Measuring and controlling data quality in biological assemblage surveys with special reference to stream benthic macroinvertebrates

1. Biological assemblage surveys primarily aim to characterise species composition and relative abundance at one or more spatial or temporal scales. Data interpretation and conclusions are dependent on how well samples characterise the assemblage of interest. 2. Conventional measures of data quality, e.g. standard deviations or coefficients of variation, were designed for single variable estimation, and they are either insufficient or invalid for assessing the quality of data describing entire assemblages. Similarity indices take species composition and relative abundance into account and may be used to effectively measure and control the quality of data used to characterise assemblage structure. 3. The average Jaccard coefficient (JC) calculated across multiple pairs of replicate samples, i.e. autosimilarity JC (AJC), is conceptually and numerically related to the average coefficient of variation in the densities of all species recorded, a measure of sampling precision, and to the proportion of total species richness sampled, a measure of sampling accuracy. 4. We explored how AJC can be used to assess the effect of different potential sources of error on the quality of assemblage survey data, including the sampling effort used both within regions and at individual sites, the individuals collecting samples, sub‐sampling procedures, and consistency of taxon identification. 5. We found that the autosimilarity‐based approach overcomes most weaknesses associated with conventional measures of data quality and can be used to effectively measure and control the quality of assemblage survey data.     

CpG methylation recruits sequence specific transcription factors essential for tissue specific gene expression

CG methylation is an epigenetically inherited chemical modification of DNA found in plants and animals. In mammals it is essential for accurate regulation of gene expression and normal development. Mammalian genomes are depleted for the CG dinucleotide, a result of the chemical deamination of methyl-cytosine in CG resulting in TpG. Most CG dinucleotides are methylated, but ~ 15% are unmethylated. Five percent of CGs cluster into ~ 20,000 regions termed CG islands (CGI) which are generally unmethylated. About half of CGIs are associated with housekeeping genes. In contrast, the gene body, repeats and transposable elements in which CGs are generally methylated. Unraveling the epigenetic machinery operating in normal cells is important for understanding the epigenetic aberrations that are involved in human diseases including cancer. With the advent of high-throughput sequencing technologies, it is possible to identify the CG methylation status of all 30 million unique CGs in the human genome, and monitor differences in distinct cell types during differentiation and development. Here we summarize the present understanding of DNA methylation in normal cells and discuss recent observations that CG methylation can have an effect on tissue specific gene expression. We also discuss how aberrant CG methylation can lead to cancer. This article is part of a Special Issue entitled: Chromatin in time and space.     

In vitro rearing of Campoletis sonorensis, a larval endoparasitoid of Heliothis virescens from egg to third instar in an artificial medium devoid of insect sources

Campoletis sonorensis is a solitary larval endoparasitoid of several Heliothis spp. pests. This study was carried out to develop media devoid of insect sources for in vitro rearing the parasitoid. Trehalose, lysine, threonine, asparagine, glutamine, hydroxyproline, serine, bovine serum albumin, and lactalbumin were beneficial to C. sonorensis. Addition of fresh chicken egg yolk at a low level improved the artificial media. Addition of 20-hydroxyecdysone increased the molting rate, reduced the critical size at molt and decreased development time. Parasitoid development in vitro was dependent on eggs that had been in the host for at least 22 h. Luminosity was also critical for the development of C. sonorensis in vitro. Optimal development occurred in a L14:D10 photoperiod at 43 Lux light intensity. Utilizing the best media and conditions, 100% of the parasitoid larvae reached the second instar and over 37% molted to the third instar. However, no further development occurred.     

Effect of a virus associated with the reproductive system of the parasitoid wasp,Campoletis sonorensis,on host weight gain

The particulate fraction of the calyx fluid of the endoparasitoid, Campoletis sonorensis, reduces host weight gain when manually injected into healthy Heliothis virescens larvae. Reduced weight gain of the host, H. virescens, is normally associated with parasitism by C. sonorensis. Electron microscopy has confirmed that the particulate fraction of the calyx fluid is composed of virus particles and it appears that this virus, injected with the egg at oviposition, actually reduces host weight gain. The effect of the virus is negated when the calyx fluid is exposed to ultraviolet light prior to injection. Furthermore, the calyx fluid is effective only if injected into hosts; there is no effect on host weight gain when hosts are fed or topically treated with the virus-containing calyx fluid.     

Characterization of a cDNA encoding a putative chitinase from teratocytes of the endoparasitoid Toxoneuron nigriceps

Females of insect endoparasitoids inject substances along with the egg at oviposition, which can regulate or induce changes in a number of host physiological processes to benefit the developing parasitoid. These changes can be caused by substances such as venoms, calyx fluids, or symbiotic‐associated virus particles (polydnavirus), which are injected by females along with their eggs, and by substances secreted by parasitoid‐derived tissues (teratocytes) or the developing parasitoid larvae. Teratocytes (dissociated cells of the serosal membrane after parasitoid eclosion) release substances that have roles (i) in parasitoid nutrition, (ii) in the digestion of host tissues, and (iii) in the regulation of host development. Teratocytes of Toxoneuron nigriceps (Viereck) (Hymenoptera: Braconidae) have been implicated in the arrestment of the host development and in the regulation of circulating levels of host ecdysteroids. Here we describe the cDNA of a teratocyte‐secreted chitinase and its expression during parasitoid development, and discuss its putative role in this host–parasitoid association.     

Effect of parasitism by Cardiochiles nigriceps on food consumption and utilization by Heliothis virescens

Parasitism of Heliothis virescens larvae by the endoparasitoid Cardiochiles nigriceps resulted in a reduction in the amount of food consumed by parasitized larvae. This effect was attributed in part to inoculation of material from the accessory reproductive glands of the female at the time of oviposition. Injection of solutions of either the calyx fluid or the poison gland (0·04 gl/larva) into non-parasitized larvae resulted in a reduction in the amount of food consumed by these larvae. A 1 : 1 mixture of these glands (total of 0·04 gl/larva) appeared to be more active than either of the two glands alone. Both of these glands were essential for total activity since larvae parasitized by females lacking the poison gland (poi gl^? female) continued to eat and consumed more food than did those parasitized by a normal female.Parasitism resulted in a slower rate of crop-emptying. This effect was, however, shown to be a result of the quantity of food consumed. Inhibition of gut movement was therefore not considered the cause for the reduction in the amount of food consumed by parasitized larvae.The effect of parasitism on the ability of H. virescens larvae to utilize ingested food was partially reduced by parasitism. Larvae parasitized by a normal female were less efficient than non-parasitized larvae in digesting food. Those larvae parasitized by a poi gl^? female did not convert as much of their food to body substance as did non-parasitized larvae. Injection of solutions of accessory glands into non-parasitized larvae did not cause these effects.