scholarly journals Interpreting deep mutational scanning data resulting from selections on solid media

2016 ◽  
Author(s):  
Justin R. Klesmith ◽  
Sarah Thorwall ◽  
Timothy A. Whitehead
Keyword(s):  
Growth Rate ◽  
Directed Evolution ◽  
Relative Growth Rate ◽  
Deep Sequencing ◽  
Growth Rates ◽  
Mixed Population ◽  
Relative Growth ◽  
Survival Percentage ◽  
Solid Media ◽  
Proper Interpretation

AbstractDeep mutational scanning is now used in directed evolution experiments to quantify the change in frequency of a cellular variant in a mixed population. A key concern is the extent to which the enrichment of a variant in a population corresponds to a fitness metric like relative growth rate or survival percentage. We present here analytical equations converting the enrichment of a variant to fitness metrics for plate-based selections. Using isogenic and mixed cultures we show that growth rates and survival percentages correlate for antibiotic plate-based selections. These results are important for proper interpretation of data resulting from deep sequencing.

Effect of a pesticide pentachlorophenol on soil microflora. III. Growth rates as an index of pesticide resistance of bacterial groups isolated from soil

1987 ◽  
Vol 33 (9) ◽  
pp. 819-822 ◽  
Author(s):  
Kyo Sato
Keyword(s):  
Growth Rate ◽  
Relative Growth Rate ◽  
Growth Rates ◽  
Bacterial Species ◽  
Bacterial Flora ◽  
Soil Microflora ◽  
Pesticide Resistance ◽  
Relative Growth ◽  
Bacterial Groups

Pentachlorophenol resistance was investigated in bacteria isolated from glycine- or water-percolated soils where the bacterial flora was modified by the addition of pentachloropenol. The strains isolated from the water-percolated soil amended with PCP had the highest resistance, and the addition of glycine to the percolated soil weakened the resistance. The strains from the glycine-percolated soil without pentachlorophenol had a medium degree of resistance, and the resistance of the strains from the water-percolated soil without PCP was the lowest. The bacterial groups were sorted taxonomically; differences in pentachloropenol resistance were correlated with taxonomic groupings. Relative growth rate in the presence of pentachlorophenol was proposed as a useful means to distinguish among the bacterial species.

Analyzing growth in cell cultures. I. Calculating growth rates

1986 ◽  
Vol 64 (1) ◽  
pp. 233-237 ◽  
Author(s):  
Susan R. Singer
Keyword(s):  
Growth Rate ◽  
Relative Growth Rate ◽  
Growth Rates ◽  
Rate Equations ◽  
Constant Growth Rate ◽  
Relative Growth ◽  
Relative Growth Rates ◽  
Growing Cell ◽  
Absolute Growth ◽  
Plant Tissue Cultures

Growth is the major parameter used to assess novel phenotypes derived from plant tissue cultures. Any quantitative analysis of growth must have an explicit rational basis. Frequently this criterion is not met. For example, the calculation (W2 − W1)/W1(W1 = initial weight; W2 = final weight) approximates neither linear nor exponential growth. Yet, it is a common method of analysis, as is the related calculation W2/W1. When absolute growth values provide insufficient information, meaningful relative growth rate equations can be utilized. Relative growth rates should be evaluated as ln (W2/W1)/(t2 − t1) for t = time, thereby yielding a constant growth rate for exponentially growing cell lines. Linear growth (root growth, for example) can be approximated by 2(W2 − W1)/((W1 + W2)(t2 − t1)). All methods of analysis we have encountered assume that relative growth at a given instant depends on total mass. The possibility exists that growth may actually be proportional to mass raised to some power less than one. For example, growth could be limited to a thin outer shell of a spherical callus. Then the relative growth rate would equal 3(W21/3 − W11/3)/(t2 − t1). Data can be seriously distorted when inappropriate calculations are used. Such distortions are exacerbated when comparisons are made. In all cases an adequate assessment of growth kinetics for each cell line and each treatment is essential.

scholarly journals Interrelationship of Nitrogen and Light on Episodic Growth of Ligustrum japonicum

1994 ◽  
Vol 12 (1) ◽  
pp. 43-46
Author(s):  
Jeff S. Kuehny ◽  
Dennis R. Decoteau
Keyword(s):  
Growth Rate ◽  
Root Growth ◽  
Relative Growth Rate ◽  
Growth Rates ◽  
Shoot Growth ◽  
Fertilizer Application ◽  
Relative Growth ◽  
Mature Leaves ◽  
Episodic Growth ◽  
Ligustrum Japonicum

Abstract Exclusion of nitrogen and light from existing leaves at initiation of an episode of shoot growth decreased shoot and root relative growth rate. The combination of both nitrogen and light exclusion synergistically impacted relative growth rate for shoot (RGRs) and relative growth rate for root (RGRr). The next episode of shoot growth provided sufficient leaf area for carbohydrate assimilation and maintaining shoot and root growth rates when light was excluded from mature leaves. A better understanding of the developmental and biochemical changes of this episodic species provided useful information for timing of fertilizer application and transplanting of Ligustrum and other episodic species.

Temperature and day length response of some cocksfoot populations

1967 ◽  
Vol 18 (1) ◽  
pp. 1 ◽  
Author(s):  
P BrouT ◽  
CN Williams ◽  
CA Neal-Smith ◽  
L Albrecht
Keyword(s):  
Growth Rate ◽  
Relative Growth Rate ◽  
Growth Rates ◽  
Leaf Size ◽  
Day Length ◽  
Relative Growth ◽  
Dactylis Glomerata L ◽  
Leaf Appearance ◽  
Rate Of Leaf Appearance ◽  
Short Days

Seedling plants of seven cocksfoot (Dactylis glomerata L.) populations were exposed to day/night temperatures of 20/15, 15/10, 12/7, and 9/4°C at day lengths of either 8 or 16 hr. Leaf size, rate of leaf appearance, and relative growth rate decreased as temperature decreased. At higher temperatures, relative growth rate was greater in long than in short days, but at 9/4° it was greater in short days. Long days increased leaf size but slightly reduced the rate of leaf appearance at higher temperatures; the increased leaf size, however, more than compensated for the slightly lower rate of leaf appearance, so that relative growth rate was greater in long than in short days. At 9/4°, however, greater leaf size did not compensate for the much slower rate of leaf appearance in long days. Growth rates were consequently lower in long than in short days at 9/4°. The populations showed a general similarity in response, although significant differences between populations were recorded for particular treatments. There was no apparent relationship between seedling growth rates at low temperatures in this experiment and winter growth of these populations under field conditions.

scholarly journals GROWTH OF MANGROVE COCKLE (Anandara antiquata) CULTURED IN CAGES

2009 ◽  
Vol 34 (2) ◽  
pp. 91-96
Author(s):  
Jesaja A. Pattikawa ◽  
Elizabeth Ferdinandus
Keyword(s):  
Growth Rate ◽  
Relative Growth Rate ◽  
Growth Rates ◽  
Condition Factor ◽  
Intertidal Area ◽  
Relative Growth ◽  
Relative Growth Rates ◽  
Weight Relationship ◽  
Large Size ◽  
Length Increment

Study on growth of mangrove cockle (Anadara antiquata) was conducted in the intertidal area of Passo, Inner Ambon Bay. Three size-classes of 25 individual cockles were cultured in 1 m3 cage. Length increment data was collected every two weeks for seven periods of observation. Relative growth rate, length-weight relationship and condition factor were estimated using formula proposed by Effendie, Pauly and King, respectively. The results showed that the small size had the highest length increment and relative growth rates while the large size had the best condition factor. Length-weight relationship showed isometric growth for all categories.

scholarly journals Soil flood tolerance of seven genotypes of Panicum maximum Jacq.

2009 ◽  
Vol 52 (6) ◽  
pp. 1341-1348 ◽  
Author(s):  
Adriane Schio Silva ◽  
Valdemir Antônio Laura ◽  
Liana Jank
Keyword(s):  
Growth Rate ◽  
Relative Growth Rate ◽  
Growth Rates ◽  
Root Biomass ◽  
Flood Tolerance ◽  
Panicum Maximum ◽  
Above Ground Biomass ◽  
Relative Growth ◽  
Relative Growth Rates ◽  
Commercial Cultivars

The soil flood tolerance of seven genotypes of Panicum maximum Jacq. (PM11, PM34, PM40 and PM45, and the commercial cultivars Massai, Mombaça and Tanzânia) was evaluated in plants subjected to two conditions: flooded and not flooded, during a period of 14 days. Flooding significantly decreased the total and above ground biomass of PM40 and PM45. For cultivar Tanzânia, flooding decreased these two variables and also root biomass. The root, total and above ground relative growth rates were significantly reduced by flooding in cultivar Tanzânia, while in PM45 only the above ground relative growth rate was reduced. Cultivar Tanzânia showed significant differences for all variables analyzed, thus was not flood tolerant, as well as PM40 and PM45. It could be concluded that Massai, PM34, Mombaça and PM11 were the most flood tolerant genotypes.

Analysis of antigenic types appearing in first relapse populations of clones of Trypanosoma brucei

Parasitology ◽  
1981 ◽  
Vol 82 (1) ◽  
pp. 63-80 ◽  
Author(s):  
E. N. Miller ◽  
M. J. Turner
Keyword(s):  
Growth Rate ◽  
Trypanosoma Brucei ◽  
Growth Rates ◽  
Surface Antigens ◽  
Mixed Population ◽  
Immunofluorescent Staining ◽  
Relative Growth ◽  
Relative Growth Rates ◽  
First Relapse

SUMMARYVariant antigenic types (VATs) represented in a total of 47 first relapse populations of 6 clones of Trypanosoma brucei LUMP 227 were identified by immunofluorescent staining of living trypanosomes, using antiserum raised against purified surface antigens. The relative growth rates of these 6 clones were measured both individually and when grown together in a mixed population, and were found to be different under these two sets of conditions. A pattern emerged in the VATs represented in relapses of each clone, with some types being expressed more frequently than others and certain VATs being only very rarely expressed. It is suggested that new VATs are expressed according to a statistically definable order of priority which is different for each parent VAT, and that some VATs may be able to change to certain others only after passing through an intermediate VAT. The order of priority of appearance of VATs does not appear to correlate with growth rate measured either in individual clones or when clones are grown in a mixed population.

Evolution of model specific relative growth rate: Its genesis and performance over Fisher’s growth rates

2018 ◽  
Vol 444 ◽  
pp. 11-27 ◽  
Author(s):  
Arijit Pal ◽  
Amiya Ranjan Bhowmick ◽  
Farhana Yeasmin ◽  
Sabyasachi Bhattacharya
Keyword(s):  
Growth Rate ◽  
Relative Growth Rate ◽  
Growth Rates ◽  
Relative Growth ◽  
And Performance

Response of Common Ragweed (Ambrosia artemisiifolia) and Giant Ragweed (Ambrosia trifida) to Postemergence Imazethapyr

Weed Science ◽  
1996 ◽  
Vol 44 (2) ◽  
pp. 248-251 ◽  
Author(s):  
Thomas O. Ballard ◽  
Michael E. Foley ◽  
Thomas T. Bauman
Keyword(s):  
Growth Rate ◽  
Relative Growth Rate ◽  
Growth Rates ◽  
Growth Response ◽  
Ambrosia Artemisiifolia ◽  
Ambrosia Trifida ◽  
Relative Growth ◽  
Common Ragweed ◽  
Relative Growth Rates ◽  
Giant Ragweed

A study was conducted to evaluate the response of common and giant ragweed to postemergence applications of imazethapyr using relative growth rate parameters. The relative growth rate was the same for untreated common and giant ragweed through the 21 d harvest interval. Relative growth rates of treated common and giant ragweed were 50% lower than the relative growth rates of untreated ragweeds 21 d after treatment. Between 21 and 56 d after treatment, the relative growth rate of common ragweed declined an additional 13%, while the relative growth rate of giant ragweed declined an additional 38%. The sharp continued decline in the relative growth rate of giant ragweed indicated plant death. The moderation and slight increase in the relative growth rate of common ragweed between 21 and 56 d corresponded with the initiation of lateral axillary buds and the regeneration of plant growth. Relative growth rate parameters identified differences in the response of common and giant ragweed to imazethapyr as early as 21 d after treatment. Relative growth rate demonstrated utility by objectively measuring differences in the growth response of these two weeds that are moderately susceptible to imazethapyr under laboratory conditions.

scholarly journals Uptake and Transport of Ions in Barley Seedlings III. Correlation Between Transport to the Shoot and Relative Growth Rate

1972 ◽  
Vol 25 (5) ◽  
pp. 905 ◽  
Author(s):  
MG Pitman
Keyword(s):  
Growth Rate ◽  
Relative Growth Rate ◽  
Growth Rates ◽  
Potassium Transport ◽  
Culture Solution ◽  
Relative Growth ◽  
Relative Growth Rates ◽  
Transport Of Ions ◽  
Total Potassium ◽  
Uptake And Transport

Determinations of potassium transport are described for plants growing at varied relative growth rates. These determinations were based on differences in total potassium content of the shoot over a 3.day period for plants growing on culture solution. It is shown that rate of transport from root to shoot is correlated with relative growth rate. The concentration of potassium in the shoot was independent of ratio of root to shoot, and little affected by relative growth rate (potassium was the only available univalent cation).

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