Mixed longitudinal study (6 years) of bone mineral density,muscle mass and muscle strength in the leg of aged females--relations to gravitational load and aging

Researchers examined the relationship between changes in physiological function in space and aging in older females. The hypotheses were that some of the changes may be due to a decrease in gravitational stimulation, but that some could be caused by aging itself. Data are based on a mixed longitudinal research study performed in aged females since 1995.     

Identification of a gene involved in plasmid structural instability in Corynebacterium glutamicum

Expression plasmids that facilitate production of bio-based products are susceptible to toxic effects that frequently affect plasmid structural stability in recombinant microbial cells. In order to enhance plasmid stability in recombinant Corynebacterium glutamicum, an expression plasmid containing genes of the Clostridium acetobutylicum butyryl-CoA synthesis operon with high structural instability within wild-type C. glutamicum was employed. From a total of 133 mutants exhibiting disruptions in 265 suspect genes, only cgR_0322-deficient mutant was able to maintain the expression plasmid intact. The mutant exhibited normal growth under standard laboratory conditions but its transformation efficiency was about one order of magnitude lower than that of wild-type strain. The cgR_0322 gene encodes an endonuclease that is active against single- as well as double-stranded DNA substrates in the presence of Mg²⁺. The cgR_0322-deficient strain should therefore facilitate the development of more robust C. glutamicum strains to be used as microbial production hosts.     

Adult monozygotic twins discordant for intra-uterine growth have indistinguishable genome-wide DNA methylation profiles

Background

Low birth weight is associated with an increased adult metabolic disease risk. It is widely discussed that poor intra-uterine conditions could induce long-lasting epigenetic modifications, leading to systemic changes in regulation of metabolic genes. To address this, we acquire genome-wide DNA methylation profiles from saliva DNA in a unique cohort of 17 monozygotic monochorionic female twins very discordant for birth weight. We examine if adverse prenatal growth conditions experienced by the smaller co-twins lead to long-lasting DNA methylation changes.

Results

Overall, co-twins show very similar genome-wide DNA methylation profiles. Since observed differences are almost exclusively caused by variable cellular composition, an original marker-based adjustment strategy was developed to eliminate such variation at affected CpGs. Among adjusted and unchanged CpGs 3,153 are differentially methylated between the heavy and light co-twins at nominal significance, of which 45 show sensible absolute mean β-value differences. Deep bisulfite sequencing of eight such loci reveals that differences remain in the range of technical variation, arguing against a reproducible biological effect. Analysis of methylation in repetitive elements using methylation-dependent primer extension assays also indicates no significant intra-pair differences.

Conclusions

Severe intra-uterine growth differences observed within these monozygotic twins are not associated with long-lasting DNA methylation differences in cells composing saliva, detectable with up-to-date technologies. Additionally, our results indicate that uneven cell type composition can lead to spurious results and should be addressed in epigenomic studies.     

Dialogue and causality: global description from local observations and vague communications

We propose a dialogue-based society model which explains how the transitive law of the causality is originated. Causality is, in general, formalized by using axiomatic approaches. Instead of using axiomatic methods, we, however, compose a model consisting of agents who have knowledge about causal relations among objects. The model society can reveal the transitive law through interactional dialogues among themselves. The agents are reciprocally influenced, if they have either completely same opinions, or a particular pattern of opinions, that are regarded as the extension of such exact accordance. In addition, we add some vagueness to the dialogue, which is closer to a real communication than the former model. A set of knowledge of each agent is expressed as a directed graph, hence the every model can be construed as mere transformations of directed graphs through the interactions among directed graphs themselves. Following this perspective, the models are the systems that connect local logic with global one, while the union of the directed graphs is regarded as the global.     

Circulating AIM as an Indicator of Liver Damage and Hepatocellular Carcinoma in Humans

Background

Hepatocellular carcinoma (HCC), the fifth most common cancer type and the third highest cause of cancer death worldwide, develops in different types of liver injuries, and is mostly associated with cirrhosis. However, non-alcoholic fatty liver disease often causes HCC with less fibrosis, and the number of patients with this disease is rapidly increasing. The high mortality rate and the pathological complexity of liver diseases and HCC require blood biomarkers that accurately reflect the state of liver damage and presence of HCC.

Methods and Findings

Here we demonstrate that a circulating protein, apoptosis inhibitor of macrophage (AIM) may meet this requirement. A large-scale analysis of healthy individuals across a wide age range revealed a mean blood AIM of 4.99±1.8 µg/ml in men and 6.06±2.1 µg/ml in women. AIM levels were significantly augmented in the younger generation (20s–40s), particularly in women. Interestingly, AIM levels were markedly higher in patients with advanced liver damage, regardless of disease type, and correlated significantly with multiple parameters representing liver function. In mice, AIM levels increased in response to carbon tetrachloride, confirming that the high AIM observed in humans is the result of liver damage. In addition, carbon tetrachloride caused comparable states of liver damage in AIM-deficient and wild-type mice, indicating no influence of AIM levels on liver injury progression. Intriguingly, certain combinations of AIM indexes normalized to liver marker score significantly distinguished HCC patients from non-HCC patients and thus could be applicable for HCC diagnosis.

Conclusion

AIM potently reveals both liver damage and HCC. Thus, our results may provide the basis for novel diagnostic strategies for this widespread and fatal disease.     

Time reverse automata patterns generated by Spencer-Brown's modulator: invertibility based on autopoiesis

In the present paper the self-consistency or operational closure of autopoiesis is described by introducing time explicitly. It is an extension of Spencer-Brown's idea of time, however. The definition of time is segregated into two parts, corresponding to the syntax and semantics of language, respectively. In this context, time reversibility is defined by the formalization of the relationship between time and self-consistency. This idea has also been discussed in the context of designation and/or naming. Here we will discuss it in the context of cellular automata and explain the structure of one-to-many type mappings. Our approach is the first attempt to extend autopoietic systems in terms of dynamics. It illustrates how to introduce an autopoietic time which looks irreversible, but without the concept of entropy.     

A model of network formation by Physarum plasmodium: Interplay between cell mobility and morphogenesis

The plasmodium of Physarum polycephalum has attracted much attention due its intelligent adaptive behavior. In this study, we constructed a model of the organism and attempted to simulate its locomotion and morphogenetic behavior. By modifying our previous model, we were able to get closer to the actual behavior. We also compared the behavior of the model with that of the real organism, demonstrating remarkable similarity between the two.     

Autonomous Learning in Maze Solution by Octopus

We tested seven octopuses, Octopus vulgaris, in maze-learning experiments. They tried to reach the goal, so as to get a reward, by using various locomotory actions in the path, and sometimes encountered obstacles. They came to select efficient swimming actions in the path; afterwards less efficient tactile actions (crawling, staying put, and so on: these reduce the speed of movement) gradually increased, while time to detour around the obstacle was reduced. To investigate whether octopuses reduce time spent detouring around obstacles by estimating their actions in the path, we devised a trade-off situation in which octopuses were obliged to use tactile actions even though the set-up also encouraged them to use swimming actions. As a result, we could observe that they reduced the detouring time. In that way, we experimentally constituted a perspective as if octopuses looked around the whole maze and estimated their actions. Such a perspective appeared to be autonomous learning.