Me write pretty one day: how to write a good scientific paper

The scientific literature is exploding in quantity even as it stands still in literary quality. In this brief guide, I suggest a few small steps that the individual can take to make his or her writing clear, straightforward, and digestible.     

Functional response: rigorous estimation and sensitivity to genetic variation in prey

Holling's type II functional response is a cornerstone of community ecology and coevolutionary theory. The so‐called disc equation is the most widely used model of the type II response, yet thus far no robust experimental assessment has been achieved in any single system. Fundamental issues that remain to be assessed include whether the assumptions of the disc equation are fulfilled, whether the disc equation yields accurate estimates of predation‐related individual traits, and whether differences in disc equation parameters can capture genetic variation in prey behaviour. This paper provides a rigorous approach to all of these questions. The functional response of the predatory mite Pergamasus crassipes on three genetically distinct clones of the springtail Folsomia candida was measured at six levels of prey density in controlled conditions where prey number and arena size were concomitantly manipulated. A crucial assumption of Holling's disc equation was fulfilled by maintaining a constant prey density for the entire experimental period of predation. The timing of each attack and capture, as well as the duration of the handling time, were recorded by constant observation. We contrasted three different methods to calculate functional response curves: (1) indirect estimation of the disc equation's parameters from the number of prey killed by the end of each experimental run; (2) direct estimation of the parameters via a unique protocol of constant observation; and (3) independently deriving a function based on direct measurements of encounter rate and attack success. The basic assumptions of the disk equation were globally fulfilled. Estimations of the functional response's parameters (type II) were remarkably congruent across approach (1) and (2). A single genetic effect was detected – the relationship between the encounter rate and prey density differed significantly between clones – whereas a direct comparison of functional response across clones failed to reveal genetic variation.     

Trials to assess equivalence: the importance of rigorous methods.

The aim of an equivalence trial is to show the therapeutic equivalence of two treatments, usually a new drug under development and an existing drug for the same disease used as a standard active comparator. Unfortunately the principles that govern the design, conduct, and analysis of equivalence trials are not as well understood as they should be. Consequently such trials often include too few patients or have intrinsic design biases which tend towards the conclusion of no difference. In addition the application of hypothesis testing in analysing and interpreting data from such trials sometimes compounds the drawing of inappropriate conclusions, and the inclusion and exclusion of patients from analysis may be poorly managed. The design of equivalence trials should mirror that of earlier successful trials of the active comparator as closely as possible. Patient losses and other deviations from the protocol should be minimised; analysis strategies to deal with unavoidable problems should not centre on an "intention to treat" analysis but should seek to show the similarity of results from a range of approaches. Analysis should be based on confidence intervals, and this also carries implications for the estimation of the required numbers of patients at the design stage.     

Silylation of triacylglycerol: an easy route to new biosiloxanes

A new approach to functionalize triacylglycerol fish oils has been achieved. For the first time, hydrosilylation of various terminal and internal C=C double bonds in ethylenic triacylglycerol was performed under radical initiation sequence, which, after ethanolysis, gave the sol-gel processable triethoxysilyltriacylglycerol P(2). By the use of silyltriflate, new metalated triglycerides P(3), in which silyl fragments are C-bonded in alpha-position to glycerol groups, were synthesized. The sol-gel hydrolysis and polycondensation of triethoxysilyltriacylglycerol led to hybrid materials in which organic and inorganic moieties are covalently linked. These materials open new applications in drug delivery and pharmaceutical formulation.     

Behavioral neuroscience: no easy path from genes to cognition

Two recent studies illustrate the limits of a strictly molecular approach toward understanding learning and memory.     

Tree age estimates in Fagus sylvatica and Quercus robur: testing previous and improved methods

The accuracy of direct (based on increment cores) and indirect (based on age-size relationships) methods of tree age estimation in Fagus sylvatica and Quercus robur was tested. This was done through increment cores and stem discs taken in an old-growth forest of Northern Spain. It was found that cross-dating was more precise than ring counting by up to 7 years per tree. Furthermore, cross-dating permitted the estimation of the age of trees with floating ring-width series, which were 7% of cored F. sylvatica and 40% of Q. robur ones. In partial cores with the arcs of the inner rings, the length of the missing radius was estimated with both a geometric method, based on the curvature of the arcs, and a new graphical method, based on the convergence of xylem rays at the pith. The graphical method was more accurate when the radial growth was eccentric, as happens in Q. robur, while both methods showed a similar accuracy for F. sylvatica, whose growth is relatively concentric. Empirical models of initial radial growth (IRG), built to estimate the number of missing rings, reduced the errors associated with other methods that assume constant growth rates. Age estimates obtained from the graphical method combined with the IRG models were within 4% of the actual age. This combination ensured age estimates with a mean accuracy of 8 years for 98% of the F. sylvatica trees, and 4 years for 89% of the Q. robur. In partial cores without the arcs of the inner rings, the length of the missing radius was estimated as the distance to the geometric centre of the tree. In that case, age estimates obtained by extrapolating the mean growth rate of the 20 innermost rings in the cores were from 10 to 20% of actual age, which coincided with results obtained in other tree species with this method. Finally, the age-diameter equations of the different cohorts produced better age estimates (from 8 to 14% of actual age) than equations of the population as a whole (from 20 to 40% of actual age). These results proved that the errors derived from doubtful assumptions, such as concentric radial growth, constant growth and recruitment rates, or the absence of anomalous rings, could be reduced by applying more realistic methods of tree age estimation.     

Stories,fun and games: Teaching genetics in primary school

Nuggets are suggestions with practical advice to help in communicating biology to students. They are shorter than the formal papers and have not been peer-reviewed, but may provide ideas for the classroom. Please send contributions to the editor at: jbe@iob.org     

CRISPR-STAT: an easy and reliable PCR-based method to evaluate target-specific sgRNA activity

CRISPR/Cas9 has emerged as a versatile genome-engineering tool that relies on a single guide RNA (sgRNA) and the Cas9 enzyme for genome editing. Simple, fast and economical methods to generate sgRNAs have made targeted mutagenesis routine in cultured cells, mice, zebrafish and other model systems. Pre-screening of sgRNAs for target efficacy is desirable both for successful mutagenesis and minimizing wasted animal husbandry on targets with poor activity. Here, we describe an easy, quick and cost-effective fluorescent polymerase chain reaction (PCR)-based method, CRISPR Somatic Tissue Activity Test (CRISPR-STAT), to determine target-specific efficiency of sgRNA. As a proof of principle, we validated our method using 28 sgRNAs with known and varied levels of germline transmission efficiency in zebrafish by analysis of their somatic activity in injected embryos. Our data revealed a strong positive correlation between the fluorescent PCR profiles of the injected embryos and the germline transmission efficiency. Furthermore, the assay was sensitive enough to evaluate multiplex gene targeting. This method is easy to implement by laboratories with access to a capillary sequencer. Although we validated the method using CRISPR/Cas9 and zebrafish, it can be applied to other model systems and other genome targeting nucleases.     

Information processing limits: the effects of information load and age.

As a test of the effects of age and information load Ss performed a visual and auditory discrimination task under conditions requiring division of attention. Amount of stimulus information was determined by the number of stimulus alternatives which could occur in a set of trials. Performance by 12 Ss over age 40 was impaired in comparison to 12Ss under age 40. Performance for all Ss was a function of amount of information, but there was no Age X Information Load interaction. It has been reported in the literature that age-related performance decrements are correlated with task complexity. These data indicate that amount of information is not a critical dimension of task complexity as it contributes to age-related performance deficits.