A model for nucleotide sequences.

We propose a model for generating "artificial" nucleotide sequences and, by the method of mapping those sequences onto a "DNA-walk," we analyze the presence of correlation between nucleotides. Artificial sequences are constructed considering, basically, interactions between first neighbors and between more distant units. We show that long-range correlations may be favored by the occurrence of intrastrand interactions, which give a nonlinear characteristic to the sequence.     

雄性麋鹿的交配机会、社会等级和皮质醇水平

我们在北京麋鹿苑研究了发情期雄性麋鹿的社会行为、社会等级和血清皮质醇水平,并分析了三者间的相互关系。按照雄性麋鹿的行为,将雄性麋鹿分为优势群和从属群。优势群包括群主和挑战者,从属群包括单身汉和被淘汰群主。使用SJ—Ⅰ型事件记录器进行常规行为取样,用放射免疫分析法测定血清皮质醇含量。发现：(1)优势雄鹿的发情行为频次明显高于从属雄鹿;(2)攻击行为的发生频次在两组间无显著差异;(3)血清皮质醇含量在两组间也无显著差异。由此我们认为,发情期雄性麋鹿的社会等级序位影响许多行为的表达,优势雄鹿成功交配的机会比从属雄鹿多。而攻击行为和肾上腺皮质醇的分泌与社群等级无明显相关,可能是麋鹿在圈养状态下的一种适应策略,这将有利于缓解发情期雄鹿的紧张,从而允许更多的能量投放在发情交配上。     

Proliferation and degeneration of circulating CFU-GM in 15 adult normal subjects. Can any ontogenetic relationship be deduced from these data?

We studied, in 15 normal adults, the "in vitro" proliferation and differentiation of circulating CFU-GM, in order to assess their implication in the processes that regulate the dynamic equilibrium of granulopoiesis, analogous to bone marrow CFU-GM, and to deduce by their growth behaviour the ontogenetic relationship between CFU-GM subpopulations in the circulating and bone marrow compartments respectively. We found that "in vitro" proliferation of circulating CFU-GM predominates over their degeneration. We believe circulating CFU-GM and bone marrow CFU-GM are not implicated in granulopoiesis regulation in the same manner, and that circulating CFU-GM are more immature than bone marrow CFU-GM when taking proliferation and GM-CSF response into account. One cannot ignore the hypothesis that cells that "in vivo" are quiescent, are recruited "in vitro" with GM-CSF. Finally we would like to draw attention to the parallelism between CFU-GM classification in types 1 and 2 using monoclonal antibodies to track surface antigens, and our classification obtained by using a new mathematical model that takes the "birth" and "dead" of cellular aggregates into account.     

Genomic ancestry, self-reported "color" and quantitative measures of skin pigmentation in Brazilian admixed siblings

A current concern in genetic epidemiology studies in admixed populations is that population stratification can lead to spurious results. The Brazilian census classifies individuals according to self-reported "color", but several studies have demonstrated that stratifying according to "color" is not a useful strategy to control for population structure, due to the dissociation between self-reported "color" and genomic ancestry. We report the results of a study in a group of Brazilian siblings in which we measured skin pigmentation using a reflectometer, and estimated genomic ancestry using 21 Ancestry Informative Markers (AIMs). Self-reported "color", according to the Brazilian census, was also available for each participant. This made it possible to evaluate the relationship between self-reported "color" and skin pigmentation, self-reported "color" and genomic ancestry, and skin pigmentation and genomic ancestry. We observed that, although there were significant differences between the three "color" groups in genomic ancestry and skin pigmentation, there was considerable dispersion within each group and substantial overlap between groups. We also saw that there was no good agreement between the "color" categories reported by each member of the sibling pair: 30 out of 86 sibling pairs reported different "color", and in some cases, the sibling reporting the darker "color" category had lighter skin pigmentation. Socioeconomic status was significantly associated with self-reported "color" and genomic ancestry in this sample. This and other studies show that subjective classifications based on self-reported "color", such as the one that is used in the Brazilian census, are inadequate to describe the population structure present in recently admixed populations. Finally, we observed that one of the AIMs included in the panel (rs1426654), which is located in the known pigmentation gene SLC24A5, was strongly associated with skin pigmentation in this sample.     

Use of a FACS III for fluorescence depolarization with DPH

We have previously demonstrated age-related differences in human lymphocyte membrane fluidity, by use of steady-state polarization measurements on bulk cell suspensions with the fluorescence probe DPH. However, for exact analysis of the possible functional importance of these changes, single-cell measurements were deemed of interest. We have now used an analog division device to measure fluorescence depolarization "p" of DPH in real time with a FACS III flow cytometer. The measurements are reliable, as we have been able to confirm the differences in DPH "p" between monocytes and lymphocytes previously shown in bulk suspension and to demonstrate the expected differences in fluidity of lipid-modulated cells. We also found significant differences in DPH "p" between lymphocytes of young and elderly blood donors. Lymphocyte subsets did not differ in polarization values but did differ in fluorescence intensity with Th less than Ts less than B = NK cells.     

Cell Surface Proteins of Agrobactevium tumefaciens Involved in the Transfer of T-DNA to the Host

We investigated the taste synergy between L-theanine and the flavour enhancer, inosine 5′-monophosphate (IMP), by using a human sensory evaluation. When L-theanine was added to IMP, only the umami taste was enhanced. We then investigated this synergistic effect of L-theanine in mice by gustatory nerve recording. We confirmed the synergism between L-theanine and IMP for the umami taste.     

Insights into allosteric control of vinculin function from its large scale conformational dynamics

Vinculin is an important constituent of both cell-cell and cell-matrix junctions, where it plays crucial roles in the regulation of cell adhesion and migration. When activated, it mediates the linkage between cadherins (cell-cell) or integrins (cell-matrix) and the actin cytoskeleton through interactions with various proteins. The activation of vinculin requires structural conversions from an autoinhibited conformation to the "open" conformations in which the occluded binding sites of its different ligands become exposed, while the structural dynamics underlying the vinculin activation remains largely unknown. Here we report the first computational study of large scale conformational dynamics of full-length vinculin. We find that the "holding" and "releasing" motions between vinculin tail and pincer-like structure formed by first three domains of vinculin are the dominant motions near the native state of vinculin, indicating that an inherent flexibility of vinculin has a large influence on its allostery. We also find a cooperative dissociation between the head and tail domains of vinculin with increasing temperature in both thermodynamic and kinetic simulations, implying that vinculin may function as an allosteric switch in response to external signals. We show that the kinetics of vinculin unfolding exhibits specific sequential patterns, suggesting that a sophisticated interplay between domains may synergistically contribute to vinculin activation. We further find that the interaction between vinculin-binding site peptide from talin and vinculin significantly destabilizes the intramolecular head-tail interactions, suggesting a direct role of talin binding in vinculin activation.     

Minimalist protein model as a diagnostic tool for misfolding and aggregation

We propose a realistic coarse-grained protein model and a technique to "anchor" the model to available experimental data. We apply this procedure to characterize the effect of multiple mutations on the folding mechanism of protein S6. We show that the mutation of a few "gatekeeper" residues triggers significant changes on the folding landscape of S6. These results suggest that gatekeeper residues control the flexibility of critical regions of S6, that in turn regulates the delicate balance between folding and aggregation. Although obtained with a minimalist protein model, these results are fully consistent with experimental evidence and offer a clue to understand the interplay between folding and aggregation in protein S6.     

Removing the bottlenecks of cell culture metabolomics: fast normalization procedure,correlation of metabolites to cell number,and impact of the cell harvesting method

Introduction

Although cultured cells are nowadays regularly analyzed by metabolomics technologies, some issues in study setup and data processing are still not resolved to complete satisfaction: a suitable harvesting method for adherent cells, a fast and robust method for data normalization, and the proof that metabolite levels can be normalized to cell number.

Objectives

We intended to develop a fast method for normalization of cell culture metabolomics samples, to analyze how metabolite levels correlate with cell numbers, and to elucidate the impact of the kind of harvesting on measured metabolite profiles.

Methods

We cultured four different human cell lines and used them to develop a fluorescence-based method for DNA quantification. Further, we assessed the correlation between metabolite levels and cell numbers and focused on the impact of the harvesting method (scraping or trypsinization) on the metabolite profile.

Results

We developed a fast, sensitive and robust fluorescence-based method for DNA quantification showing excellent linear correlation between fluorescence intensities and cell numbers for all cell lines. Furthermore, 82–97 % of the measured intracellular metabolites displayed linear correlation between metabolite concentrations and cell numbers. We observed differences in amino acids, biogenic amines, and lipid levels between trypsinized and scraped cells.

Conclusion

We offer a fast, robust, and validated normalization method for cell culture metabolomics samples and demonstrate the eligibility of the normalization of metabolomics data to the cell number. We show a cell line and metabolite-specific impact of the harvesting method on metabolite concentrations.

     

An empirical comparison of knowledge and skill in the context of traditional ecological knowledge

Background

We test whether traditional ecological knowledge (TEK) about how to make an item predicts a person’s skill at making it among the Tsimane’ (Bolivia). The rationale for this research is that the failure to distinguish between knowledge and skill might account for some of the conflicting results about the relationships between TEK, human health, and economic development.

Methods

We test the association between a commonly-used measure of individual knowledge (cultural consensus analysis) about how to make an arrow or a bag and a measure of individual skill at making these items, using ordinary least-squares regression. The study consists of 43 participants from 3 villages.

Results

We find no association between our measures of knowledge and skill (core model, p?>?0.5,?R ² ?=?.132).

Conclusions

While we cannot rule out the possibility of a real association between these phenomena, we interpret our findings as support for the claim that researchers should distinguish between methods to measure knowledge and skill when studying trends in TEK.

     

Attributional and consequential LCA in the ILCD handbook

Purpose

This discussion article aims to highlight two problematic aspects in the International Reference Life Cycle Data System (ILCD) Handbook: its guidance to the choice between attributional and consequential modeling and to the choice between average and marginal data as input to the life cycle inventory (LCI) analysis.

Methods

We analyze the ILCD guidance by comparing different statements in the handbook with each other and with previous research in this area.

Results and discussion

We find that the ILCD handbook is internally inconsistent when it comes to recommendations on how to choose between attributional and consequential modeling. We also find that the handbook is inconsistent with much of previous research in this matter, and also in the recommendations on how to choose between average and marginal data in the LCI.

Conclusions

Because of the inconsistencies in the ILCD handbook, we recommend that the handbook be revised.

     

A stronger coordination of litter decomposability between leaves and fine roots for woody species in a warmer region

Key message

There is a positive correlation between leaf and root decomposition across species, both in a warm-temperate forest in Japan, as well as globally.

Abstract

Evaluating the effects of plant species traits on litter decomposition would increase our understanding of plant–soil feedbacks in forest ecosystems. Currently, an assessment of a possible coordination between leaf and root decomposition across different species is required. However, previous studies have generated conflicting results. We hypothesized that such inconsistencies may be attributed to differences in local climatic effects on the decomposition process. We focused on the linkages between leaf and fine-root decomposition of woody species in a warm-temperate forest, which have not been addressed in previous studies. We found a significant positive correlation between leaf and root decomposition, and this linkage may be attributed to a wider range of decomposition rates across the species in our study forest. Additionally, we combined our data with those of previous studies of woody species to infer a global linkage in the decomposition process between leaves and roots. We found a positive correlation in decomposition rates between leaves and roots at the global scale, as well as a relatively strong correlation in warmer regions. These results support the importance of litter quality on biogeochemical processes and suggest that synergetic interactions between climate and plant communities could be amplified in a warmer future.

     

肺与大肠相表里的微生态学解释

“肺与大肠相表里”、“肺在志为悲（忧）”均是传统中医所特有的思维,现代临床实践也发现肠道疾病与肺部疾病常相伴而发,而情志失调常为肺肠疾病的诱因。但没有物质基础的经脉如何联系肺与肠,用经脉络属或是五行理论来解释的“肺在志为悲（忧）”观点有没有明确的物质基础仍有待研究。目前各项研究发现肺与大肠在解剖及生理病理过程方面存在相似性,而菌群在肺—肠联系中起着重要的作用,很可能是经脉联系肺肠的物质基础之一,随着对肠道菌群研究的进一步深入,其与抑郁症等情志障碍疾病的潜在关系被逐渐揭示,也让“肺在志为悲（忧）”的观点获得认同和深化,借助最新研究成果深度认识理论术语与客观实在的关系,是中医发展的必由之路。     

Transnational migration and the redefinition of the state: Variations and explanations

In this article, we examine the shifting policies of sending country states towards communities living abroad, demonstrate the ways in which these are redefining the relationship between the state and its territorial boundaries, and highlight how these reconfigure conventional understandings of sovereignty, citizenship and membership. We begin by delineating the ­different types of policies that sending states are adapting in order to break down categories like "global nations policies" and to identify similarities and differences between states. We then suggest some possible explanations both for the convergence we see on the "repertoire" of policies that states employ and divergence we see in how far states are willing to go to ensure that migrants remain enduring long-distance membership. We draw on material from several countries, but look most closely at Brazil, Mexico, the Dominican Republic and Haiti.     

Sex differences in hepatic one-carbon metabolism

Background

There are large differences between men and women of child-bearing age in the expression level of 5 key enzymes in one-carbon metabolism almost certainly caused by the sex hormones. These male-female differences in one-carbon metabolism are greatly accentuated during pregnancy. Thus, understanding the origin and consequences of sex differences in one-carbon metabolism is important for precision medicine.

Results

We have created a mathematical model of hepatic one-carbon metabolism based on the underlying physiology and biochemistry. We use the model to investigate the consequences of sex differences in gene expression. We give a mechanistic understanding of observed concentration differences in one-carbon metabolism and explain why women have lower S-andenosylmethionine, lower homocysteine, and higher choline and betaine. We give a new explanation of the well known phenomenon that folate supplementation lowers homocysteine and we show how to use the model to investigate the effects of vitamin deficiencies, gene polymorphisms, and nutrient input changes.

Conclusions

Our model of hepatic one-carbon metabolism is a useful platform for investigating the mechanistic reasons that underlie known associations between metabolites. In particular, we explain how gene expression differences lead to metabolic differences between males and females.

     

Roost switching, roost sharing and social cohesion: forest-dwelling big brown bats, Eptesicus fuscus, conform to the fission-fusion model

We used radiotelemetry to quantify roost switching and assess associations between members of maternity colonies of forest-dwelling big brown bats. Bats remained loyal to small roosting areas of forest within and between years and switched trees often (). For radiotagged bats from the colony in one of these areas, roost-switching frequency was positively correlated with the number of different individuals with which tagged bats shared roosts. We quantified associations between pairs of bats using a pairwise sharing index and found that bats associated more often than predicted when roost and roostmate selection were random but that all tagged bats spent at least some days roosting in different trees, apart from preferred roostmates. Our results suggest that forest-dwelling big brown bats conform to a fission-fusion roosting pattern. Roost switching in forests may reflect the maintenance of long-term social relationships between individuals from a colony that is spread among a number of different trees on a given night. In this fission-fusion scenario, switching between trees, within a local area, could serve to increase the numbers of individuals with which bats maintain associations. We contend that roosting areas in forests are analogous to spatially large roosts in caves, mines and buildings.     

Silicon cellular morphology

We describe a design technique for neuromorphic engineering that exploits both Mead's notion of physical equivalence between transistors and ion channels and the intrinsic properties of the materials of which transistors are composed. This is in contrast to the "algorithmic" design technique in common use. A "physical" design technique allows us to emphasise the morphology of cells. We hope to use this in an exploration of the effect of cell morphology upon function.     

Coupling effects on turning points of infectious diseases epidemics in scale-free networks

Background

Pandemic is a typical spreading phenomenon that can be observed in the human society and is dependent on the structure of the social network. The Susceptible-Infective-Recovered (SIR) model describes spreading phenomena using two spreading factors; contagiousness (β) and recovery rate (γ). Some network models are trying to reflect the social network, but the real structure is difficult to uncover.

Methods

We have developed a spreading phenomenon simulator that can input the epidemic parameters and network parameters and performed the experiment of disease propagation. The simulation result was analyzed to construct a new marker VRTP distribution. We also induced the VRTP formula for three of the network mathematical models.

Results

We suggest new marker VRTP (value of recovered on turning point) to describe the coupling between the SIR spreading and the Scale-free (SF) network and observe the aspects of the coupling effects with the various of spreading and network parameters. We also derive the analytic formulation of VRTP in the fully mixed model, the configuration model, and the degree-based model respectively in the mathematical function form for the insights on the relationship between experimental simulation and theoretical consideration.

Conclusions

We discover the coupling effect between SIR spreading and SF network through devising novel marker VRTP which reflects the shifting effect and relates to entropy.

     

Type I burst excitability

We introduce the concept of type I burst excitability, which is a generalization of the normal excitability that is well-known in cardiac and neural systems. We demonstrate this type of burst excitability in a specific model system, a pyramidal cell from the electrosensory lateral line lobe of the weakly electric fish Apteronotus leptorhynchus. As depolarizing current is increased, a saddle-node bifurcation of periodic orbits occurs, which separates tonic and burst activity. This bifurcation is responsible for the excitable nature of the system, and is the basis for the type I designation. We verify the existence of this transition from in vitro recordings of a number of actual pyramidal cells. A scaling relationship between the magnitude and duration of a current pulse required to induce a burst is derived. We also observe this type of burst excitability and the scaling relationships in a multicompartmental model that is driven by realistic stochastic synaptic inputs mimicking sensory input. We conclude by discussing the relevance of burst excitability to communication between weakly electric fish.     

Distribution and Geographic Variation in the Western Woolly Lemur (Avahi occidentalis) with Description of a New Species (A. unicolor

The western woolly lemur is distributed through central western, northwestern and possibly northern Madagascar and is traditionally viewed as a monotypic species (Avahi occidentalis) or as a subspecies of A. laniger. We present new data on body weights of Avahi which, together with previously available body weights, provide additional evidence for recognizing eastern and western woolly lemurs as two distinct species. We then reexamine the distributions of, and chromatic variation within and between, populations of western woolly lemurs. A comparative study of wild subjects and museum skins reveals that several geographically discrete morphs exist in western Avahi, which is clearly polytypic. Marked differences between populations in fur coloration suggest that 3 distinct taxa should be recognized. The populations differ considerably in their habitat structure. In addition, field observations suggest clear differences in population density between 2 of the populations. We describe and name one new species.