MASQOT-GUI: spot quality assessment for the two-channel microarray platform

MASQOT-GUI provides an open-source, platform-independent software pipeline for two-channel microarray spot quality control. This includes gridding, segmentation, quantification, quality assessment and data visualization. It hosts a set of independent applications, with interactions between the tools as well as import and export support for external software. The implementation of automated multivariate quality control assessment, which is a unique feature of MASQOT-GUI, is based on the previously documented and evaluated MASQOT methodology. Further abilities of the application are outlined and illustrated. AVAILABILITY: MASQOT-GUI is Java-based and licensed under the GNU LGPL. Source code and installation files are available for download at http://masqot-gui.sourceforge.net/     

Pastoralist Responses to Floodplain Rehabilitation in North Cameroon

This paper examines the responses of mobile pastoralists to a floodplain rehabilitation program in north Cameroon. From 1993 to 1999, we measured changes in number of camps and herds, and the time they spent in the 600 km² of the Logone floodplain that was reflooded in 1994. The first year, few pastoralists anticipated the reflooding or its impact, and the increase in grazing intensity was caused by a prolonged stay of pastoralists who already used the area for transit. The following three years showed a sharp increase in the number of camps and herds, which stabilized from 1997 onwards. Overall, grazing intensity increased threefold, following the gradually recovering perennial grasslands, with no signs of overexploitation of the area. These developments closely match the ideal preemptive distribution model. We also examined how reflooding affected pastoral incursions in the Waza National Park located in the floodplain.

Genetic population structure and call variation in a passerine bird, the satin bowerbird, Ptilonorhynchus violaceus

Geographic variation in vocalizations is widespread in passerine birds, but its origins and maintenance remain unclear. One hypothesis to explain this variation is that it is associated with geographic isolation among populations and therefore should follow a vicariant pattern similar to that typically found in neutral genetic markers. Alternatively, if environmental selection strongly influences vocalizations, then genetic divergence and vocal divergence may be disassociated. This study compared genetic divergence derived from 11 microsatellite markers with a metric of phenotypic divergence derived from male bower advertisement calls. Data were obtained from 16 populations throughout the entire distribution of the satin bowerbird, an Australian wet-forest-restricted passerine. There was no relationship between call divergence and genetic divergence, similar to most other studies on birds with learned vocalizations. Genetic divergence followed a vicariant model of evolution, with the differentiation of isolated populations and isolation-by-distance among continuous populations. Previous work on Ptilonorhynchus violaceus has shown that advertisement call structure is strongly influenced by the acoustic environment of different habitats. Divergence in vocalizations among genetically related populations in different habitats indicates that satin bowerbirds match their vocalizations to the environment in which they live, despite the homogenizing influence of gene flow. In combination with convergence of vocalizations among genetically divergent populations occurring in the same habitat, this shows the overriding importance that habitat-related selection can have on the establishment and maintenance of variation in vocalizations.     

Natal origin and dispersal of problem saltwater crocodiles in the Darwin Harbor,Australia

Management programs that successfully recovered wild saltwater crocodile (Crocodylus porosus) populations in the Northern Territory of Australia did so with an expanding commitment to maintaining public safety. One aspect of the program is the ongoing removal of resident and immigrant crocodiles within Darwin Harbor (since 1979), the main urban center. We determined the likely sources of crocodiles caught as problem animals between 2015–2017 by comparing recently developed methods for population assignment. Depending on the assignment model used, we estimated that between 30% and 50% of crocodiles in Darwin Harbor originated from the Adelaide and Mary rivers, and the Kakadu region east of Darwin, and between 20% and 30% of crocodiles originated from the Finniss, Reynolds, and Daly rivers southwest of Darwin. Saltwater crocodiles occur at particularly high densities in these catchments. The remainder came from a mixture of different sources across the Northern Territory. The most common animals captured were immature (150–180 cm) males that have traveled 100–200 km. We did not identify any relationships between the distance from the inferred origin to Darwin Harbor and the size and sex of the crocodiles, or the year of capture. The targeted removal of crocodiles from specific sites such as Darwin Harbor, near where most people live, improves public safety in the highest risk areas, without compromising abundant source populations in most areas.     

Renal responses to furosemide are significantly attenuated in male sheep at 6 months of age following fetal uninephrectomy

We have previously shown that fetal uninephrectomy (uni-x) at 100 days of gestation (term = 150 days) in male sheep results in a 30% nephron deficit, reduction in glomerular filtration rate (GFR) and renal blood flow, and elevation in arterial pressure at 6 mo of age. Furthermore, in response to an acute 0.9% saline load, sodium excretion was significantly delayed in uni-x animals leading us to speculate that tubuloglomerular feedback (TGF) activity was reset in uni-x animals. In the present study, we induced TGF blockade by furosemide administration (1.5 mg/kg iv over 90 min) and determined GFR, effective renal plasma flow, and urine and sodium excretion responses in 6-mo-old male sheep. In response to furosemide, a significant diuresis and natriuresis was observed in the sham group; however, the response was significantly delayed and reduced in uni-x animals (both, P(treatment×time) < 0.001). Cummulative urinary and sodium output was significantly less in the uni-x compared with the sham sheep (both, P(treatment×time) < 0.001). GFR was increased in the sham but not the uni-x sheep (P(treatment×time) < 0.0001). In conclusion, the excretory response to furosemide was attenuated in the uni-x sheep, and this suggests a rightward resetting of the TGF operating point. The TGF mechanism is important in the fine tuning of sodium homeostasis and is likely a contributing factor for the dysfunction in sodium regulation we have previously observed in the uni-x animals.     

Interactions among flavonoids of propolis affect antibacterial activity against the honeybee pathogen Paenibacillus larvae

Propolis is derived from plant resins, collected by honeybees (Apis mellifera) and renown for its antibacterial properties. Here we test the antibacterial effects of ethanolic extracts of propolis from different origins on Paenibacillus larvae, the bacterial pathogen that causes American Foulbrood, a larval disease that can kill the honeybee colony. All tested propolis samples inhibited significantly the growth of P. larvae tested in vitro. The extracts showed major differences in the content of total flavonoids (ranging from 2.4% to 16.4%) and the total polyphenols (ranging between 23.3% and 63.2%). We found that it is not only the content of compounds in propolis, which influences the strength of antimicrobial effects but there is also a significant interaction effect among flavonoids of the propolis extracts. We propose that interaction effects among the various chemical compounds in propolis should be taken into account when considering the antibacterial effects against honeybee pathogens.     

Crystal structure of p44, a constitutively active splice variant of visual arrestin

Visual arrestin specifically binds to photoactivated and phosphorylated rhodopsin and inactivates phototransduction. In contrast, the p44 splice variant can terminate phototransduction by binding to nonphosphorylated light-activated rhodopsin. Here we report the crystal structure of bovine p44 at a resolution of 1.85 Å. Compared to native arrestin, the p44 structure reveals significant differences in regions crucial for receptor binding, namely flexible loop V–VI and polar core regions. Additionally, electrostatic potential is remarkably positive on the N-domain and the C-domain. The p44 structure represents an active conformation that serves as a model to explain the ‘constitutive activity’ found in arrestin variants.