Transcriptomic response to differentiation induction

Background  

Microarrays used for gene expression studies yield large amounts of data. The processing of such data typically leads to lists of differentially-regulated genes. A common terminal data analysis step is to map pathways of potentially interrelated genes.     

The effect of oligonucleotide microarray data pre-processing on the analysis of patient-cohort studies

Background  

Intensity values measured by Affymetrix microarrays have to be both normalized, to be able to compare different microarrays by removing non-biological variation, and summarized, generating the final probe set expression values. Various pre-processing techniques, such as dChip, GCRMA, RMA and MAS have been developed for this purpose. This study assesses the effect of applying different pre-processing methods on the results of analyses of large Affymetrix datasets. By focusing on practical applications of microarray-based research, this study provides insight into the relevance of pre-processing procedures to biology-oriented researchers.     

Time-matched grooming in female primates? New analyses from two species

The parcelling model of reciprocity predicts that grooming partners will alternate between giving and receiving grooming within grooming bouts, and that each partner will perform approximately as much grooming as it receives within each bout (‘time matching’). Models of allogrooming based on biological markets theory predict that individuals of lower dominance rank will exchange grooming for tolerance from high-rankers, and therefore an inverse relation will be found between grooming partners' dominance rank distance and how closely they match each other's grooming contributions within each bout. We used weighted logistic regression and weighted least-squares regression to test these predictions using data from female white-faced capuchins, Cebus capucinus, and bonnet macaques, Macaca radiata. Only 5-7% of macaque grooming bouts, and 12-27% of capuchin grooming bouts, were reciprocated. However, (1) the duration of grooming by the first groomer significantly predicted whether the groomee would reciprocate at all, and (2) when bouts were reciprocated, the duration of grooming by the first groomer significantly predicted the duration of grooming by the second groomer. Grooming was most balanced among females of similar dominance ranks. Both the time-matching and rank-related effects were weak, although significant. These results indicate that although some form of time matching may be a general characteristic of grooming in female-bonded primate species, time matching accounts for relatively little of the variation in the distribution of grooming within bouts. We also draw attention to weighted regression as a technique that avoids pseudoreplication while using all available data.     

Use of contact chemical cues in prey discrimination by Cerceris fumipennis

Cerceris fumipennis Say (Hymenoptera: Crabronidae) uses a wide range of adult buprestid beetles to provision nests. Wasps seldom make ‘mistakes’ and attack beetles in other families. Bioassays showed that the wasps use contact chemical cues in the beetles’ epicuticle to discriminate buprestids from other beetles. Wasps rejected buprestids that had their cuticular hydrocarbons (CHC) removed by being washed in solvents. The washed, rejected buprestids became acceptable to 70% of wasps when they were coated with an extract of buprestids’ own CHC. Washed buprestids coated with extracts of non‐buprestid beetle CHC were not accepted. Analyses of buprestid CHC profiles showed that they are relatively simple, consisting of five classes. Other coleopteran families that may co‐occur in the arboreal hunting habitat of C. fumipennis have a broader range of CHC classes. Experiments adding buprestid hydrocarbons to a non‐buprestid beetle, unwashed Popillia japonica Newman (Coleoptera: Scarabaeidae), suggested that wasps may be deterred by the presence of CHC classes not found in Buprestidae. Adding a synthesized dimethyl‐branched hydrocarbon, a class of CHC found in Chrysomelidae but not Buprestidae, to the cuticle of unwashed buprestid beetles, caused wasps to reject the buprestid beetles. We propose that CHC act as a kairomone for C. fumipennis, triggering attack, whereas classes of CHC not found in Buprestidae disrupt this response, and thus help to determine the prey range of the wasp.     

Kinematics of plant growth.

Many of the concepts and equations which have been used in the study of compressible fluids can be applied to problems of plant development. Growth field variables, i.e. functions of position in the plant and of time, can be specified in either Eulerian (spatial) or Lagrangian (material) terms. The two specifications coincide only when the spatial distribution of the variable is steady, and steady patterns are most likely to emerge when an apex is chosen as origin of the co-ordinate system. The growth field itself can be described locally by the magnitude and orientation of the principal axes of the rate of strain tensor and by the vorticity tensor. Material derivatives can be calculated if the temporal and spatial variation in both growth velocity, u (rate of displacement from a material origin), and the variable of interest are known. The equation of continuity shows the importance of including both growth velocity, u, and growth rate, ▽ ·u in estimates of local biosynthesis and transport rates in expanding tissue, although the classical continuity equation must be modified to accommodate the compartmentalized distributions characteristic of plant tissue. Relatively little information on spatial variation in plant organs can be found in the botanical literature, but the current availability of interactive computer graphics equipment suggests that analysis of the spatial distribution of growth rates at least is no longer difficult.     

Evidence for limited spatial spread in an exotic longhorn beetle, Tetropium fuscum (Coleoptera: Cerambycidae)

The longhorn beetle Tetropium fuscum F. (Coleoptera: Cerambycidae) has become established in Nova Scotia, Canada, where it coexists with Tetropium cinnamopterum Kirby. The two Tetropium species share a similar ecological niche and use the same volatile cues for mate attraction. Exotic T. fuscum was introduced near Halifax, Nova Scotia, in approximately 1990, but the rate of its spread 20 yr later has not been documented. We report a large-scale, 3-yr study that investigates the distribution of T. fuscum relative to its site of introduction. Traps baited with male-produced pheromone and host volatiles were used to estimate the relative abundance of the two Tetropium species. Adult T. fuscum emerged 1-2 wk earlier than T. cinnamopterum each year between 2008 and 2010. The spatial distribution of T. fuscum was characterized by a sharp decline in abundance in relation to its point of introduction, up to a threshold distance of approximately 80 km beyond which T. fuscum is rare in comparison with native T. cinnamopterum. The restricted range of T. fuscum 20 yr after its introduction may be attributed to limited dispersal of adults or reproductive failures of low-density populations. The distribution of T. fuscum seemed stable between 2008 and 2010. In 1 of 3 yr, the abundance of T. cinnamopterum increased with the distance to the site of introduction of T. fuscum, which suggests competitive interactions between the two Tetropium species.