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William R. Jacobs - One of the best experts on this subject based on the ideXlab platform.
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Conjugal Rites of mycobacteria
Nature Genetics, 2003Co-Authors: Apoorva Bhatt, William R. JacobsAbstract:Gene products involved in the naturally occurring process of bacterial conjugation are usually encoded on plasmids. A new study shows that in Mycobacterium smegmatis , a unique conjugative transfer is mediated by multiple cis -acting sequences present on the chromosome and requires host recombination functions.
Krzysztof Kaczmarek - One of the best experts on this subject based on the ideXlab platform.
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population wide body mass increment at stopover sites is an unreliable indicator of refuelling rates in migrating waders
Ibis, 2013Co-Authors: Piotr Minias, Krzysztof KaczmarekAbstract:Estimates of refuelling rates in migrating waders are best based on intra-seasonal recaptures of individually marked birds. This method, however, has methodological problems associated with capture effects and difficulties in attaining sufficient sample sizes. An alternative method had been proposed whereby refuelling rates are approximated by the body mass increment from the slope of the regression between body masses of all birds caught at a site and date. We investigated the appropriateness of this indicator with a simulation study in non-synchronized migratory species (i.e. arrivals and departures of individuals at the stopover site are not synchronized). Simulation results indicated that the mass increment across the population may be used as an approximation of refuelling rate only in populations with low turnover rates (percentage of birds arriving at/departing from stopover site per day <2%) and ideally with constant numbers of staging birds. The mass increment of non-synchronized populations with moderate or high turnover rates (higher than 5%) depends mainly on body masses of arriving birds and is not indicative of the individual rate of refuelling. The results of the simulation study were confirmed with empirical data gathered from Wood Sandpiper Tringa glareola and Common Snipe Gallinago gallinago during their autumn migration at a stopover site in Poland. The population mass increment methods considerably underestimated refuelling rate obtained from the recapture-based approach of individual birds in both species. As a consequence, we suggest that population mass increment should not be used as an indicator of refuelling rates in non-synchronized stopover populations of migrating waders.
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Population‐wide body mass increment at stopover sites is an unreliable indicator of refuelling rates in migrating waders
Ibis, 2012Co-Authors: Piotr Minias, Krzysztof KaczmarekAbstract:Estimates of refuelling rates in migrating waders are best based on intra-seasonal recaptures of individually marked birds. This method, however, has methodological problems associated with capture effects and difficulties in attaining sufficient sample sizes. An alternative method had been proposed whereby refuelling rates are approximated by the body mass increment from the slope of the regression between body masses of all birds caught at a site and date. We investigated the appropriateness of this indicator with a simulation study in non-synchronized migratory species (i.e. arrivals and departures of individuals at the stopover site are not synchronized). Simulation results indicated that the mass increment across the population may be used as an approximation of refuelling rate only in populations with low turnover rates (percentage of birds arriving at/departing from stopover site per day
Ziheng Yang - One of the best experts on this subject based on the ideXlab platform.
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approximate methods for estimating the pattern of nucleotide substitution and the variation of substitution rates among sites
Molecular Biology and Evolution, 1996Co-Authors: Ziheng Yang, Sudhir KumarAbstract:We propose two approximate methods (one based on parsimony and one on pairwise sequence comparison) for estimating the pattern of nucleotide substitution and a parsimony-based method for estimating the gamma parameter for variable substitution rates among sites. The matrix of substitution rates that represents the substitution pattern can be recovered through its relationship with the observable matrix of site pattern frequences in pairwise sequence comparisons. In the parsimony approach, the ancestral sequences reconstructed by the parsimony algorithm were used, and the two sequences compared are those at the ends of a branch in the phylogenetic tree. The method for estimating the gamma parameter was based on a reinterpretation of the numbers of changes at sites inferred by parsimony. Three data sets were analyzed to examine the utility of the approximate methods compared with the more reliable likelihood methods. The new methods for estimating the substitution pattern were found to produce estimates quite similar to those obtained from the likelihood analyses. The new method for estimating the gamma parameter was effective in reducing the bias in conventional parsimony estimates, although it also overestimated the parameter. The approximate methods are computationally very fast and appear useful for analyzing large data sets, for which use of the likelihood method requires excessive computation.
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maximum likelihood phylogenetic estimation from dna sequences with variable rates over sites approximate methods
Journal of Molecular Evolution, 1994Co-Authors: Ziheng YangAbstract:Two approximate methods are proposed for maximum likelihood phylogenetic estimation, which allow variable rates of substitution across nucleotide sites. Three data sets with quite different characteristics were analyzed to examine empirically the performance of these methods. The first, called the "discrete gamma model," uses several categories of rates to approximate the gamma distribution, with equal probability for each category. The mean of each category is used to represent all the rates falling in the category. The performance of this method is found to be quite good, and four such categories appear to be sufficient to produce both an optimum, or near-optimum fit by the model to the data, and also an acceptable approximation to the continuous distribution. The second method, called "fixed-rates model", classifies sites into several classes according to their rates predicted assuming the star tree. Sites in different classes are then assumed to be evolving at these fixed rates when other tree topologies are evaluated. Analyses of the data sets suggest that this method can produce reasonable results, but it seems to share some properties of a least-squares pairwise comparison; for example, interior branch lengths in nonbest trees are often found to be zero. The computational requirements of the two methods are comparable to that of Felsenstein's (1981, J Mol Evol 17:368-376) model, which assumes a single rate for all the sites.
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maximum likelihood estimation of phylogeny from dna sequences when substitution rates differ over sites
Molecular Biology and Evolution, 1993Co-Authors: Ziheng YangAbstract:: Felsenstein's maximum-likelihood approach for inferring phylogeny from DNA sequences assumes that the rate of nucleotide substitution is constant over different nucleotide sites. This assumption is sometimes unrealistic, as has been revealed by analysis of real sequence data. In the present paper Felsenstein's method is extended to the case where substitution rates over sites are described by the gamma distribution. A numerical example is presented to show that the method fits the data better than do previous models.
Apoorva Bhatt - One of the best experts on this subject based on the ideXlab platform.
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Conjugal Rites of mycobacteria
Nature Genetics, 2003Co-Authors: Apoorva Bhatt, William R. JacobsAbstract:Gene products involved in the naturally occurring process of bacterial conjugation are usually encoded on plasmids. A new study shows that in Mycobacterium smegmatis , a unique conjugative transfer is mediated by multiple cis -acting sequences present on the chromosome and requires host recombination functions.
J. Henrich Bruggemann - One of the best experts on this subject based on the ideXlab platform.
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Food intake by the parrotfish Scarus ferrugineus varies seasonally and is determined by temperature, size and territoriality
Marine Ecology Progress Series, 2013Co-Authors: Y. Afeworki, Z. A. Zekeria, J. J. Videler, J. Henrich BruggemannAbstract:On coral reefs, feeding by parrotfishes may prevent coral to macroalgal phase shifts by keeping algae in a cropped state. To predict the response of grazers to changing conditions, knowledge of the factors that affect feeding intensity is needed. Therefore, we studied food intake of the parrotfish Scarus ferrugineus on an inshore fringing reef in the southern Red Sea, Eritrea, where seasonality and extreme summer temperatures were expected to influence feeding rates. Bite rates (bites min(-1)), defecation rates (defecations min(-1)) and yield per bite (mass ingested bite(-1)) were estimated for 3 life-phase categories: 20 to 25 cm initial phase (IP), 30 to 35 cm terminal phase (TP) and 30 to 35 cm territorial terminal phase (TTP). The bite rates increased from low levels in the morning to peak values in the afternoon. IP bite rates increased linearly with seawater temperature. For TP, the temperature-bite rate relationship was quadratic, with maximum bite rates at similar to 32 degrees C and lower rates at higher temperatures. Yield per bite in both IP and TP did not differ with time of year. Throughout the year, the total daily bites were highest in IP and lowest in TTP, resulting in similar to 23% lower daily intake in TTP compared to similar-sized TP males. Daily intake of ash-free dry mass of epilithic algal matrix (g AFDM d(-1)) was 7.5 to 9.6 for IP, 12.4 to 17.5 for TP and 8.7 to 13.2 for TTP. Intake and defecation rates and hence gut turnover rates peaked from April to July. The quadratic temperature response of TP suggests that large individuals may be close to their upper thermal limit, implying that temperature rises are likely to negatively affect grazing by large-bodied parrotfishes.
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Food intake by the parrotfish Scarus ferrugineus varies seasonally and is determined by temperature, size and territoriality
Marine Ecology Progress Series, 2013Co-Authors: Y. Afeworki, Z. A. Zekeria, J. J. Videler, J. Henrich BruggemannAbstract:ABSTRACT: On coral reefs, feeding by parrotfishes may prevent coral to macroalgal phase shifts by keeping algae in a cropped state. To predict the response of grazers to changing conditions, knowledge of the factors that affect feeding intensity is needed. Therefore, we studied food intake of the parrotfish Scarus ferrugineus on an inshore fringing reef in the southern Red Sea, Eritrea, where seasonality and extreme summer temperatures were expected to influence feeding rates. Bite rates (bites min-1), defecation rates (defecations min-1) and yield per bite (mass ingested bite-1) were estimated for 3 life-phase categories: 20 to 25 cm initial phase (IP), 30 to 35 cm terminal phase (TP) and 30 to 35 cm territorial terminal phase (TTP). The bite rates increased from low levels in the morning to peak values in the afternoon. IP bite rates increased linearly with seawater temperature. For TP, the temperature-bite rate relationship was quadratic, with maximum bite rates at ~32°C and lower rates at higher temperatures. Yield per bite in both IP and TP did not differ with time of year. Throughout the year, the total daily bites were highest in IP and lowest in TTP, resulting in ~23% lower daily intake in TTP compared to similar-sized TP males. Daily intake of ash-free dry mass of epilithic algal matrix (g AFDM d-1) was 7.5 to 9.6 for IP, 12.4 to 17.5 for TP and 8.7 to 13.2 for TTP. Intake and defecation rates and hence gut turnover rates peaked from April to July. The quadratic temperature response of TP suggests that large individuals may be close to their upper thermal limit, implying that temperature rises are likely to negatively affect grazing by large-bodied parrotfishes.
