomów jako innowacyjne narzedzie do badania procesu syntezy bialek.

The ribosome profiling approach (Ribo-seq) is currently the most effective method to study the protein synthesis in vivo. This technique relies on sequencing of ribosome protected mRNA fragments (so-called ribosomal footprints) allowing to indicate the exact positions of ribosomes on transcripts. Advanced bioinformatic analysis of Ribo-seq data enables selection of ribosomal footprints originated from translating ribosomes, providing information about authentic translational status of mRNA. Here, authors present principles of ribosome profiling method with special attention to basic experimental and bioinformatics strategies important for obtaining satisfactory results. Review includes examples of applications of ribosome profiling technique in various biological systems, giving the significant insight into the translation process and its regulation.

Freeware tool for analysing numbers and sizes of cell colonies.

The clonogenic cell survival assay is a basic method to study the cytotoxic effect of radiation and chemical toxins. In large experimental setups, counting of colonies by eye is tiresome and prone to bias. Moreover, it is often interesting to quantify the size of individual colonies. Such analyses are largely facilitated by computerised image analysis systems. Although a number of such systems exist, they all focus on enumerating colonies and not on analysing the colony size. We have developed a new software package for both counting colonies and plotting their size distributions. The software called count and Plot HIstograms of Colony Size (countPHICS) consists of two parts: (1) a macro written for ImageJ which analyses computerised images of cell culture dishes or 6-well plates, counts colonies, estimates their size and saves the results in a text file; (2) a program written with QT Creator which reads the text file, plots histograms of colony size distribution and fits the best function. The full program is freely available at: http://www.fuw.edu.pl/~bbrzozow/FizMed/countPHICS.html . In conclusion, our new publically available software will facilitate colony counting and provide additional information on the colony growth rate, which is relevant especially for radiosensitisation studies.

Biological effects of mixed-ion beams. Part 2: The relative biological effectiveness of CHO-K1 cells irradiated by mixed- and single-ion beams.

The relative biological effectiveness (RBE) values were determined for single- and mixed-ion beams containing carbon and oxygen ions. The CHO-K1 cells were irradiated with beams with the linear energy transfer (LET) values of 236-300 and 461-470 keV/µm for 12C and 16O ions, respectively. The RBE was estimated as a function of dose, survival fraction (SF) and LET. The SF was not affected by varying contributions of the constituent ions to the total mixed dose. The RBE has the same value for single-ion exposures with ions with LET 300 (12C) and 470 keV/µm (16O).

Biological effects of mixed-ion beams. Part 1: Effect of irradiation of the CHO-K1 cells with a mixed-ion beam containing the carbon and oxygen ions.

Carbon and oxygen ions were accelerated simultaneously to estimate the effect of irradiation of living cells with the two different ions. This mixed ion beam was used to irradiate the CHO-K1 cells, and a survival test was performed. The type of the effect of the mixed ion beam on the cells was determined with the isobologram method, whereby survival curves for irradiations with individual ion beams were also used. An additive effect of irradiation with the two ions was found.

Investigation of the bystander effect in CHO-K1 cells.

AIM: Investigation of the bystander effect in Chinese Hamster Ovary cells (CHO-K1) co-cultured with cells irradiated in the dose range of 0.1-4 Gy of high LET 12C ions and X-rays. BACKGROUND: The radiobiological effects of charged heavy particles on a cellular or molecular level are of fundamental importance in the field of biomedical applications, especially in hadron therapy and space radiation biology. MATERIALS AND METHODS: A heavy ion 12C beam from the Heavy Ion Laboratory of the University of Warsaw (HIL) was used to irradiate CHO-K1 cells. Cells were seeded in Petri dishes specially designed for irradiation purposes. Immediately after irradiation, cells were transferred into transwell culture insert dishes to enable co-culture of irradiated and non-irradiated cells. Cells from the membrane and well shared the medium but could not touch each other. To study bystander effects, a clonogenic survival assay was performed. RESULTS: The survival fraction of cells co-cultured with cells irradiated with 12C ions and X-rays was not reduced. CONCLUSIONS: The bystander effect was not observed in these studies.

The influence of active exercise in low positions on the functional condition of the lumbar-sacral segment in patients with discopathy.

BACKGROUND: Pain in the lower segments of the spine is among the most frequent symptoms in industrialized countries. Injuries to intervertebral discs are the cause of this kind of discomfort in 90% of cases. The factors promoting the disease are: physical activity limitation, prolonged sitting position, overweight and bad movement stereotypes. New methods of treating sacral pain ignore the aspect of weakening the muscle force and do not introduce active exercise to the program of rehabilitation. OBJECTIVES: The aim of the work was to describe the influence of active exercise in low positions on the functional condition of patients with L-S segment discopathy. MATERIAL AND METHODS: The examination group consisted of 20 patients, including 17 women and 3 men. The examination was conducted twice, before and after a two-week long series of rehabilitation. The examined patients practiced a 20-minute exercise program for 10 days. The subjective part of the examination referred to pain discomfort felt by the patients and existing difficulties in performing everyday activities. The objective part included the measurement of movement range of the lumbar segment with the use of Schober's test, finger-to-floor test and spine rotation in the sitting position. RESULTS: It was shown that intervertebral disc disease may lead to spine flexibility limitation and to pain occurrence. CONCLUSIONS: Practicing active exercise in low positions significantly improves the movement range and body posture and it reduces pain in the lower segments of the spine. Moreover, the patient's functional abilities are improved while performing everyday activities.

Discopathy of the lumbar-sacral segment and its influence on sexual dysfunction.

BACKGROUND: Intervertebral disc disease is a widespread medical and social problem. Degeneration of intervertebral discs can lead to disc disease, commonly known as discopathy. One of the consequences of discopathy is pressure on the spinal cord or nerve roots that supply the genitals and sexual centers located in the core. In addition, the accompanying pain and limitation of mobility can lead to the occurrence of sexual dysfunction. OBJECTIVES: The goal of the study was to ascertain the influence of discopathy in the lumbosacral (L-S) segment on the occurrence of sexual dysfunction. MATERIAL AND METHODS: The study involved 50 hospitalized patients with discopathy in the L-S segment were asked to complete a specially prepared questionnaire (11 questions). The goal of the survey was to compare the patients' satisfaction with their sex life before and after the disease. The questions were constructed in a way that excluded other indicators that could affect their sexual activity, i.e.: bad moods, bad family relations, or a lack of sexual activity due to age or the lack of a partner. RESULTS: Discopathy in the lumbar-sacral segment has an influence on sexual activity. A decrease in the assessment of satisfaction with one's sex life can be observed among patients with discopathy. CONCLUSIONS: The pain and neurological symptoms associated with intervertebral disc disease reduce the patients' satisfaction with their sex lives. Patients in the group surveyed noted a change in sexual performance, often resulting in passivity, discouragement, weakness or a complete lack of interest in sex. The disorders also affect the emotional state. The patients also noted a significant decrease in physical activity.

The primary study on influence of fitness camps on rehabilitation efficiency of full laryngectomy patients.

The objective of this study was to estimate the efficiency of exercise driven rehabilitation procedure after laryngectomy. A retrospective review of case notes from the Ludwig Rydygier Hospital, Bydgoszcz, Poland archives was performed. The setting was the Rehabilitation Unit in Department of Occupational Therapy and Rehabilitation of Collegium Medicum, Nicolas Copernicus University, Poland. Thirty male laryngectomy patients with no signs of recurrence were analyzed using modified Harvard Step Test. Also, t-test, Wilcoxon u-paired test and Friedman analysis of variance analyses were performed. A significant increase in the level of physical fitness was observed. The test results showed high effectiveness of rehabilitation camps in respect to the improvement in both physical efficiency and physical exertion tolerance.