Improved pulse sequences for measuring coupling constants in 13C, 15N-labeled proteins

Summary NMR pulse sequences for measuring coupling constants in ¹³C, ¹⁵N-labeled proteins are presented. These pulse sequences represent improvements over earlier experiments with respect to resolution and number of radiofrequency pulses. The experiments are useful for measuring J_NH , J_NCO, J_NC , J_H ^N _CO and J_H ^N _H . Applications to chymotrypsin inhibitor 2 (CI-2) are shown.     

Variation between strains of the cyanobacterium Microcystis aeruginosa isolated from a Portuguese river

AIMS: The aim of this study was to investigate toxicological differences between strains of the cyanobacterium Microcystis aeruginosa isolated from a potable water supply in the north of Portugal over a 2-month period. METHODS AND RESULTS: Twenty-six strains of M. aeruginosa were isolated, grown in pure culture, and tested using a range of techniques including matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), ELISA and a PCR procedure targeting the genes implicated in the production of toxic microcystins. There was considerable variation with respect to the amounts of microcystin produced by each of the strains as measured by ELISA, with values ranging from 0.02 to 0.53% dry weight. The results of the MALDI-TOF MS analysis demonstrated the presence of several chemically distinct forms of microcystin as well as aeruginosins, anabaenopeptins and several other unidentified peptide-like compounds. CONCLUSIONS: The growth of individual strains that comprise bloom populations, with unique 'chemotypes' can potentially be an important factor affecting the toxicity of bloom populations. Molecular probes, targeting the genes responsible for microcystin production were shown to be useful for distinguishing between toxic and nontoxic strains and showed good agreement with the results obtained from the other analyses. SIGNIFICANCE AND IMPACT OF THE STUDY: The results of this study show that the analysis of cyanobacterial bloom populations at the subspecies (strain) level can potentially provide important information regarding the toxin-producing potential of a cyanobacterial bloom and could be used as an 'early warning' for toxic bloom development.     

Fully Automated Enhanced Tumor Compartmentalization: Man vs. Machine Reloaded

ObjectiveComparison of a fully-automated segmentation method that uses compartmental volume information to a semi-automatic user-guided and FDA-approved segmentation technique.MethodsNineteen patients with a recently diagnosed and histologically confirmed glioblastoma (GBM) were included and MR images were acquired with a 1.5 T MR scanner. Manual segmentation for volumetric analyses was performed using the open source software 3D Slicer version 4.2.2.3 (www.slicer.org). Semi-automatic segmentation was done by four independent neurosurgeons and neuroradiologists using the computer-assisted segmentation tool SmartBrush® (referred to as SB), a semi-automatic user-guided and FDA-approved tumor-outlining program that uses contour expansion. Fully automatic segmentations were performed with the Brain Tumor Image Analysis (BraTumIA, referred to as BT) software. We compared manual (ground truth, referred to as GT), computer-assisted (SB) and fully-automated (BT) segmentations with regard to: (1) products of two maximum diameters for 2D measurements, (2) the Dice coefficient, (3) the positive predictive value, (4) the sensitivity and (5) the volume error.ResultsSegmentations by the four expert raters resulted in a mean Dice coefficient between 0.72 and 0.77 using SB. BT achieved a mean Dice coefficient of 0.68. Significant differences were found for intermodal (BT vs. SB) and for intramodal (four SB expert raters) performances. The BT and SB segmentations of the contrast-enhancing volumes achieved a high correlation with the GT. Pearson correlation was 0.8 for BT; however, there were a few discrepancies between raters (BT and SB 1 only). Additional non-enhancing tumor tissue extending the SB volumes was found with BT in 16/19 cases. The clinically motivated sum of products of diameters measure (SPD) revealed neither significant intermodal nor intramodal variations. The analysis time for the four expert raters was faster (1 minute and 47 seconds to 3 minutes and 39 seconds) than with BT (5 minutes).ConclusionBT and SB provide comparable segmentation results in a clinical setting. SB provided similar SPD measures to BT and GT, but differed in the volume analysis in one of the four clinical raters. A major strength of BT may its independence from human interactions, it can thus be employed to handle large datasets and to associate tumor volumes with clinical and/or molecular datasets ("-omics") as well as for clinical analyses of brain tumor compartment volumes as baseline outcome parameters. Due to its multi-compartment segmentation it may provide information about GBM subcompartment compositions that may be subjected to clinical studies to investigate the delineation of the target volumes for adjuvant therapies in the future.     

Potential toxicity of chrysophytes affiliated with Poterioochromonas and related 'Spumella-like' flagellates

The chrysophyte genera Poterioochromonas and Ochromonas andtheir heterotrophic analogons, i.e. the ‘Spumella-like’flagellates, account for a significant and often dominatingfraction of the pelagic nanoplankton. Even though several osmotrophicallyand autotrophically grown strains of Ochromonas and Poterioochromonasare assumed to produce toxins, the potential toxicity has beeninvestigated neither for its association with bacterivorousnutrition nor within the related exclusively heterotrophic ‘Spumella-like’flagellates. We investigated the toxic potential of severalflagellate strains using cultures of flagellates, cell extractsand filtrate of flagellate cultures. The effect on potentialpredators was exemplarily tested for the cladoceran Daphniamagna and the rotifer Platyias sp. All tested heterotrophicand mixotrophic flagellate strains were toxic to zooplanktonat abundances exceeding 10⁴ flagellates mL^–1. For therotifers, survival on any of the flagellate strains was significantlylower than that in the control treatment (P < 0.001) alreadyafter 24 h. We conclude that (i) ‘Spumella-like’flagellates can be toxic to zooplankton, (ii) all tested flagellates,i.e. heterotrophic and mixotrophic flagellates, feeding phagotrophicallycan be toxic to zooplankton and (iii) sublethal effects maybe observed at typical field abundances, even though acute toxicityseems to be restricted to flagellate abundances observed onlyat peak events.     

Influence of prey foraging posture on flight behavior and predation risk: predators take advantage of unwary prey

Foraging in animals is often associated with characteristicbody postures, such as the head-down posture. When foragingconflicts with the ability to detect predators or to flee, individualsmay incur a greater risk of mortality to predation than otherwise.Here we investigate the influence of different foraging postures(horizontal versus nose-down body posture) on the ability ofindividuals to respond to approaching predators and on the riskof mortality to predation in the guppy (Poecilia reticulata).Individuals engaged in nose-down foraging were assumed to beable to visually scan a smaller area for predators and to escapeless effectively due to their body posture, and thus are morevulnerable to stalking predators than horizontally foragingones. In a first experiment, we separately exposed nonforaging,horizontally foraging, and nose-down foraging guppies to anapproaching cichlid fish predator model. Nonforaging guppiesreacted sooner to and initiated flight further away from theapproaching model than did foraging fish collectively, and horizontallyforaging individuals responded sooner to the model than nose-downforaging ones. Comparing all test guppies, nose-down foragingindividuals were the most likely not to exhibit any responseto the predator model. When presented with a simultaneous choiceof two guppies behind a one-way mirror, individual blue acaracichlid (Aequidens pulcher), a natural predator of the guppy,preferred to attack foraging guppies over nonforaging ones andnose-down foraging guppies over horizontally foraging individuals.In a final experiment with free-swimming cichlids and guppies,we demonstrated that individual risk of predation for guppiesforaging nose down was greater than for guppies foraging horizontally,and both were at greater risk than nonforaging guppies. Thislatter result is consistent with the above differences in theguppy's responsiveness to approaching predators depending ontheir foraging behavior, and with the finding that cichlid predatorspreferred fish that were less likely to show any response tothem. Our results therefore indicate that the ability to respondto approaching predators and the risk of mortality to predationin the guppy is strongly influenced by their foraging activity,and in particular their foraging posture, and that cichlid predatorspreferentially select less wary and more vulnerable guppies.[BehavEcol 7: 264–271 (1996)]     

Is reproduction of the Australian house mouse (<Emphasis Type="Italic">Mus domesticus</Emphasis>) constrained by food? A large-scale field experiment

Food quantity and especially food quality are thought to be key factors driving reproductive changes in the house mouse, Mus domesticus, leading to outbreaks of house mouse populations in the Australian grain-growing region. Characteristic changes during an incipient mouse plague are an early start of breeding, a high proportion of females breeding at a young age and a prolonged breeding season. We conducted a large-scale food manipulation during an incipient mouse plague, which started with early breeding and relatively high spring numbers of mice. We measured background food availability in four farms throughout the study and conducted a food manipulation experiment from November to March in two of them. After harvest in December 100-200 kg/ha spilled grain remained in the stubble. This was depleted by March. In two treatment farms we added high-protein food pellets on a weekly basis between November and March and two farms served as controls. We measured changes in mouse numbers by capture-mark-recapture trappings and changes in reproduction by scoring embryos and recent placental scars at necropsy. Mouse numbers did not differ between treatments and controls. There were no differences in the litter size or the proportion of females breeding between treatments and controls. We observed the normal pattern of high litter size in spring and decreasing litter size towards the end of summer in treatments and controls. In all farms reproduction stopped in March. Mouse numbers were high but not at plague densities. Contrary to our prediction we did not observe food constraint affecting the reproduction of female mice. Our field experiment seems to rule out food quality as the driving factor for improved reproduction and formation of an outbreak of mice. We suggest that physiological mechanisms in mice might not enable them to take advantage of food with a high protein content in arid summers in southeastern Australian grain fields because of the lack of free-standing water.