Estimation Of Fragment Size Research Articles

Assessing RNA integrity by digital RT-PCR: Influence of extraction, storage, and matrices

Abstract The development of high-throughput sequencing has greatly improved our knowledge of microbial diversity in aquatic environments and its evolution in highly diverse ecosystems. Relevant microbial diversity description based on high-throughput sequencing relies on the good quality of the nucleic acid recovered. Indeed, long genetic fragments are more informative for identifying mutation combinations that characterize variants or species in complex samples. This study describes a new analytical method based on digital Polymerase Chain Reaction (PCR) partitioning technology for assessing the fragmentation of nucleic acid and more specifically viral RNA. This method allows us to overcome limits associated with hydrolysis probe-based assay by focusing on the distance between different amplicons, and not, as usual, on the size of amplicons. RNA integrity can thus be determined as a new fragmentation index, the so-called Fragment size 50. The application of this method has provided information on issues that are inherent in environmental analyses, such as the storage impact of raw samples or extracted RNA, extraction methods, and the nature of the sample on the integrity of viral RNA. Finally, the estimation of fragment size by digital PCR (dPCR) showed a very strong similarity with the fragment size sequenced using Oxford Nanopore Technology. In addition to enabling objective improvements in analytical methods, this approach could become a systematic quality control prior to any long-read sequencing, avoiding insufficiently productive sequencing runs or biases in the representativeness of sequenced fragments.

Fragment size distribution and its probability distribution in blasted rock mass in a natural stone quarry

The key objectives in the drilling and blasting design is the determination of a powder factor, explosive weight and distribution in rock mass, as well as some other parameters required to ensure the wanted quality of rock fragmentation by blasting. These objectives have different complexities but their common feature is the probabilistic nature of fragmentation results. An integral distribution function can provide an insight into the probability of yield of certain fragment sizes. This article describes fragment size estimation of blasted rock mass at Mikashevichi granite quarry. Mikashevichi quarry has 10 producing benches mostly 12 m high and uses the blasting method of quarrying. The quarry rock mass is watered, has a hardness factor of 15–20 on Protodyakonov’s scale and belongs to jointing categories III and IV. The multiple-row and short-delay blasting uses nonelectric detonators Iskra manufactured in Russia. The explosive is nitronite E-70. The continuous explosive charges are installed in polypropylene hoses placed in jointed rock mass. The workability of different models of fragment size distribution in rock mass after blasting in evaluation of blasting results in a natural stone quarry is analyzed. The theoretical and applied research and estimation of fragment sizes after blasting in different geological conditions uses various theoretical models, including the most popular gamma-distribution (Pearson type III distribution), Weibull distribution and log-normal distribution. The comparison of the theoretical distributions and in-situ estimates of fragment sizes in blasted rock mass using Pearson’s chi-squared test shows that the best model of fragment size distribution in blasted rock mass for a natural stone quarry is the Weibull distribution.

Lunar Orientale Impact Basin Secondary Craters: Spatial Distribution, Size‐Frequency Distribution, and Estimation of Fragment Size

AbstractSecondary impact craters, features created by projectiles ejected from a primary impact, contain important information about the primary cratering event and the nature and distribution of its ejecta. The Orientale impact basin (D ~ 930 km) is the youngest and the least degraded large impact basin on the Moon and has the most recognizable secondary impact craters. We identified and mapped 2,728 secondary craters in the investigated area of ~1.66 × 107 km2, covering an area from the rim of Orientale to six radii. Secondary crater diameters range from ~2 to 27 km, and the median diameter decreases as distance increases. Secondary craters are concentrated predominantly in the northwest and southwest. The ejecta deposit pattern inferred from secondary crater distribution suggests that the Orientale basin was formed by an oblique impact in which the downrange direction was 240°–265° in azimuth, and the incidence angle was steeper than 20°. The cumulative size‐frequency distribution of mapped secondary craters steepens as diameter increases and is very well approximated with a Weibull distribution with an exponent 1.32. A widely used crater scaling relationship predicts that the fragments that produced the secondary craters were predominantly in ~0.5–2‐km diameter range over the investigated area; the diameter of the largest fragment, however, decreases with increasing distance from Orientale. On the basis of the diameter of the largest secondary crater of Orientale, and other craters and basins, the largest secondary crater of the South Pole‐Aitken basin is estimated to be ~40 km in diameter. We explore the implications of these findings for the evolution of the megaregolith and future sample return missions.

Rock fracturing mechanisms by blasting

Optimizing blast fragmentation and reducing the damage from it are two important research subjects in this field. Detonation and explosive charge induces three sets of tension cracks in the monolith rock. Radial tension cracks are formed under the influence of the pressure wave whose cylindrical propagation induces tension. Along with the explanation of how radial cracks are formed, formulation is given as to how their length can be calculated using laboratory and drill and blast parameters. Cracks subparallel with the free surface (face) are related with amounts of absorbed and recoverable strain energies. The distance between subsequent cracks can be calculated using the results of simple load-unload laboratory tests. Third sets of tension cracks are formed as a result of excessive deformation of the beam or cantilever formed by radial cracks. Once the length of the cracks and the distance between them are known, it is possible to apply these results for estimation of fragment sizes and blasting pattern design.

Energy transform in a brittle fragmentation process and the estimation of fragment size

The dynamic fracture process of a material containing an array of cracks is studied. By symmetry a unit crack body is analyzed, with the material separation behavior described by a linear cohesive law. Exact solutions of the problem are obtained by using Laplace transform, rendering the theoretical expressions for the crack and the boundary stresses, and the energy flux into the crack body during fracture. For a prescribed strainrate, the energy flux is evaluated for different crack spacing. It is found that there exists a preferred crack spacing corresponding to the minimum energy flux, and the value of this spacing is a reasonable estimate of the average fragment size in a natural brittle fragmentation process.

Observations and Studies of NEOs and the SL‐9 Impact at the Purple Mountain Observatory

Annals of the New York Academy of SciencesVolume 822, Issue 1 p. 174-175 Observations and Studies of NEOs and the SL-9 Impact at the Purple Mountain Observatory HEQI ZHANG, HEQI ZHANG Purple Mountain Observatory Academia Sinica Nanjing 210008 Peoples Republic of ChinaSearch for more papers by this authorJIAXIANG ZHANG, JIAXIANG ZHANG Purple Mountain Observatory Academia Sinica Nanjing 210008 Peoples Republic of ChinaSearch for more papers by this authorSICHAO WANG, SICHAO WANG Purple Mountain Observatory Academia Sinica Nanjing 210008 Peoples Republic of ChinaSearch for more papers by this authorQI WANG, QI WANG Purple Mountain Observatory Academia Sinica Nanjing 210008 Peoples Republic of ChinaSearch for more papers by this authorJIEXING YANG, JIEXING YANG Purple Mountain Observatory Academia Sinica Nanjing 210008 Peoples Republic of ChinaSearch for more papers by this author HEQI ZHANG, HEQI ZHANG Purple Mountain Observatory Academia Sinica Nanjing 210008 Peoples Republic of ChinaSearch for more papers by this authorJIAXIANG ZHANG, JIAXIANG ZHANG Purple Mountain Observatory Academia Sinica Nanjing 210008 Peoples Republic of ChinaSearch for more papers by this authorSICHAO WANG, SICHAO WANG Purple Mountain Observatory Academia Sinica Nanjing 210008 Peoples Republic of ChinaSearch for more papers by this authorQI WANG, QI WANG Purple Mountain Observatory Academia Sinica Nanjing 210008 Peoples Republic of ChinaSearch for more papers by this authorJIEXING YANG, JIEXING YANG Purple Mountain Observatory Academia Sinica Nanjing 210008 Peoples Republic of ChinaSearch for more papers by this author First published: 17 December 2006 https://doi.org/10.1111/j.1749-6632.1997.tb48341.xRead the full textAboutRelatedInformationPDFPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessClose modalShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL No abstract is available for this article. Volume822, Issue1Near‐Earth Objects: The United Nations ConferenceMay 1997Pages 174-175 RelatedInformation RecommendedShoemaker-Levy 9 and Plume-forming Collisions on EarthMARK B. E. BOSLOUGH, DAVID A. CRAWFORD, Annals of the New York Academy of SciencesComet Shoemaker-Levy 9 Fragment Size Estimates: How Big Was the Parent Body?DAVID A. CRAWFORD, Annals of the New York Academy of SciencesMigration of Jupiter‐Family Comets and Resonant Asteroids to Near‐Earth SpaceS I IPATOV, J C MATHER, Annals of the New York Academy of SciencesLagrange L4/L5 Points and the Origin of Our Moon and Saturn's Moons and RingsJ RICHARD GOTT, Annals of the New York Academy of SciencesHomes for Extraterrestrial LifeDAVID W. LATHAM, Annals of the New York Academy of Sciences

Comet Shoemaker‐Levy 9 Fragment Size Estimates: How Big Was the Parent Body?a

ABSTRACT: The impact of Comet Shoemaker‐Levy 9 on Jupiter in July, 1994 was the largest, most energetic impact event on a planet ever witnessed. Because it broke up during a close encounter with Jupiter in 1992, it was bright enough to be discovered more than a year prior to impact, allowing the scientific community an unprecedented opportunity to assess the effects such an event would have. Many excellent observations were made from Earth‐based telescopes, the Hubble Space Telescope (HST), and the Galileo spacecraft en route to Jupiter. In this paper, these observations are used in conjunction with computational simulations performed with the CTH shock‐physics hydrocode to determine the sizes of the fifteen fragments that made discernible impact features on the planet. To do this, CTH was equipped with a radiative ablation model and a postprocessing radiative ray‐trace capability that enabled light‐flux predictions (often called the impact flash) for the viewing geometries of Galileo and ground‐based observers. The five events recorded by Galileo were calibrated to give fragment size estimates. Compared against ground‐based and HST observations, these estimates were extended using a least‐squares analysis to assess the impacts of the remaining ten fragments. Some of the largest impacts (L, G, and K) were greater that 1 km in diameter, but the density of the fragments was low, about 0.25 g/cm3. The volume of the combined fifteen fragments would make a sphere 1.8 km in diameter. Assuming a prebreakup density of 0.5 g/cm3, the parent body of Shoemaker‐Levy 9 had a probable diameter of 1.4 km. The total kinetic energy of all the impacts was equivalent to the explosive yield of 300 Gigatons of TNT.

Numerical modeling of Shoemaker‐Levy 9 impacts as a framework for interpreting observations

Computational models of the impacts of Comet Shoemaker‐Levy 9 onto Jupiter may provide the best framework by which the observational data can be interpreted. Among the observations that have already been at least partially explained in a way that appears to be consistent with the impact models are: the sources and timings of multiple flashes observed from Earth, the temperatures and durations of the single flashes observed from the Galileo spacecraft, and the asymmetry of the plumes and ejecta patterns observed by the Hubble Space Telescope. Further modeling subsequent to the impacts has shown that (contrary to our pre‐impact expectations) fireball trajectory data do not provide strong constraints on either fragment mass or maximum penetration depth. Instead, it is the cross‐sectional area of the fragment (or swarm of sub‐fragments) at the time of impact that determines the ejection velocity and trajectory of the fireball. The observation of seemingly consistent plume heights, coupled with this computational result, suggests that SL‐9 fragments were loosely‐bound “rubble piles,” possibly with widely varying masses, that in most cases dispersed to about the same diameter (2.0±0.5 km) by the time they reached the Jovian atmosphere. After more data become available and correlated, and more simulations are performed, we expect that fragment size estimates will become more precise.

PFGE analysis of the rice genome: estimation of fragment sizes, organization of repetitive sequences and relationships between genetic and physical distances

Pulsed-field gel electrophoresis (PFGE) has been applied to analyze the rice nuclear genome. Probing 56 RFLP probes selected from the 12 rice chromosomes to PFGE blots of nine rare-cutting restriction enzymes revealed that there are relatively high numbers of 'rare-cutting' restriction sites in the rice genome. The average sizes of restriction fragments detected by single-copy probes are smaller than 200 kb for all of the rare-cutting restriction enzymes examined. Sizes of fragments detected by repetitive probes are variable, depending on the probes analyzed. By using PFGE, a tandemly repeated sequence, Os48, was found to be tightly linked to telomeric tandem repeats but not physically linked to r5s genes with which sequence homology had been observed. Relationships between genetic and physical distances have been established for three different chromosomal segments. In these regions 1 cm corresponds to ca. 260 kb on average. Analysis of a cluster of RFLP markers on chromosome 3 revealed that genetically clustered RFLP markers are also physically closely linked, suggesting that clustering of genetic markers may result in part from uneven distribution of single-copy sequences.

Correlated physical and genetic map of the Bradyrhizobium japonicum 110 genome.

We describe a compilation of 79 known genes of Bradyrhizobium japonicum 110, 63 of which were placed on a correlated physical and genetic map of the chromosome. Genomic DNA was restricted with enzymes PacI, PmeI, and SwaI, which yielded two, five, and nine fragments, respectively. Linkage of some of the fragments was established by performing Southern blot hybridization experiments. For probes we used isolated, labelled fragments that were produced either by PmeI or by SwaI. Genes were mapped on individual restriction fragments by performing gene-directed mutagenesis. The principle of this method was to introduce recognition sites for all three restriction enzymes mentioned above into or very near the desired gene loci. Pulsed-field gel electrophoresis of restricted mutant DNA then resulted in an altered fragment pattern compared with wild-type DNA. This allowed us to identify overlapping fragments and to determine the exact position of any selected gene locus. The technique was limited only by the accuracy of the fragment size estimates. After linkage of all of the restriction fragments we concluded that the B. japonicum genome consists of a single, circular chromosome that is approximately 8,700 kb long. Genes directly concerned with nodulation and symbiotic nitrogen fixation are clustered in a chromosomal section that is about 380 kb long.

Spatial normalization of one-dimensional electrophoretic gel images

A strategy for using processed, digitized images of one-dimensional electrophoretic gels to facilitate the analysis of large sets of overlapping clones is described. The images are acquired from fluorescently stained gels or from transilluminated gel photographs using a cooled, solid-state charge-coupled device camera. By employing sets of bands in the size-standard lanes as reference points, all the gel images are spatially normalized to a common reference template. After normalization, lane images from different gels can be compared as though the gels had been electrophoresed resed under identical, uniform-field conditions. Applications of this procedure to the analysis of a large set of overlapping λ clones from chromosome VII of Saccharomyces cerevisiae and to the estimation of fragment sizes are illustrated.

Pulsed field gradient electrophoresis of DNA digested in agarose allows the sizing of the large duplication unit of a surface antigen gene in trypanosomes

Intact chromosome-sized DNA molecules from eukaryotes may be prepared by performing lysis and enzymic deproteinization on cells embedded in agarose [Schwartz and Cantor, Cell 37 (1984), 67–75]. Here we show that DNA prepared by this method may be cut with restriction enzymes, or modified with site-specific methylases and cut by DpnI. As the DNA remains incorporated in the gel matrix, shear degradation of large fragments is avoided. The fragments can then be sized by conventional or pulsed field gradient gel electrophoresis. Phage λ genomic oligomers are used as size markers, allowing the estimation of fragment sizes up to about 1200 kb. We apply these techniques to show that activation of the telomeric gene encoding variant surface antigen 1.3 in Trypanosoma brucei strain 427, involves the duplication of a DNA segment that starts between 29 and 42 kb upstream of the gene and to assign a chromosomal fragment into which the duplicated 1.3 gene may have transposed.