Online exercise for the design and simulation of PCR and PCR-RFLP experiments

[EN] Background: Polymerase Chain Reaction (PCR) and Restriction Fragment Length Polymorphism of PCR products (PCR-RFLP) are extensively used molecular biology techniques. An exercise for the design and simulation of PCR and PCR-RFLP experiments will be a useful educational tool. Findings: An online PCR and PCR-RFLP exercise has been create that requires users to find the target genes,compare them, design primers, search for restriction endonucleases, and finally to simulate the experiment. Each user of the service is randomly assigned a gene from Escherichia coli; to complete the exercise, users must design an experiment capable of distinguishing among E. coli strains. By applying the experimental procedure to all completely sequenced E. coli, a basic understanding of strain comparison and clustering can also be acquired. Comparison of results obtained in different experiments is also very instructive. Conclusions: The exercise is freely available at http://insilico.ehu.es/edu.

Population dynamics of the anchoveta, Cetengraulis mysticetus, in the Gulf of Panama, as determined by tagging experiments

ENGLISH: The anchoveta is the major constituent of the important bait and reduction fisheries of the Gulf of Panama. It is a short-lived species, the great majority of the catch consisting of fish in their first year of life. Fish for reduction are caught chiefly in the Isla Verde area, between Punta Chame and the entrance of the Panama Canal. In 1960 and 1961 anchovetas were tagged with metal internal tags and released in the major areas of occurrence of this species. The tags were recovered from the meal in the reduction plants with magnets. From the 53,380 fish tagged in 1960, 745 tags were returned during the 1960 season, 246 during the 1961 season, and 8 during the 1962 season. From the 113,202 tagged in 1961, 373 tags were returned during the 1961 season and 48 during the 1962 season. Complete catch statistics are available, and length-frequency and length-weight data were used to convert these from pounds to numbers of fish of each year class. The annual survival rate for the fish of the 1959 year class in the Isla Verde area was estimated to be 0.086 by the Chapman-Robson method, 0.102 by the year-class method, and 0.088 by the Jackson positive method. The first method is considered to give the best estimate. Six estimates of the population of fish of the 1959 year class in the Isla Verde area were obtained from the sample tag ratios of six experiments conducted in that area in 1960. The estimates differed due to the temporal decrease in the population, but the downward trend corresponded fairly well to what was expected from the total annual mortality rate. It was estimated that the population of 1959-year class fish was about 818 million on March 8, 1960, and about 70 million on March 8, 1961. As the population of anchovetas decreases during the season the effort increases sufficiently that the catch remains roughly constant. This is described as the "constant absolute catch" type fishery. Of the original population of fish in the Isla Verde area at the beginning of the 1960 season, about 11 per cent were caught and 81 per cent died of natural causes. Evaluation of growth and mortality data demonstrated that beginning the fishery for the youngest age group later than March 8 (the date it began in 1960) would reduce the yield per recruit, while increasing the fishing effort would greatly increase it. Further, it is believed unlikely that increases in the catch in the Isla Verde area alone would noticeably decrease the number of recruits to that area. Therefore there is no foreseeable need for regulation of the fishery. SPANISH: El principal constituyente de la importante pesquería para carnada y para reducción en el Golfo de Panamá es la anchoveta. Es una especie de vida corta cuya pesca, en su mayor parte, está constituida por peces que se encuentran en su primer año de vida. Para la industria de reducción los peces son capturados principalmente en el área de Isla Verde, entre Punta Chame y la entrada del Canal de Panamá. En 1960 y 1961 las anchovetas fueron marcadas con marcas metálicas internas y liberadas en las áreas más importantes en que se encuentra esta especie. Las marcas fueron recobradas de la harina en las plantas de reducción por medio de magnetos. De los 53,380 peces marcados en 1960, fueron devueltas 745 marcas durante la temporada pesquera de 1960, 246 durante la de 1961, y 8 durante la de 1962. De los 113,202 marcados en 1961, 373 marcas fueron devueltas durante la temporada pesquera de 1961 y 48 durante la de 1962. Se dispone de estadísticas completas de captura, y los datos de frecuencia-longitud y de longitud-peso fueron usados para convertir éstos de libras a números de peces de cada clase anual. La tasa anual de supervivencia correspondiente a la clase anual de 1959 en el área de Isla Verde estimó en 0.086 por medio del método Chapman-Robson; en 0.102 por método de la clase anual; y en 0.088 por el método positivo de Jackson. Se considera que el primer método dé la mejor estimación. Seis estimaciones de la población de peces de la clase anual 1959 en el área de Isla Verde fueron obtenidas según la proporción de marcas halladas en las muestras correspondientes a seis experimentos efectuados en aquella área en 1960. Las estimaciones variaron debido a la disminución temporal de la población, pero esta tendencia descendente correspondió bastante bien a lo que se esperaba según la tasa total de mortalidad anual. Se estimó que la población de peces de la clase anual de 1959 era de unos 818 millones el 8 de marzo de 1960, y aproximadamente de unos 70 millones el 8 de marzo de 1961. Conforme a que la población de anchovetas disminuye durante la temporada pesquera, el esfuerzo aumenta lo suficientemente como para que la pesca se mantenga más o menos constante. Este es el tipo de pesquería descrito como de "captura absoluta constante". De la población original de peces en el área de Isla Verde al comienzo de la temporada pesquera de 1960, cerca del 11 por ciento fue capturada y el 81 por ciento murió por causas naturales. La evaluación de los datos del crecimiento mortalidad demostraron que al comenzar la pesquería a explotar grupo de edad más joven en una fecha posterior al 8 de marzo (la fecha en que comenzó en 1960) se reduciría el rendimiento por recluta, mientras que al aumentar el esfuerzo de pesca lo aumentaría considerablemente. Más aún, se cree improbable que el aumento en la pesca en el área de Isla Verde de por sí disminuyera perceptiblemente el número de reclutas en esa área. En consecuencia no se prevé la necesidad de una reglamentación de la pesquería. (PDF contains 172 pages.)

Estimates of the rates of mortality of yellowfin tuna in the Eastern Pacific Ocean derived from tagging experiments

ENGLISH: Tag release and return data for the Baja California and Gulf of Guayaquil areas were selected for this study because substantial numbers of returns resulted from these releases and because the effects of emigration are small in these areas. The returns of tags per unit of fishing effort for several experiments in each area were used to estimate the coefficients of total mortality and shedding. The coefficient of annual natural mortality was estimated to be less than 2.0, which is in agreement with a previous estimate of 0.8, but does not improve upon it. The estimates for the average coefficients of catchability are 2.02 X 10-3 for the Baja California area and 0.67 X 10-3 for the Gulf of Guayaquil area. SPANISH: Se seleccionaron para este estudio algunos da tos de liberación y retorno de marcas en las áreas de Baja California y el Golfo de Guayaquil debido a que cantidades substanciales de retornos resultaron de estas liberaciones y porque los efectos de migración son pequeños en estas áreas. Los retornos de marcas por unidad de esfuerzo de pesca de varios experimentos en cada área fueron empleados para estimar los coeficientes de mortalidad total y desprendimiento. Se estimó que el coeficiente de mortalidad natural anual fue inferior a 2.0, lo que está de acuerdo con una estimación anterior de 0.8, pero no la mejora. Las estimaciones de los coeficientes promedios de capturabilidad son 2.02 X 10-3 en el área de Baja California y 0.67 X 10-3 en el área del Golfo de Guayaquil. (PDF contains 58 pages.)

Migrations of yellowfin and skipjack tuna in the Eastern Pacific Ocean as determined by tagging experiments, 1952-1964

ENGLISH: Totals of 59,547 tagged yellowfin and 90,412 tagged skipjack were released during 1952-1964 throughout the range of the fishery in the eastern Pacific Ocean during that period. Most of the fish were released from commercial baitboats, either on regular fishing trips or on chartered trips to catch fish for tagging. There we re 8,397 yellowfin and 4,381 skipjack returned from these releases. There appear to be two main groups of yellowfin in the eastern Pacific Ocean. There is considerable intermingling among the fish of the two groups, however. The fish of the northern group (west coast of Baja California, Gulf of California, and Revillagigedo Islands) first appear in the Revillagigedo Islands in about April, and migrate north along the Baja California coast during the spring and summer and south along that coast during the fall. Recruits to the southern group (Tres Marias Islands to northern Chile) appear at many points or continuously along most of the coast. The fish which first appear in the northern Panama Bight in April migrate rapidly northwest to Central America and Mexico and south to the Gulf of Guayaquil. There also appear to be two main groups of skipjack in the eastern Pacific Ocean. The fish of the northern group (west coast of Baja California, Gulf of California, and Revillagigedo Islands ) perform about the same migration as do the yellowfin of the same area, but most of the skipjack apparently then migrate to the central Pacific Ocean during the fall and/or winter. Recruits to the southern group (Central America to northern Chile) appear mostly in or near the Panama Bight. The fish which first appear in the northern Panama Bight in April migrate rapidly northwest to Central America and south to the Gulf of Guayaquil. The proportions which migrate in these directions vary considerably from year to year, this perhaps being dependent on differences in the sea-surface temperatures. SPANISH: Durante el período de 1952-1964 se liberó a través de todos los límites de distribución de la pesquería en el Océano Pacífico oriental un total de 59,547 aleta amarilla y 90,412 barriletes marcados. La mayoria de los peces fueron liberados de barcos de carnada comerciales, o en viajes regulares de pesca o en viajes en los que se fletaron los barcos para capturar atunes y marcarlos. De estas líberaciones se recapturaron 8,397 aleta amarilla y 4,381 barriletes. Parece que haya dos grupos principales de aleta amarilla en el Océano Pacífico oriental. Sin embargo, existe una entremezcla considerable entre los peces de los dos grupos. Los peces del grupo septentrional (costa occidental de Baja California, Golfo de California y Islas Revillagigedo) aparecen primero en las Islas Revillagigedo alrededor de abril, y durante la primavera y el verano se desplazan al norte a lo largo de la costa de Baja California y durante el otoño al sur a lo largo de la costa. Los reclutas del grupo meridional (Islas Tres Marias hasta el norte de Chile) aparecen en muchas partes o continuamente a lo largo de la mayoría de la costa. Los peces que aparecen primero en la región septentrional del Panamá Bight en abril se desplazan rápidamente al noroeste a la América Central y México y al sur al Golfo de Guayaquil. Parece también que existen dos grupos principales de barrilete en el Océano Pacífico oriental. Los peces del gr upo septentrional (costa occidental de Baja California, Golfo de California e Islas Revillagigedo ) realizan casi la misma migración que el atún aleta amarilla de la misma área, pero aparentemente la mayor parte del barrilete se desplaza luego al Océano Pacífico central durante el otoño y/o en el invierno. Los reclutas al grupo meridional (América Central al norte de Chile) aparecen en su mayoría en el Panamá Bight o cerca a este lugar. Los peces que aparecen primero en la región septentrional del Panamá Bight en abril se desplazan rápidamente al noroeste a la América Central y al sur al Golfo de Guayaquil. Las proporciones que se desplazan en estas direcciones varían considerablemente de año a año; tal vez esto depende en las diferencias de temperatura de la superficie del mar. (PDF contains 227 pages.)

Migrations of yellowfin tuna in the Eastern Pacific Ocean as determined from tagging experiments initiated during 1968-1974

ENGLISH: Data from tagging experiments initiated during 1968-1974 in the eastern Pacific Ocean were used to study the migrations of yellowfin tuna in that area. The map method, the parallel-area method, and the Jones method were employed in the analyses. The map method gives a useful impression of the distances and directions traveled, but does not express these parameters in quantitative terms. The parallel-area method is particularly useful for determining whether or not there is net movement in particular directions, i.e. inshore-offshore, east-west, or north-south. The first of these is of particular interest, as the incidence of smaller fish is much higher in the catches made inshore than in those made offshore, and it is desirable to know whether this is due to relatively greater abundance or to relatively greater vulnerability of the smaller fish in the inshore areas. If the former were the case an offshore movement of the fish as they grew older would probably be detected. Such a movement was not detected, however, so it appears likely that the differences in the catches of smaller fish in the inshore and offshore areas are due mainly to differences in vulnerability. Few or no east-west or north-south tendencies in the movements of the fish were detected. The Jones method indicates that the movement is not random, but reveals no pronounced directional tendencies. SPANISH: Se emplearon los datos de los experimentos de marcado, iniciados en el Océano Pacífico oriental durante 1968-1974 para estudiar los desplazamientos del atún aleta amarilla en esa zona. En los análisis se emplearon los métodos cartográficos, de las zonas paralelas y de Jones. El método cartográfico ofrece una idea útil sobre la distancia y dirección de los desplazamientos, pero no expresa estos parámetros en términos cuantitativos. El método de las zonas paralelas es particularmente conveniente para determinar si existe o nó un desplazamiento neto en una dirección especial, es decir, hacia la costa-fuera de la costa, este-oeste o norte-sur. El primero de éstos tiene un interés especial, ya que la incidencia de peces más pequeños es muy superior en las capturas realizadas cerca de la costa que en las de mar afuera, y se desea conocer si ésto se debe a la abundancia relativamente superior o a las vulnerabilidad relativamente mayor de los pequeños peces en las zonas costeras. Si el caso fuera el primero, se podría descubrir probablemente un movimiento de los peces mar afuera a medida que crecen. Sin embargo, no se ha descubierto tal movimiento, así que es probable que las diferencias en las capturas de peces pequeños en las zonas costeras y mar afuera se deban principalmente a diferencias en la vulnerabilidad. Se descubrió poca o ninguna tendencia en los peces a desplazarse este-oeste o norte-sur. El método de Jones indica que el movimiento no es aleatorio, pero no revela una tendencia pronunciada a orientarse direccionalmente.

Parallel Fully-Implicit Computation of MHD Acceleration Experiments

A three-dimensional MHD solver is described in the paper. The solver simulates reacting flows with nonequilibrium between translational-rotational, vibrational and electron translational modes. The conservation equations are discretized with implicit time marching and the second-order modified Steger-Warming scheme, and the resulted linear system is solved iteratively with Newton-Krylov-Schwarz method that is implemented by PETSc package. The results of convergence tests are plotted, which show good scalability and convergence around twice faster when compared with the DPLR method. Then five test runs are conducted simulating the experiments done at the NASA Ames MHD channel, and the calculated pressures, temperatures, electrical conductivity, back EMF, load factors and flow accelerations are shown to agree with the experimental data. Our computation shows that the electrical conductivity distribution is not uniform in the powered section of the MHD channel, and that it is important to include Joule heating in order to calculate the correct conductivity and the MHD acceleration.

Some experiments on commercial pond fish culture in the tidal mangrove area of Niger delta of Nigeria

A pilot fish culture project was initiated by Shell Petroleum Development Company of Nigeria Limited in 1981 with specific aims and objectives. Site selection, survey, pond construction method and fish production with regards to experiences gathered and gained, problems and solutions so far obtained are discussed. Trials of freshwater fish species to check their adaptability to brackishwater ponds were carried out and the promising results of the growth rate of these species when compared with the traditional local brackishwater species selected for culture are reported. The extension programme so far carried out is briefly described

Nucleon structure functions from ν_µ-Fe interactions and a study of the valence quark distribution

Data were taken in 1979-80 by the CCFRR high energy neutrino experiment at Fermilab. A total of 150,000 neutrino and 23,000 antineutrino charged current events in the approximate energy range 25 < E_v < 250GeV are measured and analyzed. The structure functions F2 and xF_3 are extracted for three assumptions about σ_L/σ_T:R=0., R=0.1 and R= a QCD based expression. Systematic errors are estimated and their significance is discussed. Comparisons or the X and Q^2 behaviour or the structure functions with results from other experiments are made.

We find that statistical errors currently dominate our knowledge of the valence quark distribution, which is studied in this thesis. xF_3 from different experiments has, within errors and apart from level differences, the same dependence on x and Q^2, except for the HPWF results. The CDHS F_2 shows a clear fall-off at low-x from the CCFRR and EMC results, again apart from level differences which are calculable from cross-sections.

The result for the the GLS rule is found to be 2.83±.15±.09±.10 where the first error is statistical, the second is an overall level error and the third covers the rest of the systematic errors. QCD studies of xF_3 to leading and second order have been done. The QCD evolution of xF_3, which is independent of R and the strange sea, does not depend on the gluon distribution and fits yield

ʌ_(LO) = 88^(+163)_(-78) ^(+113)_(-70) MeV

The systematic errors are smaller than the statistical errors. Second order fits give somewhat different values of ʌ, although α_s (at Q^2_0 = 12.6 GeV^2) is not so different.

A fit using the better determined F_2 in place of xF_3 for x > 0.4 i.e., assuming q = 0 in that region, gives

ʌ_(LO) = 266^(+114)_(-104) ^(+85)_(-79) MeV

Again, the statistical errors are larger than the systematic errors. An attempt to measure R was made and the measurements are described. Utilizing the inequality q(x)≥0 we find that in the region x > .4 R is less than 0.55 at the 90% confidence level.

Searches for new symmetries in pp collisions with the razor kinematic variables at √s = 7 TeV

The construction and LHC phenomenology of the razor variables M_R, an event-by-event indicator of the heavy particle mass scale, and R, a dimensionless variable related to the transverse momentum imbalance of events and missing transverse energy, are presented.  The variables are used  in the analysis of the first proton-proton collisions dataset at CMS  (35 pb^-1) in a search for superpartners of the quarks and gluons, targeting indirect hints of dark matter candidates in the context of supersymmetric theoretical frameworks. The analysis produced the highest sensitivity results for SUSY to date and extended the LHC reach far beyond the previous Tevatron results.  A generalized inclusive search is subsequently presented for new heavy particle pairs produced in √s = 7 TeV proton-proton collisions at the LHC using 4.7±0.1 fb^-1 of integrated luminosity from the second LHC run of 2011.  The selected events are analyzed in the 2D razor-space of M_R and R and the analysis is performed in 12 tiers of all-hadronic, single and double leptons final states in the presence and absence of b-quarks, probing the third generation sector using the event heavy-flavor content.   The search is sensitive to generic supersymmetry models with minimal assumptions about the superpartner decay chains. No excess is observed in the number or shape of event yields relative to Standard Model predictions. Exclusion limits are derived in the CMSSM framework with  gluino masses up to 800 GeV and squark masses up to 1.35 TeV excluded at 95% confidence level, depending on the model parameters. The results are also interpreted for a collection of simplified models, in which gluinos are excluded with masses as large as 1.1 TeV, for small neutralino masses, and the first-two generation squarks, stops and sbottoms are excluded for masses up to about 800, 425 and 400 GeV, respectively.

With the discovery of a new boson by the CMS and ATLAS experiments in the γ-γ and 4 lepton final states, the identity of the putative Higgs candidate must be established through the measurements of its properties. The spin and quantum numbers are of particular importance, and we describe a method for measuring the J^PC of this particle using the observed signal events in the H to ZZ^* to 4 lepton channel developed before the discovery. Adaptations of the razor kinematic variables are introduced for the H to WW^* to 2 lepton/2 neutrino channel, improving the resonance mass resolution and increasing the discovery significance. The prospects for incorporating this channel in an examination of the new boson J^PC is discussed, with indications that this it could provide complementary information to the H to ZZ^* to 4 lepton final state, particularly for measuring CP-violation in these decays.

Discovery of non-zero neutrino mixing angle θ_13 using Daya Bay antineutrino detectors

The Daya Bay Reactor Antineutrino Experiment observed the disappearance of reactor $\bar{\nu}_e$ from six $2.9~GW_{th}$ reactor cores in Daya Bay, China. The Experiment consists of six functionally identical $\bar{\nu}_e$ detectors, which detect $\bar{\nu}_e$ by inverse beta decay using a total of about 120 metric tons of Gd-loaded liquid scintillator as the target volume. These $\bar{\nu}_e$ detectors were installed in three underground experimental halls, two near halls and one far hall, under the mountains near Daya Bay, with overburdens of 250 m.w.e, 265 m.w.e and 860 m.w.e. and flux-weighted baselines of 470 m, 576 m and 1648 m. A total of 90179 $\bar{\nu}_e$ candidates were observed in the six detectors over a period of 55 days, 57549 at the Daya Bay near site, 22169 at the Ling Ao near site and 10461 at the far site. By performing a rate-only analysis, the value of $sin^2 2\theta_{13}$ was determined to be $0.092 \pm 0.017$.