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The importance of analyzing neighbor competitive response in the target-neighbor experimental design.

ABSTRACT: The role of competition in community structure and species interactions is universal. However, how one quantifies the outcome of competitive interactions is frequently debated. Here, we review the strengths and weaknesses of the target-neighbor design, a type of additive design where one of the competing species is reduced to a single individual and where controls and analyses are used for the target, but not for the neighbors. We conducted a literature review to determine how the target-neighbor design has been typically used and analyzed. We found that historically, targets were often smaller than neighbors and introduced after neighbor establishment; thus, targets would have little effect on neighbors. However, as co-establishment of targets and neighbors of similar size is now common, the target is more likely to affect the neighbors than in its earlier usage. This can be problematic, because if targets have a significant effect on neighbor performance, bias is introduced into the assessment of the target results. As target treatment controls are necessary to determine the absolute effect of neighbors on target growth, we advocate that analysis of the neighbor competitive response serves as a necessary control for unexpected target x neighbor interactions.

SUBMITTER: Barry KJ

PROVIDER: S-EPMC6102521 | biostudies-literature | 2015 Nov

REPOSITORIES: biostudies-literature

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The importance of analyzing neighbor competitive response in the target-neighbor experimental design.

Barry Kevin J KJ Dudash Michele R MR

Ecology and evolution 20151026 22

The role of competition in community structure and species interactions is universal. However, how one quantifies the outcome of competitive interactions is frequently debated. Here, we review the strengths and weaknesses of the target-neighbor design, a type of additive design where one of the competing species is reduced to a single individual and where controls and analyses are used for the target, but not for the neighbors. We conducted a literature review to determine how the target-neighbo ...[more]

PMID: 30151129

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Project description:AIM:To determine the influence of the construction design over the biological component's performance in an experimental bio-artificial liver (BAL) device. METHODS:Two BAL models for liver microorgans (LMOs) were constructed. First, we constructed a cylindrical BAL and tested it without the biological component to establish its correct functioning. Samples of blood and biological compartment (BC) fluid were taken after 0, 60, and 120 min of perfusion. Osmolality, hematocrit, ammonia and glucose concentrations, lactate dehydrogenase (LDH) release (as a LMO viability parameter), and oxygen consumption and ammonia metabolizing capacity (as LMO functionality parameters) were determined. CPSI and OTC gene expression and function were measured. The second BAL, a "flat bottom" model, was constructed using a 25 cm2 culture flask while maintaining all other components between the models. The BC of both BALs had the same capacity (approximately 50 cm3) and both were manipulated with the same perfusion system. The performances of the two BALs were compared to show the influence of architecture. RESULTS:The cylindrical BAL showed a good exchange of fluids and metabolites between blood and the BC, reflected by the matching of osmolalities, and glucose and ammonia concentration ratios after 120 min of perfusion. No hemoconcentration was detected, the hematocrit levels remained stable during the whole study, and the minimal percentage of hemolysis (0.65% ± 0.10%) observed was due to the action of the peristaltic pump. When LMOs were used as biological component of this BAL they showed similar values to the ones obtained in a Normothermic Reoxygenation System (NRS) for almost all the parameters assayed. After 120 min, the results obtained were: LDH release (%): 14.7 ± 3.1 in the BAL and 15.5 ± 3.2 in the NRS (n = 6); oxygen consumption (?mol/min·g wet tissue): 1.16 ± 0.21 in the BAL and 0.84 ± 0.15 in the NRS (n = 6); relative expression of Cps1 and Otc: 0.63 ± 0.12 and 0.67 ± 0.20, respectively, in the BAL, and 0.86 ± 0.10 and 0.82 ± 0.07, respectively, in the NRS (n = 3); enzymatic activity of CPSI and OTC (U/g wet tissue): 3.03 ± 0.86 and 222.0 ± 23.5, respectively, in the BAL, and 3.12 ± 0.73 and 228.8 ± 32.8, respectively, in the NRS (n = 3). In spite of these similarities, LMOs as a biological component of the cylindrical BAL were not able to detoxify ammonia at a significant level (not detected vs 35.1% ± 7.0% of the initial 1 mM NH4 + dose in NRS, n = 6). Therefore, we built a second BAL with an entirely different design that offers a flat base BC. When LMOs were placed in this "flat bottom" device they were able to detoxify 49.3% ± 8.8% of the initial ammonia overload after 120 min of perfusion (n = 6), with a detoxification capacity of 13.2 ± 2.2 ?mol/g wet tissue. CONCLUSION:In this work, we demonstrate the importance of adapting the BAL architecture to the biological component characteristics to obtain an adequate BAL performance.

Project description:BackgroundThe enumeration of tetrameric and other sequence motifs that are positively or negatively correlated with in vivo antisense DNA effects has been a useful addition to the arsenal of information needed to predict effective targets for antisense DNA control of gene expression. Such retrospective information derived from in vivo cellular experiments characterizes aspects of the sequence dependence of antisense inhibition that are not predicted by nearest-neighbor (NN) thermodynamic parameters derived from in vitro experiments. However, quantitation of the antisense contributions of motifs is problematic, since individual motifs are not isolated from the effects of neighboring nucleotides, and motifs may be overlapping. These problems are circumvented by a next-nearest-neighbor (NNN) analysis of antisense DNA effects in which the overlapping nature of nearest-neighbors is taken into account.ResultsNext-nearest-neighbor triplet combinations of nucleotides are the simplest that include overlapping sequence effects and therefore can encompass interactions beyond those of nearest neighbors. We used singular value decomposition (SVD) to fit experimental data from our laboratory in which phosphorothioate-modified antisense DNAs (S-DNAs) 20 nucleotides long were used to inhibit cellular protein expression in 112 experiments involving four gene targets and two cell lines. Data were fitted using a NNN model, neglecting end effects, to derive NNN inhibition parameters that could be combined to give parameters for a set of 49 sequences that represents the inhibitory effects of all possible overlapping triplet interactions in the cellular targets of these antisense S-DNAs. We also show that parameters to describe subsets of the data, such as the mRNAs being targeted and the cell lines used, can be included in such a derivation. While NNN triplet parameters provided an adequate model to fit our data, NN doublet parameters did not.ConclusionsThe methodology presented illustrates how NNN antisense inhibitory information can be derived from in vivo cellular experiments. Subsequent calculations of the antisense inhibitory parameters for any mRNA target sequence automatically take into account the effects of all possible overlapping combinations of nearest-neighbors in the sequence. This procedure is more robust than the tallying of tetrameric motifs that have positive or negative antisense effects. The specific parameters derived in this work are limited in their applicability by the relatively small database of experiments that was used in their derivation.

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The importance of analyzing neighbor competitive response in the target-neighbor experimental design.

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The importance of analyzing neighbor competitive response in the target-neighbor experimental design.

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