Frequency distribution of TATA box and extension sequences on human promoters

TATA box is one of the most important transcription factor binding sites. But the exact sequences of TATA box are still not very clear yet. In this study, we conducted a dedicated analysis on the frequency distribution of TATA Box and its extension sequences on human promoters. Sixteen TATA elements derived from TATA Box motif, TATAWAWN, were classified into three distribution patterns: peak, bottom-peak and bottom. Fourteen TATA extension sequences (up to two base extensions) were predicted to be the new TATA Box elements because of their high motif factors, which indicate their statistical significance. Statistical analysis on the promoters of mouse, zebrafish and drosophila melanogaster verified seven of these elements. It was also observed that the distribution of TATA elements on the promoters of housekeeping genes are very similar with their distribution on the promoters of tissue specific genes in human.

Plasma cholinesterase characteristics in native Australian birds : significance for monitoring avian species for pesticide exposure

Cholinesterase-inhibiting pesticides are applied throughout Australia to control agricultural pests. Blood plasma cholinesterase (ChE) activity is a sensitive indicator of exposure to organophosphorus insecticides in vertebrates. To aid biomonitoring and provide reference data for wildlife pesticide-risk assessment, plasma acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) activities were characterised in nine species of native bird: King Quails (Excalfactoria chinensis), Budgerigars (Melopsittacus undulatus), White-plumed Honeyeaters (Lichenostomas penicillatus), Yellow-throated Miners (Manorina flavigula), Willie Wagtails (Rhipidura leucophrys), Australian Reed-Warblers (Acrocephalus australis), Brown Songlarks (Cincloramphus cruralis), Double-barred Finches (Taeniopygia bichenovii) and Australasian Pipits (Anthus novaeseelandiae). Plasma ChE activities in all species were within the range of most other avian species and all but one contained AChE and BChE; no AChE was present in King Quail, which has not previously been reported for any species. The lowest detectable plasma AChE activity was 0.10 μmol min^–1 mL^–1 in Budgerigars and the highest was 0.86 μmol min^–1 mL^–1 in Australian Reed-Warblers. BChE in the plasma ranged from 0.37 μmol min^–1 mL^–1 in Double-barred Finches to 0.90 μmol min^–1 mL^–1 in White-plumed Honeyeaters and Australian Reed-Warblers. The lowest proportion of AChE was found in Budgerigars (12.8%) and highest in Willie Wagtails (67.8%). No differences were detected in ChE activity at any time of day in Budgerigars and Zebra Finches (Taeniopygia guttata), although there was a significant difference in all ChE activity between seasons in Zebra Finches.

The effect of acute fenitrotion exposure on a variety of physiological indices, including avian aerobic metabolism during exercise and cold exposure

The effect of fenitrothion exposure on birds was examined by measuring aerobic metabolism, blood hemoglobin content, plasma cholinesterases, and body weight for up to 21 d postdose. Peak metabolic rate was measured in a flight chamber in three-dose groups of house sparrows (Passer domesticus; 100 mg/kg = high, 60 mg/kg = medium, 30 mg/kg = low) and one-dose groups of zebra finches (Taeniopygia guttata; 3 mg/kg) and king quails (Coturnix chinensis; 26 mg/kg). Aerobic metabolism was measured during 1 h of exposure to subfreezing thermal conditions in low-dose house sparrows and king quails (26 mg/kg). Fenitrothion had no effect on metabolic rate during cold exposure or on blood hemoglobin at any time. By contrast, aerobic performance during exercise in sparrows was reduced by 58% (high), 18% (medium), and 20% (low), respectively, 2 d postdose. House sparrows (high) had the longest recovery period for peak metabolic rate (21 d) and plasma cholinesterase activity (14 d). House sparrows (high) and treated king quails had significantly lower myoglobin at 48 h postdose, whereas myoglobin was invariant in zebra finches and house sparrows (medium and low). Cholinesterase was maximally inhibited at 6 h postdose, and had recovered within 24 h, in house sparrows (low), king quails, and zebra finches. Exercise peak metabolic rate in zebra finches and king quails was reduced by 23% at 2 d and 3 d, respectively, despite these birds being asymptomatic in both behavior and plasma cholinesterase activities.

Cholinesterase response in native birds exposed to fenitrothion during locust control operations in Eastern Australia

Huge aggregations of flightless locust nymphs pose a serious threat to agriculture when they reach plague proportions but provide a very visible and nutritious resource for native birds. Locust outbreaks occur in spring and summer months in semiarid regions of Australia. Fenitrothion, an organophosphate pesticide, is sprayed aerially to control locust plagues. To evaluate fenitrothion exposure in birds attending locust outbreaks, we measured total plasma cholinesterase (ChE), butrylcholinesterase (BChE), and acetylcholinesterase (AChE) activities in four avian species captured pre- and postfenitrothion application and ChE reactivation in birds caught postspray only. Eleven of 21 plasma samples from four species had ChE activity below the diagnostic threshold (two standard deviations below the mean ChE activity of prespray samples). Granivorous zebra finches (Taeniopygia guttata) and insectivorous white-winged trillers (Lalage sueurii) had significantly lower mean plasma total ChE, BChE, and AChE activity postspray, while other insectivores, white-browed (Artamus superciliosus) and masked woodswallows (Artamus personatus), did not. Cholinesterase was reactivated in 19 of the 73 plasma samples and in one of three brain samples. We conclude that native bird species are exposed to fenitrothion during locust control operations. This exposure could have detrimental impacts, as both locust outbreaks and avian reproductive events are stimulated by heavy summer rainfall, leading to co-occurrence of locust control and avian breeding activities.

Diacetone alcohol, a dispersant solvent, contributes to acute toxicity of a fipronil-based insecticide in a passerine bird

Fipronil, a phenyl pyrazole pesticide, is aerially applied in eastern Australia to control locust outbreaks, usually as “Adonis 3UL Insecticide^®” (BASF), an ultra low (UL) volume formulation containing 0.3% active pesticide. We tested the toxicities of technical-grade fipronil, the Adonis 3UL formulation and its components in zebra finch, a native bird at risk of exposure in locust control regions. We estimated oral-dose LD50 by the Up-and-Down method. Under laboratory conditions, we identified unexpectedly high toxicities due exclusively to diacetone alcohol (DAA), a solvent making up 12.5% of the Adonis 3UL formulation. In contrast, finches were asymptomatic when exposed to 0.3% technical grade fipronil dissolved in a minimum amount of acetone. Depending upon the behaviour and persistence of DAA under field conditions, this formulation of Adonis 3UL may pose a far greater threat to the health of small birds and possibly other vertebrates than expected for fipronil alone.

Is the ultraviolet waveband a special communication channel in avian mate choice?

There is growing evidence that ultraviolet (UV) wavelengths play an important role in avian mate choice. One of the first experiments to support this idea showed that female zebra finches (Taeniopygia guttata) prefer UV-reflecting males to males whose ultraviolet reflection has been removed. The effect was very strong despite little or no UV reflection from several plumage areas. However, it is not clear how the importance of the UV waveband compares to other regions of the bird-visible spectrum. We tested whether the response of female zebra finches to the removal of male UV reflection is greater than to the removal of other wavebands. We presented females with a choice of males whose appearance was manipulated using coloured filters. The filters removed single blocks of the avian visible spectrum corresponding closely to the spectral sensitivities of each of the zebra finch's single cone classes. This resulted in males that effectively had no UV (UV-), no short-wave (SW-), no medium-wave (MW-) or no long-wave (LW-) plumage reflection. Females preferred UV- and SW- males. LW- and MW- males were least preferred, suggesting that female zebra finches show the greatest response to the removal of longer wavelengths. Quantal catches of the single cone types viewing body areas of the male zebra finch are presented for each treatment. Our study suggests it is important to consider the role of the UV waveband in avian mate choice in conjunction with the rest of the avian visible spectrum.

Context-dependent visual preferences in starlings and blue tits: mate choice and light environment

There is considerable interest in the role that ultraviolet (UV) cues play in the foraging and mate choice decisions of birds. However, with the exception of the zebra finch, Taeniopygia guttata, it is not yet clear whether ultraviolet preferences are context specific, or whether birds show a general preference for full-avian-spectrum environments 320-700 nm) irrespective of the activity in which they are engaged. We investigated whether European starlings, Sturnus vulgaris, and blue tits, Parus caeruleus, show general (nonresource based) or context-specific preferences for full-spectrum environments. We found that neither species showed a general preference for UV-present (UV+) over UV-deficient (UV-) environments, when those environments contained no resources (experiment 1). Furthermore, neither species showed a UV+ preference when cages contained food, water and perches (starlings; experiment 2) or food, perches and heterospecifics (blue tits; Hunt et al. 1999. Animal Behaviour, 58, 809-815). However, both species did show highly significant preferences for UV+ conditions when viewing potential mates. Such experiments are necessary before one can conclude that particular wavebands have specific relevance to mate choice. In fact, our results suggest that the importance of particular wavelength compositions do indeed vary with behavioural context. (C) 2002 The Association for the Study of Animal Behaviour.

Study of myeloid leukemogenesis in Zebrafish

In this study zebrafish were used to identify, characterize and study leukemic "cancer"-genes as well as to investigate their role in normal development, particularly blood cell development. The experiments demonstrated that zebrafish represent an excellent tool for studying leukemogenesis, the genes involved in this process and for testing anti-cancer therapeutics.

Dissecting the role of SOCS proteins using zebrafish

Suppressors of cytokine signalling (SOCS) proteins are negative regulators of the JAK-STAT pathway which is perturbed in certain disease states including cancers and inflammatory diseases. This thesis ascertained the suitability of zebrafish as an alternative animal model to study the SOCS proteins which established new and additional roles during development.

Permanent genetic resources added to molecular ecology resources database 1 August 2010 – 30 September 2010

This article documents the addition of 229 microsatellite marker loci to the Molecular Ecology Resources Database. Loci were developed for the following species: Acacia auriculiformis · Acacia mangium hybrid, Alabama argillacea, Anoplopoma fimbria, Aplochiton zebra, Brevicoryne brassicae, Bruguiera gymnorhiza, Bucorvus leadbeateri, Delphacodes detecta, Tumidagena minuta, Dictyostelium giganteum, Echinogammarus berilloni, Epimedium sagittatum, Fraxinus excelsior, Labeo chrysophekadion, Oncorhynchus clarki lewisi, Paratrechina longicornis, Phaeocystis antarctica, Pinus roxburghii and Potamilus capax. These loci were cross-tested on the following species: Acacia peregrinalis, Acacia crassicarpa, Bruguiera cylindrica, Delphacodes detecta, Tumidagena minuta, Dictyostelium macrocephalum, Dictyostelium discoideum, Dictyostelium purpureum, Dictyostelium mucoroides, Dictyostelium rosarium, Polysphondylium pallidum, Epimedium brevicornum, Epimedium koreanum, Epimedium pubescens, Epimedium wushanese and Fraxinus angustifolia.

Occurrence and distribution of established and new introduced bird species in north Sulawesi, Indonesia

Distributional and habitat information on eight introduced bird species in north Sulawesi, Indonesia, is presented. The accounts are based on our observations as well as being gathered from published sources and unpublished trip reports. Three species (Sulphur-crested Cockatoo Cacatua galerita, Sooty-headed Bulbul Pycnonotus aurigaster and Red-collared Dove Steptopelia tranquebarica) have not previously been reported in north Sulawesi in the published literature, while the continued presence and status of Java Sparrow Padda oryzivora, Zebra Dove Geopelia striata and Rock Dove Columba livia was considered uncertain in the published literature. Further work is required systematically to document the distribution, status and spread of introduced species in the north and other parts of Sulawesi—an imperative from both an economic and conservation perspective.

Using an Electronic Monitoring System to Link Offspring Provisioning and Foraging Behavior of a Wild Passerine

Although the costs of parental care are at the foundations of optimal-parental-investment theory, our understanding of the nature of the underlying costs is limited by the difficulty of measuring variation in foraging effort. We simultaneously measured parental provisioning and foraging behavior in a free-living population of Zebra Finches (Taeniopygia guttata) using an electronic monitoring system. We fitted 145 adults with a passive transponder tag and remotely recorded their visits to nest boxes and feeders continuously over a 2-month period. After validating the accuracy of this monitoring system, we studied how provisioning and foraging activities varied through time (day and breeding cycle) and influenced the benefits (food received by the offspring) and costs (interclutch interval) of parental care. The provisioning rates of wild Zebra Finches were surprisingly low, with an average of only one visit per hour throughout the day. This was significantly lower than those reported for this model species in captivity and for most other passerines in the wild. Nest visitation rate only partially explained the amount of food received by the young, with parental foraging activity, including the minimum distance covered on foraging trips, being better predictors. Parents that sustained higher foraging activity and covered more distance during the first breeding attempt took longer to renest. These results demonstrate that in some species matching foraging activity with offspring provisioning may provide a better estimate of the true investment that individuals commit to a reproductive attempt.

Juvenile social experience affects pairing success at adulthood: Congruence with the loser effect?

Social interactions with adults are often critical for the development of mating behaviours. However, the potential role of other primary social partners such as juvenile counterparts is rarely considered. Most interestingly, it is not known whether interactions with juvenile females improve males’ courtship and whether, similar to the winner and loser effects in a fighting context—outcome of these interactions shapes males’ behaviour in future encounters. We investigated the combined effects of male quality and juvenile social experience on pairing success at adulthood in zebra finches (Taeniopygia guttata). We manipulated brood size to alter male quality and then placed males in either same- or mixed-sex juvenile dyads until adulthood. We found that males from reduced broods obtained more copulations and males from mixed-sex dyads had more complete courtships. Furthermore, independent of their quality, males that failed to pair with juvenile females, but not juvenile males, had a lower pairing success at adulthood. Our study shows that negative social experience with peers during adolescence may be a potent determinant of pairing success that can override the effects of early environmental conditions on male attractiveness and thereby supports the occurrence of an analogous process to the loser effect in a mating context.

All signals are not equal: acoustic signalling of individuality, sex and breeding status in a cooperative breeder

Repeated interactions between individuals in socially living animals select for the evolution of signals that convey information identifying individuals or categories of individuals, which may enable the discrimination of familiar versus unfamiliar individuals. Such information may help animals maximize their inclusive fitness by adjusting their own behaviour, allowing them to avoid conflict, preferentially direct help and/or ignore unreliable individuals. Acoustic signals in birds provide the potential to encode individual-specific information. We examined the degree to which individual identity, sex, breeding status, group membership and genetic relatedness were related to variability in six different call types, which occurred across a variety of different behavioural contexts in the apostlebird, Struthidea cinerea, a socially living and cooperatively breeding Australian passerine. We demonstrated that not all calls reflected the same extent of information. Of the six call types, call variation was related to individual identity in three call types, breeding status in two call types and sex and group relatedness in one call type. Finally, variation in two call types was not related to any of the measured variables. Our results suggest that some, but not all, acoustic signals in apostlebirds may be selected for individual distinctiveness between individuals and categories of individuals (male versus female, breeder versus nonbreeder), and these signals may be important in determining levels of cooperation and interaction between individuals in this cooperatively breeding society. © 2014 The Association for the Study of Animal Behaviour.

Personality in captivity: more exploratory males reproduce better in an aviary population

The existence of animal personality is well-established across a wide range of species, with the majority of evidence for this being obtained from individuals held in captivity. However, there has been little work assessing the influence of commonly-measured personality traits on fitness, which is pertinent when the genetic basis of personality is considered. We measured whether the reproductive behaviour and success of zebra finches in a captive mixed-sex aviary environment was influenced by an aspect of their personality, their exploratory behaviour in a single-sex social aviary. We found that more exploratory males made a greater number of breeding attempts and raised more nestlings than less exploratory males. These results were not confounded by extra-pair paternity, which was not related to personality, or by the individuals that did not initiate any reproductive attempts at all. Our work provides evidence that attributes of personality may influence the degree to which individuals cope with, and thrive in a captive environment and this should be accounted for in both experimental design and the interpretation of results. Furthermore, this suggests that there may be selection on these traits as part of the domestication process.