Random Phage Display-Based Screening of Peptides that Bind to Botulinum Neurotoxin Binding Protein, Nontoxic Nonhemagglutinin

Botulinum neurotoxin (BoNT) binds to nontoxic nonhemagglutinin (NTNHA) protein in a pH-dependent manner, and yields the protease-resistant BoNT/NTNHA complex. Here, we screened short peptides that bind to the serotype D NTNHA (NTNHA-D) using random phage display technique. NTNHA was fixed onto electrode of quartz crystal microbalance (QCM) apparatus, and then the phages displaying random heptapeptides were exposed to the NTNHA-D under the acidic condition. After rinsing with acidic buffer, the released phages under the alkaline condition were collected. The binding and release of the phage were monitored by the frequency shift on the QCM. As a result of the screening, 16 were selected as peptides that bind to NTNHA-D. The selected peptides do not share any conserved sequence, but tend to be rich in basic and/or hydrophobic amino acid. This would explain the binding manner of the BoNT to the NTNHA protein.     

Evaluating the “recovery level” of endangered species without prior information before alien invasion

For maintaining social and financial support for eradication programs of invasive species, quantitative assessment of recovery of native species or ecosystems is important because it provides a measurable parameter of success. However, setting a concrete goal for recovery is often difficult owing to lack of information prior to the introduction of invaders. Here, we present a novel approach to evaluate the achievement level of invasive predator management based on the carrying capacity of endangered species estimated using long‐term monitoring data. In Amami‐Oshima Island, Japan, where the eradication project of introduced small Indian mongoose is ongoing since 2000, we surveyed the population densities of four endangered species threatened by the mongoose (Amami rabbit, the Otton frog, Amami tip‐nosed frog, and Amami Ishikawa's frog) at four time points ranging from 2003 to 2011. We estimated the carrying capacities of these species using the logistic growth model combined with the effects of mongoose predation and environmental heterogeneity. All species showed clear tendencies toward increasing their density in line with decreased mongoose density, and they exhibited density‐dependent population growth. The estimated carrying capacities of three endangered species had small confidence intervals enough to measure recovery levels by the mongoose management. The population density of each endangered species has recovered to the level of the carrying capacity at about 20–40% of all sites, whereas no individuals were observed at more than 25% of all sites. We propose that the present approach involving appropriate monitoring data of native organism populations will be widely applicable to various eradication projects and provide unambiguous goals for management of invasive species.     

Enhancement of Glossiness Perception by Retinal-Image Motion: Additional Effect of Head-Yoked Motion Parallax

It has been argued that when an observer moves, a contingent retinal-image motion of a stimulus would strengthen the perceived glossiness. This would be attributed to the veridical perception of three-dimensional structure by motion parallax. However, it has not been investigated whether the effect of motion parallax is more than that of retinal-image motion of the stimulus. Using a magnitude estimation method, we examine in this paper whether cross-modal coordination of the stimulus change and the observer''s motion (i.e., motion parallax) is essential or the retinal-image motion alone is sufficient for enhancing the perceived glossiness. Our data show that a retinal-image motion simulating motion parallax without head motion strengthened the perceived glossiness but that its effect was weaker than that of motion parallax with head motion. These results suggest the existence of an additional effect of the cross-modal coordination between vision and proprioception on glossiness perception. That is, motion parallax enhances the perception of glossiness, in addition to retinal-image motions of specular surfaces.     

Environmental DNA as a ‘Snapshot’ of Fish Distribution: A Case Study of Japanese Jack Mackerel in Maizuru Bay,Sea of Japan

Recent studies in streams and ponds have demonstrated that the distribution and biomass of aquatic organisms can be estimated by detection and quantification of environmental DNA (eDNA). In more open systems such as seas, it is not evident whether eDNA can represent the distribution and biomass of aquatic organisms because various environmental factors (e.g., water flow) are expected to affect eDNA distribution and concentration. To test the relationships between the distribution of fish and eDNA, we conducted a grid survey in Maizuru Bay, Sea of Japan, and sampled surface and bottom waters while monitoring biomass of the Japanese jack mackerel (Trachurus japonicus) using echo sounder technology. A linear model showed a high R² value (0.665) without outlier data points, and the association between estimated eDNA concentrations from the surface water samples and echo intensity was significantly positive, suggesting that the estimated spatial variation in eDNA concentration can reflect the local biomass of the jack mackerel. We also found that a best-fit model included echo intensity obtained within 10–150 m from water sampling sites, indicating that the estimated eDNA concentration most likely reflects fish biomass within 150 m in the bay. Although eDNA from a wholesale fish market partially affected eDNA concentration, we conclude that eDNA generally provides a ‘snapshot’ of fish distribution and biomass in a large area. Further studies in which dynamics of eDNA under field conditions (e.g., patterns of release, degradation, and diffusion of eDNA) are taken into account will provide a better estimate of fish distribution and biomass based on eDNA.     

Normal Lung Quantification in Usual Interstitial Pneumonia Pattern: The Impact of Threshold-based Volumetric CT Analysis for the Staging of Idiopathic Pulmonary Fibrosis

BackgroundAlthough several computer-aided computed tomography (CT) analysis methods have been reported to objectively assess the disease severity and progression of idiopathic pulmonary fibrosis (IPF), it is unclear which method is most practical. A universal severity classification system has not yet been adopted for IPF.ObjectiveThe purpose of this study was to test the correlation between quantitative-CT indices and lung physiology variables and to determine the ability of such indices to predict disease severity in IPF.MethodsA total of 27 IPF patients showing radiological UIP pattern on high-resolution (HR) CT were retrospectively enrolled. Staging of IPF was performed according to two classification systems: the Japanese and GAP (gender, age, and physiology) staging systems. CT images were assessed using a commercially available CT imaging analysis workstation, and the whole-lung mean CT value (MCT), the normally attenuated lung volume as defined from −950 HU to −701 Hounsfield unit (NL), the volume of the whole lung (WL), and the percentage of NL to WL (NL%), were calculated.ResultsCT indices (MCT, WL, and NL) closely correlated with lung physiology variables. Among them, NL strongly correlated with forced vital capacity (FVC) (r = 0.92, P <0.0001). NL% showed a large area under the receiver operating characteristic curve for detecting patients in the moderate or advanced stages of IPF. Multivariable logistic regression analyses showed that NL% is significantly more useful than the percentages of predicted FVC and predicted diffusing capacity of the lungs for carbon monoxide (Japanese stage II/III/IV [odds ratio, 0.73; 95% confidence intervals (CI), 0.48 to 0.92; P < 0.01]; III/IV [odds ratio. 0.80; 95% CI 0.59 to 0.96; P < 0.01]; GAP stage II/III [odds ratio, 0.79; 95% CI, 0.56 to 0.97; P < 0.05]).ConclusionThe measurement of NL% by threshold-based volumetric CT analysis may help improve IPF staging.     

Large-scale profiling of brown rice ionome in an ethyl methanesulphonate-mutagenized hitomebore population and identification of high- and low-cadmium lines

Background and aim

Recycled sources of phosphorus (P), such as struvite extracted from wastewater, have potential to substitute for more soluble manufactured fertilisers and help reduce the long-term threat to food security from dwindling finite reserves of phosphate rock (PR). This study aimed to determine whether struvite could be a component of a sustainable P fertiliser management strategy for arable crops.

Methods

A combination of laboratory experiments, pot trials and mathematical modelling of the root system examined the P release properties of commercial fertiliser-grade struvite and patterns of P uptake from a low-P sandy soil by two different crop types, in comparison to more soluble inorganic P fertilisers (di-ammonium phosphate (DAP) and triple super phosphate (TSP)).

Results

Struvite had greatly enhanced solubility in the presence of organic acid anions; buckwheat, which exudes a high level of organic acids, was more effective at mobilising struvite P than the low level exuder, spring wheat. Struvite granules placed with the seed did not provide the same rate of P supply as placed DAP granules for early growth of spring wheat, but gave equivalent rates of P uptake, yield and apparent fertiliser recovery at harvest, even though only 26 % of struvite granules completely dissolved. Fertiliser mixes containing struvite and DAP applied to spring wheat have potential to provide both optimal early and late season P uptake and improve overall P use efficiency.

Conclusions

We conclude that the potential resource savings and potential efficiency benefits of utilising a recycled slow release fertiliser like struvite offers a more sustainable alternative to only using conventional, high solubility, PR-based fertilisers.

     

Fishing for jaws in early vertebrate evolution: a new hypothesis of mandibular confinement

The evolutionary origin of the vertebrate jaw persists as a deeply puzzling mystery. More than 99% of living vertebrates have jaws, but the evolutionary sequence that ultimately gave rise to this highly successful innovation remains controversial. A synthesis of recent fossil and embryological findings offers a novel solution to this enduring puzzle. The Mandibular Confinement Hypothesis proposes that the jaw evolved via spatial confinement of the mandibular arch (the most anterior pharyngeal arch within which the jaw arose). Fossil and anatomical evidence reveals: (i) the mandibular region was initially extensive and distinct among the pharyngeal arches; and (ii) with spatial confinement, the mandibular arch acquired a common pharyngeal pattern only at the origin of the jaw. The confinement occurred via a shift of a domain boundary that restricted the space the mesenchymal cells of the mandibular arch could occupy. As the surrounding domains replaced mandibular structures at the periphery, this shift allowed neural crest cells and mesodermal mesenchyme of the mandibular arch to acquire patterning programs that operate in the more posterior arches. The mesenchymal population within the mandibular arch was therefore no longer required to differentiate into specialized feeding and ventilation structures, and was remodelled into a jaw. Embryological evidence corroborates that the mandibular arch must be spatially confined for a jaw to develop. This new interpretation suggests neural crest as a key facilitator in correlating elements of the classically recognized vertebrate head ‘segmentation’.