DNA sequencing remains one of the most important problems in molecular and computational biology. One of the methods used for this purpose is sequencing by hybridization. In this approach usually DNA chips composed of a full library of oligonucleotides of a given length are used, but in principle it is possible to use another types of chips. Isothermic DNA chips, being one of them, when used for sequencing may reduce hybridization error rate. However, it was not clear if a number of errors following from subsequence repetitions is also reduced in this case. In this paper a method for estimating resolving power of isothermic DNA chips is described which allows for a comparison of such chips and the classical ones. The analysis of the resolving power shows that the probability of sequencing errors caused by subsequence repetitions is greater in the case of isothermic chips in comparison to their classical counterparts of a similar cardinality. This result suggests that isothermic chips should be chosen carefully since in some cases they may not give better results than the classical ones.
The Bulletin of the Polish Academy of Sciences: Technical Sciences (Bull.Pol. Ac.: Tech.) is published bimonthly by the Division IV Engineering Sciences of the Polish Academy of Sciences, since the beginning of the existence of the PAS in 1952. The journal is peer‐reviewed and is published both in printed and electronic form. It is established for the publication of original high quality papers from multidisciplinary Engineering sciences with the following topics preferred: Artificial and Computational Intelligence, Biomedical Engineering and Biotechnology, Civil Engineering, Control, Informatics and Robotics, Electronics, Telecommunication and Optoelectronics, Mechanical and Aeronautical Engineering, Thermodynamics, Material Science and Nanotechnology, Power Systems and Power Electronics. Journal Metrics: JCR Impact Factor 2018: 1.361, 5 Year Impact Factor: 1.323, SCImago Journal Rank (SJR) 2017: 0.319, Source Normalized Impact per Paper (SNIP) 2017: 1.005, CiteScore 2017: 1.27, The Polish Ministry of Science and Higher Education 2017: 25 points. Abbreviations/Acronym: Journal citation: Bull. Pol. Ac.: Tech., ISO: Bull. Pol. Acad. Sci.-Tech. Sci., JCR Abbrev: B POL ACAD SCI-TECH Acronym in the Editorial System: BPASTS.
In the paper, the problem of isothermic DNA sequencing by hybridization, without any errors in its input data, is presented and an exact polynomial-time algorithm solving the problem is described. The correctness of the algorithm is con.rmed by an enumerative proof.
The subject of the numerical investigation is an ellipsoidal head with a central (axis-symmetrical) nozzle. The nozzle is loaded by axial load force. The ellipsoidal head is under axial-symmetrical compression load. The numerical FEM model is elaborated. The calculation will provide the critical loads and equilibrium paths for the sample head.. The investigation will measure the influence of the diameter of the nozzle on the critical state of the ellipsoidal head.
The eurybathic isopod species Chelator insignis shows a wide distribution south of Iceland. We analysed 51 specimens from shelf (213–305 m depth), slope (885–891 m and 1380–1390 m depth) and deep−sea habitats (2750 m) south of Iceland with different DNA markers. A fragment of the mitochondrial cytochrome c oxidase subunit I gene (COI) was studied for 47 specimens, 16S was studied for 36 specimens, and a fragment for the 18S rRNA gene could be amplified for 11 specimens. For the COI data, specimens clustered into five distinct lineages each separated by ³ 20% uncorrected pairwise distances. Both the mitochondrial 16S and the nuclear 18S sequence data further support this deep divergence, suggesting the presence of overlooked species inside the nominal C. insignis . Populations on the shelf occurring east and west of the Reykjanes Ridge were genetically identical suggesting that this ridge is not a barrier to gene flow. However, populations from different depth ranges differed substantially. Our multi−gene analysis suggests that the newly found species likely have more narrow vertical distribution ranges and highlights a possible role of bathymetry in speciation processes.
Field and laboratory protocols that originally led to the success of published studies have previously been only briefly laid out in the methods sections of scientific publications. For the sake of repeatability, we regard the details of the methodology that allowed broad−range DNA studies on deep−sea isopods too valuable to be neglected. Here, a com− prehensive summary of protocols for the retrieval of the samples, fixation on board research vessels, PCR amplification and cycle sequencing of altogether six loci (three mitochondrial and three nuclear) is provided. These were adapted from previous protocols and developed especially for asellote Isopoda from deep−sea samples but have been successfully used in some other peracarids as well. In total, about 2300 specimens of isopods, 100 amphipods and 300 tanaids were sequenced mainly for COI and 16S and partly for the other markers. Although we did not set up an experimental design, we were able to analyze amplification and sequencing success of different methods on 16S and compare success rates for COI and 16S. The primer pair 16S SF/SR was generally reliable and led to better results than universal primers in all studied Janiroidea, except Munnopsidae and Dendrotionidae. The widely applied universal primers for the barcoding region of COI are problematic to use in deep−sea isopods with a success rate of 45–79% varying with family. To improve this, we recommend the development of taxon−specific primers.
Dissipative Particle Dynamics (DPD) is a simulation method at mesoscopic scales that bridges the gap between molecular dynamics and continuum hydrodynamics. It can simulate efficiently complex liquids and dense suspensions using only a few thousands of virtual particles and at speed-up factors of more than one hundred thousands compared to Molecular Dynamics. Lowes approach provides a powerful alternative to the usual DPD integrating schemes. Here, we demonstrate the details and potential of Lowes scheme. We compute viscosity, diffusivity and Schmidt number values and we present comparison of wormlike chain models under shear with experimental and Brownian Dynamics results for ll-phage DNA.
The study of liquid crystalline assemblies, with an emphasis on biological phenomena, is now accessible using newly developed microdevices integrated with X-ray analysis capability. Many biological systems can be described in terms of gradients, mixing, and confinement, all of which can be mimicked with the use of appropriate microfluidic designs. The use of hydrodynamic focusing creates well-defined mixing conditions that vary depending on parameters such as device geometry, and can be quantified with finite element modelling.We describe experiments in which geometry and strain rate induce finite changes in liquid crystalline orientation. We also demonstrate the online supramolecular assembly of lipoplexes. The measurement of lipoplex orientation as a function of flow velocity allows us to record a relaxation process of the lipoplexes, as evidenced by a remarkable 4-fold azimuthal symmetry. All of these processes are accessible due to the intentional integration of design elements in the microdevices.
This report describes the isolation and characterization of bacterial isolates that produce anti−microbial compounds from one of the South Shetland Islands, King George Is − land, Antarctica. Of a total 2465 bacterial isolates recovered from the soil samples, six (BG5, MTC3, WEK1, WEA1, MA2 and CG21) demonstrated inhibitory effects on the growth of one or more Gram−negative or Gram−positive indicator foodborne pathogens ( i.e. Escherichia coli 0157:H7, Salmonella spp., Klebsiella pneumoniae , Enterobacter cloacae , Vibrio parahaemolyticus and Bacillus cereus ). Upon examination of their 16S rRNA sequences and biochemical profiles, the six Antarctic bacterial isolates were identified as Gram−negative Pedobacter cryoconitis (BG5), Pseudomonas migulae (WEK1), P. corrugata (WEA1) and Pseudomonas spp. (MTC3, MA2, and CG21). While inhibitors produced by strains BG5, MTC3 and CG21 were sensitive to protease treatment, those produced by strains WEK1, WEA1, and MA2 were insensitive to catalase, lipase, a −amylase, and protease enzymes. In addtion, the six Antarctic bacterial isolates appeared to be resistant to multiple antibiotics.
Aeromonas hydrophila is a valuable indicator of the quality of water polluted by sewage and pathogens that pose a risk for humans and cold-blooded animals, including fi sh. The main aim of this research was to evaluate anthropogenic pollution of river water based on genetic diversity of 82 A. hydrophila strains by means of RAPD, semi-random AP-PCR (ISJ) and the rep-BOX conservative repeats test. Genetic diversity of A. hydrophila was HT = 0.28 (SD = 0.02) for all DNA markers (RAPD, semi random and rep-BOX). None of the analyzed electrophoretic patterns was identical, implying that there were many sources of strain transmission. The presence of genes for aerolysin (aerA), hemolysin (ahh1) and the cytotoxic enzyme complex (AHCYTOGEN) was verifi ed for all tested strains, and drug resistance patterns for tetracycline, enrofl oxacin and erythromycin were determined. The most diverse A. hydrophila strains isolated from river water were susceptible to enrofl oxacine (HS = 0.27), whereas less diverse strains were susceptible to erythromycin (HS = 0.24). The presence of the multidrug resistance marker (ISJ4-25; 1100 bp locus) in the examined strains (resistant to three analyzed drugs) indicates that intensive fi sh cultivation affects the microbiological quality of river water.
Silver nanoparticles (AgNPs) are widely used in numerous industries and areas of daily life, mainly as antimicrobial agents. The particles size is very important, but still not suffi ciently recognized parameter infl uencing the toxicity of nanosilver. The aim of this study was to investigate the cytotoxic effects of AgNPs with different particle size (~ 10, 40 and 100 nm). The study was conducted on both reproductive and pulmonary cells (CHO-9, 15P-1 and RAW264.7). We tested the effects of AgNPs on cell viability, cell membrane integrity, mitochondrial metabolic activity, lipid peroxidation, total oxidative and antioxidative status of cells and oxidative DNA damage. All kinds of AgNPs showed strong cytotoxic activity at low concentrations (2÷13 μg/ml), and caused an overproduction of reactive oxygen species (ROS) at concentrations lower than cytotoxic ones. The ROS being formed in the cells induced oxidative damage of DNA in alkaline comet assay. The most toxic was AgNPs<10 nm. The results indicate that the silver nanoparticles, especially less than 10 nm, may be harmful to the organisms. Therefore, risk should be considered when using nanosilver preparations and provide appropriate protective measures when they are applied.
We analyzed DNA damage, mitotic activity and polyploidization in Crepis capillaris callus cells during short- and long-term in vitro culture, and the influence of plant growth regulators on these processes. Changes in the concentration of growth regulators altered the stability of callus. The level of DNA damage was highly dependent on the growth regulator composition of the medium. Cytokinin at high concentrations damaged DNA in the absence of auxin. Short- and long-term callus differed in sensitivity to growth regulators. Mitotic activity changed when callus was transferred to medium with modified growth regulators. Callus cell nuclear DNA content increased with age and in response to plant growth regulators. Hormones played a role in the genetic changes in C. capillaris callus culture. We demonstrated the usefulness of C. capillaris callus culture as a model for analyzing the effect of culture conditions, including plant growth regulators, on genetic stability.
Intraspecific changes in genome size and chromosome number lead to divergence and species evolution. Heavy metals disturb the cell cycle and cause mutations. Areas contaminated by heavy metals (metalliferous sites) are places where microevolutionary processes accelerate: very often only a few generations are enough for a new genotype to arise. This study, which continues our long-term research on Viola tricolor (Violaceae), a species occurring on both metalliferous (Zn, Pb, Cd, Cu) and non-metalliferous soils in Western and Central Europe, is aimed at determining the influence of environments polluted with heavy metals on genome size and karyological variability. The genome size of V. tricolor ranged from 3.801 to 4.203 pg, but the differences between metallicolous and non-metallicolous populations were not statistically significant. Altered chromosome numbers were significantly more frequent in material from the polluted sites than from the non-polluted sites (43% versus 28%). Besides the standard chromosome number (2n = 26), aneuploid cells with lower (2n = 18-25) or higher (2n = 27, 28) chromosome numbers were found in plants from both types of site, but polyploid (2n = 42) cells were observed only in plants from the metalliferous locality. The lack of correlation between chromosome variability in root meristematic cells and genome size estimated from peduncle cells can be attributed to elimination of somatic mutations in generative meristem, producing chromosome-stable non-meristematic tissues in the peduncle.
Nanodiagonastic methods in plant pathology are used for enhancing detection and identification of different plant pathogens and toxigenic fungi. Improvement of the specificity and efficiency of the polymerase chain reaction (PCR) by using some nanoparticles is emerging as a new area of research. In the current research, silver, zinc, and gold nanoparticles were used to increase the yield of DNA for two plant pathogenic fungi including soil-borne fungus Rhizoctonia solani and toxigenic fungus Alternaria alternata. Gold nanoparticles combined with zinc and silver nanoparticles enhanced both DNA yield and PCR products compared to DNA extraction methods with ALB buffer, sodium dodecyl sulfate, ALBfree from protinase K, ZnNPs and AgNPs. Also, by using ZnNPs and AgNPs the DNA yield was enhanced and the sensitivity of random amplified polymorphic DNA (RAPD) PCR products was increased. Application of nanomaterials in the PCR reaction could increase or decrease the PCR product according to the type of applied nanometal and the type of DNA template. Additions of AuNPs to PCR mix increased both sensitivity and specificity for PCR products of the tested fungi. Thus, the use of these highly stable, commercially available and inexpensive inorganic nano reagents open new opportunities for improving the specificity and sensitivity of PCR amplicon, which is the most important standard method in molecular plant pathology and mycotoxicology.
The excessive use of pesticides is a problem in most parts of the world today because of their broad and unspecific target range that is considerably harmful. The accumulation of several chemical insecticide residues based on chlorpyrifos-methyl, organochlorine, different isomers of HCH, DDT etc., in Triticum aestivum L. plants can be dangerous. Hence, there is an urgent need to develop potential and safer alternative measures. Wheat (Triticum aestivum L.) is a major cereal crop grown and used for food, animal feed, beverages and furniture accessories in most parts of the world. It also serves as a host to various insect pests. Our previous studies showed the insecticidal potency and specificity of short ssDNA oligonucleotides from the inhibitor of apoptosis (IAP-2 and IAP-3) genes of Lymantria dispar multicapsid nuclear polyhedrosis virus (LdMNPV) against gypsy moth (L. dispar) larvae, a possible insect pest of non-host plants like wheat. Consequently, the present study analyzes the effects of ssDNA oligonucleotides used as DNA insecticides on wheat (T. aestivum) plant biomass, plant organs and some biochemical parameters as a marker of the safety margin on non-target organisms. The results obtained on plant biomass showed that groups treated with ssDNA oligonucleotides at concentrations of 0.01 pmol · μl−1, 0.1 pmol · μl−1 and 1 pmol · μl−1 varied in comparison with the control group, but remained harmless to plant growth and development, while the treatment concentration of 0.001 pmol · μl−1 did not affect the plant biomass. The glucose, protein and phosphorous biochemical parameters, analyzed after 21 days, showed that the ssDNA oligonucleotides used were equally safe. The data obtained for the plant organs (leaves and root lengths) indicate that the phenomenon of DNA insecticides can be further studied and developed for plant protection while improving the growth of plant organs even for a non-target organism such as wheat T. aestivum plants.
The results presented here are twofold. First, a heuristic algorithm is proposed which, through removing some unnecessary arcs from a digraph, tends to reduce it into an adjoint and thus simplifies the search for a Hamiltonian cycle. Second, a heuristic algorithm for DNA sequence assembly is proposed, which uses a graph model of the problem instance, and incorporates two independent procedures of reducing the set of arcs - one of them being the former algorithm. Finally, results of tests of the assembly algorithm on parts of chromosome arm 2R of Drosophila melanogaster are presented.
The work presented in the paper concerns a very important problem of searching for string alignments. The authors show that the problem of a genome pattern alignment could be interpreted and defined as a measuring task, where the distance between two (or more) patterns is investigated. The problem originates from modern computation biology. Hardware-based implementations have been driving out software solutions in the field recently. The complex programmable devices have become very commonly applied. The paper introduces a new, optimized approach based on the Smith-Waterman dynamic programming algorithm. The original algorithm is modified in order to simplify data-path processing and take advantage of the properties offered by FPGA devices. The results obtained with the proposed methodology allow to reduce the size of the functional block and radically speed up the processing time. This approach is very competitive compared with other related works.
We used artificial hybridization to study the crossability of the noble fir (Abies procera) with Manchurian fir (A. holophylla) and Caucasian fir (A. nordmanniana), and found compatibility between A. procera of North American origin and the Asian species A. holophylla as evidenced by the 14% fraction of filled seeds obtained in A. procera × A. holophylla crossing. Crossing of A. procera with the Mediterranean species A. nordmanniana failed completely, producing only empty seeds.
Hladnikia pastinacifolia RCHB., a narrow endemic, has an extremely restricted distribution in Trnovski gozd (Slovenia), despite the presence of many sites with suitable habitats. We compared the morphological traits of plants from different populations and habitats. The overall pattern showed that the smallest plants, with low fruit number, are found on Èaven (locus classicus or type locality); the largest individuals, with high fruit number, grow in the Golobnica gorge. As judged by plant size and seed set, the optimal habitats are screes. We used RAPD markers to estimate genetic variation between and within populations, as well as between and within the northern and the southern parts of the distribution area. Hladnikia showed only a low level of RAPD variability. AMOVA partitioned the majority of genetic diversity within selected populations. The low genetic differentiation between populations and their genetic depauperation indicates survival in situ, since the Trnovski gozd plateau most likely was a nunatak region in the southern Prealps during Pleistocene glaciations. Later range expansion of extant populations was limited by poor seed dispersal. We also analyzed the cpDNA trnL-F intergenic spacer to check whether the sequence is useful for studying the phylogenetic relationships of Hladnikia within the family Apiaceae (Umbelliferae). Our results support the assertion that H. pastinacifolia is an old taxon.
Effective control of Leptinotarsa decemlineata remains an urgent problem for agriculture worldwide. Minimization of the use of non-selective neonicotinoid insecticides, such as thiomethoxam, is an actual vector of development of potato cultivation. In this rapid communication, we show the prospect of the topical use of short unmodified antisense fragment of L. decemlineata CYP6B gene as a DNA insecticide. Investigated parameters, namely, number of larvae per plant, aboveground biomass, yield and number of potatoes produced per plant indicate the possibility of this post-genomic approach as a safe and effective method of L. decemlineata control.
To retain our cultural identity in the modern world and sensibly think about the future, we need to thoroughly study the past,” says Prof. Marek Figlerowicz from the PAS Institute of Bioorganic Chemistry, who leads the project “The Dynasty and Society of Piast-Era Poland in the Light of Integrated Historical, Anthropological, and Genomic Research.”
Sperm-mediated gene transfer (SMGT) is based on the ability of spermatozoa to bind exoge- nous DNA and transfer it into oocytes by fertilization. However, SMGT is still undergoing opti- mization to improve its efficiency to produce transgenic animals. The acrosome reaction is neces- sary for spermatozoa to carry the exogenous DNA into oocytes. In this study, the effect of the acrosome reaction on the efficiency of spermatozoa carrying exogenous DNA was evalua- ted. The results showed that the efficiency of the acrosome reaction was significantly higher (p<0.05) after incubation with 50 μmol/L progesterone compared to incubation without proges- terone. It was significantly higher (p<0.05) in the 20, 40, and 60 min of progesterone treatment groups than in the 0 min treatment group. The spermatozoa were further incubated with cyanine dye Cy5 labeled DNA (Cy5-DNA) for 30 min at 37°C, and positive fluorescence signals were detected after the acrosome reaction was induced by progesterone at concentrations of 0 and 50 μmol/L for 40 min. The percentage of positive Cy5-DNA signals in spermatozoa was 96.61±2.06% and 97.51±2.03% following exposure to 0 and 50 μmol/L progesterone, respective- ly. The percentage of partial spermatozoa heads observed following combination with Cy5-DNA was 39.73±3.03% and 56.88±3.12% following exposure to 0 and 50 μmol/L progesterone, respec- tively. The ratio of positively stained spermatozoa combined with exogenous DNA showed no reduction after the acrosome reaction. These results suggest that the acrosome reaction might not be the key factor affecting the efficiency of SMGT.
This year we are celebrating 150 anniversary of the discovery of DNA by Friedrich Miescher. His finding initiated a series of discoveries that allowed to depicts life's most famous molecule with novel features with considerable biological interest. In this article we recall the biggest mile stones of 150-year history of DNA and present the context and meaning of several key observations that have brought us closer to understanding DNA. 150 years ago, people had no idea that DNA existed, and they certainly hadn’t heard of DNA structure and sequencing. We now know that DNA is a dynamic, tortuous coil, constantly shuffling and unwinding. Today DNA is all around us, in a physical sense and in a cultural sense. It is really part of our culture. We will discuss also the little known facts, often overlooked in similar discussions. We will focus particularly on Professor Richard Altmann's from Iława, whose contribution to knowledge about nucleic acids is significant, although not well recognized so far.