Statistical Mechanics of Zooplankton

Statistical mechanics provides the link between microscopic properties of many-particle systems and macroscopic properties such as pressure and temperature. Observations of similar “microscopic” quantities exist for the motion of zooplankton, as well as many species of other social animals. Herein, we propose to take average squared velocities as the definition of the “ecological temperature” of a population under different conditions on nutrients, light, oxygen and others. We test the usefulness of this definition on observations of the crustacean zooplankton Daphnia pulicaria. In one set of experiments, D. pulicaria is infested with the pathogen Vibrio cholerae, the causative agent of cholera. We find that infested D. pulicaria under light exposure have a significantly greater ecological temperature, which puts them at a greater risk of detection by visual predators. In a second set of experiments, we observe D. pulicaria in cold and warm water, and in darkness and under light exposure. Overall, our ecological temperature is a good discriminator of the crustacean’s swimming behavior.     

Modulatory effect of Lactobacillus acidophilus KLDS 1.0738 on intestinal short‐chain fatty acids metabolism and GPR41/43 expression in β‐lactoglobulin–sensitized mice

We investigated the correlation between the beneficial effect of Lactobacillus acidophilus on gut microbiota composition, metabolic activities, and reducing cow's milk protein allergy. Mice sensitized with β‐lactoglobulin (β‐Lg) were treated with different doses of L. acidophilus KLDS 1.0738 for 4 weeks, starting 1 week before allergen induction. The results showed that intake of L. acidophilus significantly suppressed the hypersensitivity responses, together with increased fecal microbiota diversity and short‐chain fatty acids (SCFAs) concentration (including propionate, butyrate, isobutyrate, and isovalerate) when compared with the allergic group. Moreover, treatment with L. acidophilus induced the expression of SCFAs receptors, G‐protein–coupled receptors 41 (GPR41) and 43 (GPR43), in the spleen and colon of the allergic mice. Further analysis revealed that the GPR41 and GPR43 messenger RNA expression both positively correlated with the serum concentrations of transforming growth factor‐β and IFN‐γ (p < .05), but negatively with the serum concentrations of IL‐17, IL‐4, and IL‐6 in the L. acidophilus–treated group compared with the allergic group (p < .05). These results suggested that L. acidophilus protected against the development of allergic inflammation by improving the intestinal flora, as well as upregulating SCFAs and their receptors GPR41/43.     

Primate stem cells: bridge the translation from basic research to clinic application

A growing body of literature has shown that stem cells are very effective for the treatment of degenerative diseases in rodents but these exciting results have not translated to clinical practice. The difference results from the divergence in genetic, metabolic, and physiological phenotypes between rodents and humans. The high degree of similarity between non-human primates(NHPs) and humans provides the most accurate models for preclinical studies of stem cell therapy. Using a NHP model to understand the following key issues, which cannot be addressed in humans or rodents, will be helpful for extending stem cell applications in the basic science and the clinic. These issues include pluripotency of primate stem cells, the safety and efficiency of stem cell therapy, and transplantation procedures of stem cells suitable for clinical translation. Here we review studies of the above issues in NHPs and current challenges of stem cell applications in both basic science and clinical therapies. We propose that the use of NHP models, in particular combining the serial production and transplantation procedures of stem cells is the most useful for preclinical studies designed to overcome these challenges.     

Solution structure of the N‐terminal domain of DC‐UbP/UBTD2 and its interaction with ubiquitin

DC‐UbP/UBTD2 is a ubiquitin (Ub) domain‐containing protein first identified from dendritic cells, and is implicated in ubiquitination pathway. The solution structure and backbone dynamics of the C‐terminal Ub‐like (UbL) domain were elucidated in our previous work. To further understand the biological function of DC‐UbP, we then solved the solution structure of the N‐terminal domain of DC‐UbP (DC‐UbP_N) and studied its Ub binding properties by NMR techniques. The results show that DC‐UbP_N holds a novel structural fold and acts as a Ub‐binding domain (UBD) but with low affinity. This implies that the DC‐UbP protein, composing of a combination of both UbL and UBD domains, might play an important role in regulating protein ubiquitination and delivery of ubiquitinated substrates in eukaryotic cells.     

Malondialdehyde generated from peroxidized linolenic acid causes protein modification in heat-stressed plants

When polyunsaturated fatty acids (PUFAs) in biomembrane are peroxidized, a great diversity of aldehydes is formed, and some of which are highly reactive. Thus they are thought to have biological impacts in stressed plants; however, the detailed mechanism of generation and biochemical effects are unknown. In this study, we show that chloroplasts are major organelles in which malondialdehyde (MDA) generated from peroxidized linolenic acid modifies proteins in heat-stressed plants. First, to clarify the biochemical process of MDA generation from PUFAs and its attachment to proteins, we carried out in vitro experiments using model proteins (BSA and Rubisco) and methylesters of C18 PUFAs that are major components of plant biomembrane. Protein modification was detected by Western blotting using monoclonal antibodies that recognize MDA binding to proteins. Results showed that peroxidation of linolenic acid methylester by reactive oxygen species was essential for protein modification by MDA, and the MDA modification was highly dependent on temperature, leading to a loss of Rubisco activity. When isolated spinach thylakoid membrane was peroxidized at 37 degrees C, oxygen-evolving complex 33kDa protein (OEC33) was modified by MDA. These model experiments suggest that protein modification by MDA preferentially occurs under higher temperatures and oxidative conditions, thus we examined protein modification in heat-stressed plants. Spinach plants were heat-stressed at 40 degrees C under illumination, and modification of OEC33 protein by MDA was detected. In heat-stressed Arabidopsis plants, light-harvesting complex protein was modified by MDA under illumination. This modification was not observed in linolenic acid-deficient mutants (fad3fad7fad8 triple mutant), suggesting that linolenic acid is a major source of protein modification by MDA in heat-stressed plants.     

Cryopreservation of in vitro-grown shoot-tips of <Emphasis Type="Italic">Rabdosia rubescens</Emphasis> by encapsulation-dehydration and evaluation of their genetic stability

Shoot-tips of Rabdosia rubescens, excised from in vitro-grown proliferating shoots that were cold-hardened at 5°C for 3 weeks, were encapsulated in alginate beads. Subsequently, these were precultured in a mixture of 0.4 M sucrose and 2 M glycerol for 1 h and then desiccated with silica-gel to about 21% water content prior to freezing in liquid nitrogen. After thawing, about 85% of cryopreserved shoot-tips grew into true-to-type shoots and with enhanced rooting capacity. Eight single-bud sibling lines were used to assess genetic stability of these encapsulated shoot-tips. When the relative DNA content was measured by flow cytometry (FCM), no changes were observed between controls and cryopreserved shoots. Using a sequence-related amplified polymorphism (SRAP) assay, it was observed that seven out of eight cryopreserved lines showed identical banding patterns; while the eighth line displayed an absent band, amounting to a low variance rate of 0.01%. These findings suggested that it was necessary to monitor the genetic stability of recovered cryopreserved R. rubescens shoots.     

Comparative thermal unfolding study of psychrophilic and mesophilic subtilisin-like serine proteases by molecular dynamics simulations

Molecular dynamics (MD) simulations of a subtilisin-like serine protease VPR from the psychrophilic marine bacterium Vibrio sp. PA-44 and its mesophilic homologue, proteinase K (PRK), have been performed for 20 ns at four different temperatures (300, 373, 473, and 573 K). The comparative analyses of MD trajectories reveal that at almost all temperatures, VPR exhibits greater structural fluctuations/deviations, more unstable regular secondary structural elements, and higher global flexibility than PRK. Although these two proteases follow similar unfolding pathways at high temperatures, VPR initiates unfolding at a lower temperature and unfolds faster at the same high temperatures than PRK. These observations collectively indicate that VPR is less stable and more heat-labile than PRK. Analyses of the structural/geometrical properties reveal that, when compared to PRK, VPR has larger radius of gyration (Rg), less intramolecular contacts and hydrogen bonds (HBs), more protein-solvent HBs, and smaller burial of nonpolar area and larger exposure of polar area. These suggest that the increased flexibility of VPR would be most likely caused by its reduced intramolecular interactions and more favourable protein-solvent interactions arising from the larger exposure of the polar area, whereas the enhanced stability of PRK could be ascribed to its increased intramolecular interactions arising from the better optimized hydrophobicity. The factors responsible for the significant differences in local flexibility between these two proteases were also analyzed and ascertained. This study provides insights into molecular basis of thermostability of homologous serine proteases adapted to different temperatures.     

Global Patch Matching (GPM) for freehand 3D ultrasound reconstruction

Background

3D ultrasound volume reconstruction from B-model ultrasound slices can provide more clearly and intuitive structure of tissue and lesion for the clinician.

Methods

This paper proposes a novel Global Path Matching method for the 3D reconstruction of freehand ultrasound images. The proposed method composes of two main steps: bin-filling scheme and hole-filling strategy. For the bin-filling scheme, this study introduces two operators, including the median absolute deviation and the inter-quartile range absolute deviation, to calculate the invariant features of each voxel in the 3D ultrasound volume. And the best contribution range for each voxel is obtained by calculating the Euclidian distance between current voxel and the voxel with the minimum invariant features. Hence, the intensity of the filling vacant voxel can be obtained by weighted combination of the intensity distribution of pixels in the best contribution range. For the hole-filling strategy, three conditions, including the confidence term, the data term and the gradient term, are designed to calculate the weighting coefficient of the matching patch of the vacant voxel. While the matching patch is obtained by finding patches with the best similarity measure that defined by the three conditions in the whole 3D volume data.

Results

Compared with VNN, PNN, DW, FMM, BI and KR methods, the proposed Global Path Matching method can restore the 3D ultrasound volume with minimum difference.

Conclusions

Experimental results on phantom and clinical data sets demonstrate the effectiveness and robustness of the proposed method for the reconstruction of ultrasound volume.