被竹海包围的村落

在以巨树王国著称的天目山脚下,有一群特殊的农民,他们不种粮食,终年侍弄竹子,以竹笋为业,源源不断地供给周边大城市所需的鲜笋和笋干。这个巨大的竹笋市场魔幻般地把这里变成了一片竹海,在给农民带来财富的同时也伴随着隐忧。[编者按]     

Extending biochemical databases by metabolomic surveys

Metabolomics can map the large metabolic diversity in species, organs, or cell types. In addition to gains in enzyme specificity, many enzymes have retained substrate and reaction promiscuity. Enzyme promiscuity and the large number of enzymes with unknown enzyme function may explain the presence of a plethora of unidentified compounds in metabolomic studies. Cataloguing the identity and differential abundance of all detectable metabolites in metabolomic repositories may detail which compounds and pathways contribute to vital biological functions. The current status in metabolic databases is reviewed concomitant with tools to map and visualize the metabolome.     

Extending life span by increasing oxidative stress

Various nutritional, behavioral, and pharmacological interventions have been previously shown to extend life span in diverse model organisms, including Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, mice, and rats, as well as possibly monkeys and humans. This review aims to summarize published evidence that several longevity-promoting interventions may converge by causing an activation of mitochondrial oxygen consumption to promote increased formation of reactive oxygen species (ROS). These serve as molecular signals to exert downstream effects to ultimately induce endogenous defense mechanisms culminating in increased stress resistance and longevity, an adaptive response more specifically named mitochondrial hormesis or mitohormesis. Consistently, we here summarize findings that antioxidant supplements that prevent these ROS signals interfere with the health-promoting and life-span-extending capabilities of calorie restriction and physical exercise. Taken together and consistent with ample published evidence, the findings summarized here question Harman's Free Radical Theory of Aging and rather suggest that ROS act as essential signaling molecules to promote metabolic health and longevity.     

热量限制延长寿命的分子机制

很多研究均发现,热量限制在很多物种中都有延长寿命的作用.这些报道认为,寿命的延长可 能与氧化应激和炎症过程有关.值得注意的是,热量限制调节氧化应激与脂质代谢调控、抑 制细胞凋亡、DNA保护等分子过程有密切关系.最近,有研究者表明,热量限制调控氧化应激和炎症过程是通过胰岛素/胰岛素样生长因子信号通路起作用的.热量限制在所有的动物模型实验中都显示延长寿命,然而,在人类中应用热量限制,可能还存在很多对人体健康问题值得关注.本文就热量限制如何调控寿命的机制的研究进展作一综述.     

Extending the quasi-steady state approximation by changing variables

The parameter domain for which the quasi-steady state assumption is valid can be considerably extended merely by a simple change of variable. This is demonstrated for a variety of biologically significant examples taken from enzyme kinetics, immunology and ecology.     

Measuring salinity by conductivity

The simple conductivity method described here uses a home-made electrode for determining the salinity of estuarine waters     

Topological classification and enumeration of RNA structures by genus

To an RNA pseudoknot structure is naturally associated a topological surface, which has its associated genus, and structures can thus be classified by the genus. Based on earlier work of Harer–Zagier, we compute the generating function $\mathbf{D}_{g,\sigma }(z)=\sum _{n}\mathbf{d}_{g,\sigma }(n)z^n$ for the number $\mathbf{d}_{g,\sigma }(n)$ of those structures of fixed genus $g$ and minimum stack size $\sigma $ with $n$ nucleotides so that no two consecutive nucleotides are basepaired and show that $\mathbf{D}_{g,\sigma }(z)$ is algebraic. In particular, we prove that $\mathbf{d}_{g,2}(n)\sim k_g\,n^{3(g-\frac{1}{2})} \gamma _2^n$ , where $\gamma _2\approx 1.9685$ . Thus, for stack size at least two, the genus only enters through the sub-exponential factor, and the slow growth rate compared to the number of RNA molecules implies the existence of neutral networks of distinct molecules with the same structure of any genus. Certain RNA structures called shapes are shown to be in natural one-to-one correspondence with the cells in the Penner–Strebel decomposition of Riemann’s moduli space of a surface of genus $g$ with one boundary component, thus providing a link between RNA enumerative problems and the geometry of Riemann’s moduli space.     

Voting-Based Cancer Module Identification by Combining Topological and Data-Driven Properties

Recently, computational approaches integrating copy number aberrations (CNAs) and gene expression (GE) have been extensively studied to identify cancer-related genes and pathways. In this work, we integrate these two data sets with protein-protein interaction (PPI) information to find cancer-related functional modules. To integrate CNA and GE data, we first built a gene-gene relationship network from a set of seed genes by enumerating all types of pairwise correlations, e.g. GE-GE, CNA-GE, and CNA-CNA, over multiple patients. Next, we propose a voting-based cancer module identification algorithm by combining topological and data-driven properties (VToD algorithm) by using the gene-gene relationship network as a source of data-driven information, and the PPI data as topological information. We applied the VToD algorithm to 266 glioblastoma multiforme (GBM) and 96 ovarian carcinoma (OVC) samples that have both expression and copy number measurements, and identified 22 GBM modules and 23 OVC modules. Among 22 GBM modules, 15, 12, and 20 modules were significantly enriched with cancer-related KEGG, BioCarta pathways, and GO terms, respectively. Among 23 OVC modules, 19, 18, and 23 modules were significantly enriched with cancer-related KEGG, BioCarta pathways, and GO terms, respectively. Similarly, we also observed that 9 and 2 GBM modules and 15 and 18 OVC modules were enriched with cancer gene census (CGC) and specific cancer driver genes, respectively. Our proposed module-detection algorithm significantly outperformed other existing methods in terms of both functional and cancer gene set enrichments. Most of the cancer-related pathways from both cancer data sets found in our algorithm contained more than two types of gene-gene relationships, showing strong positive correlations between the number of different types of relationship and CGC enrichment -values (0.64 for GBM and 0.49 for OVC). This study suggests that identified modules containing both expression changes and CNAs can explain cancer-related activities with greater insights.     

Topological remodeling of cultured endothelial cells by characterized cyclic strains

Evaluation of mechanical environment on cellular function is a major field of study in cellular engineering. Endothelial cells lining the entire vascular lumen are subjected to pulsatile blood pressure and flow. Mechanical stresses caused by such forces determine function of arteries and their remodeling. Critical values of mechanical stresses contribute to endothelial damage, plaque formation and atherosclerosis. A device to impose cyclic strain on cultured cells inside an incubator was designed and manufactured operating with different load amplitudes, frequencies, numbers of cycles and ratios of extension to relaxation. Endothelial cells cultured on collagen coated silicon scaffolds were subjected to cyclic loading. Effects of mechanical loading on cell morphology were quantified using image processing methods. Results showed change in cell orientation from a randomly oriented before the test up to 80 degrees alignment from load axis after loading. Endothelial cells were elongated with shape index reductions up to 47% after cyclic stretch. By increase of strain amplitude, loading frequency and number of cycles, significant decrease in shape index and significant increase in orientation angle were observed. Change of load waveform similar to arterial pulse pressure waveform resulted in alteration of cell alignment with 9.7% decrease in shape index, and 10.8% increase in orientation angle. Results of cyclic loading tests in a disturbed environment with elevated PH showed lack of remodeling. It was concluded that tensile loading of endothelial cells influences cell morphology and alignment, a mechanism for structural regulation, functional adaptation and remodeling. Disturbed environment results in endothelial dysfunction and injury.     

Extending the host range of Listeria monocytogenes by rational protein design

In causing disease, pathogens outmaneuver host defenses through a dedicated arsenal of virulence determinants that specifically bind or modify individual host molecules. This dedication limits the intruder to a defined range of hosts. Newly emerging diseases mostly involve existing pathogens whose arsenal has been altered to allow them to infect previously inaccessible hosts. We have emulated this chance occurrence by extending the host range accessible to the human pathogen Listeria monocytogenes by the intestinal route to include the mouse. Analyzing the recognition complex of the listerial invasion protein InlA and its human receptor E-cadherin, we postulated and verified amino acid substitutions in InlA to increase its affinity for E-cadherin. Two single substitutions increase binding affinity by four orders of magnitude and extend binding specificity to include formerly incompatible murine E-cadherin. By rationally adapting a single protein, we thus create a versatile murine model of human listeriosis.     

Extending the NMR spatial resolution limit for RNA by motional couplings

Experimental resolution of distinct dynamical processes in molecules can prove impossible when they are correlated to one another. In nuclear magnetic resonance (NMR) spectroscopy, couplings between internal and overall motions lead to intractable complexity, depriving insights into functionally important motions. Here we demonstrate that motional couplings can be used to anchor NMR frames of reference onto different parts of an RNA molecule, thus extending the spatial resolution limit for dynamical characterization.     

Extending the diversity of cytochrome P450 enzymes by DNA family shuffling

The cytochrome P450 enzymes involved in xenobiotic metabolism are an excellent starting point for the directed evolution of novel biocatalysts due to their wide substrate specificity. A shuffled library of three highly homologous mammalian genes (for P450 2C9, P450 2C11 and P450 2C19) was constructed by applying a modified DNA family shuffling procedure. The modifications made to the traditional DNA shuffling protocols involved non-random digestion via the use of different combinations of restriction enzymes (REs) followed by isolation of fragments under 300 bp by size-selective filtration. Shuffled cytochrome P450 mutants were co-expressed in Escherichia coli with their redox partner, NADPH-cytochrome P450 reductase (NPR). We report here how non-random fragmentation may help in chimeragenesis within the areas of low sequence similarity such as substrate recognition sites (SRSs) that are generally underrepresented in recombination using the random fragmentation process. Size-selective filtration was used to limit recovery of incompletely digested fragments and consequently minimize the chances for contamination of the shuffled library with parental forms. No parental forms could be detected in the shuffled library using restriction fragment length polymorphism (RFLP) analysis, suggesting the library was free of parental contamination. Sequencing of randomly selected mutants demonstrated a high level of chimeragenesis with on average of 8.0+/-2.2 crossovers and a low level of mutagenesis with 5.2+/-2.8 spontaneous mutations per approximately 1.5 kbp of the full-length P450 sequence. The proportion of properly folded protein as indicated by the observation of characteristic Fe(II).CO vs. Fe(II) difference spectra was 15% (4/27) of analysed mutants. Screening of the shuffled library for indole oxidation revealed four clones with similar or higher levels of indigo pigment production to those of the parental P450s and two clones with elevated P450 expression. In this paper we present a method for the effective family shuffling of cytochrome P450 enzymes, applicable to the creation of mutant libraries with expanded metabolic diversity and with a significant proportion of functional clones.     

Topological examination of the bacteriophage lambda S holin by EPR spectroscopy

The S protein from bacteriophage lambda is a three-helix transmembrane protein produced by the prophage which accumulates in the host membrane during late gene expression. It is responsible for the first step in lysing the host cell at the end of the viral life cycle by multimerizing together to form large pores which permeabilize the host membrane to allow the escape of virions. Several previous studies have established a model for the assembly of holin into functional holes and the manner in which they pack together, but it is still not fully understood how the very rapid transition from monomer or dimer to multimeric pore occurs with such precise timing once the requisite threshold is reached. Here, site-directed spin labeling with a nitroxide label at introduced cysteine residues is used to corroborate existing topological data from a crosslinking study of the multimerized holin by EPR spectroscopy. CW-EPR spectral lineshape analysis and power saturation data are consistent with a three-helix topology with an unstructured C-terminal domain, as well as at least one interface on transmembrane domain 1 which is exposed to the lumen of the hole, and a highly constrained steric environment suggestive of a tight helical packing interface at transmembrane domain 2.     

Extending the time window of mammalian heart regeneration by thymosin beta 4

Recent studies demonstrated that the heart of 1‐day‐old neonatal mice could regenerate, with Wt1⁺ EPDCs migrating into myocardial regions after partial surgical resection, but this capacity was lost by 7 days of age. By treatment with Tβ4 to maintain Wt1 expression and retain the migrating feature of EPDCs in neonatal mice, we explored the possibility of restoring the cardiac regeneration potential of mice. We intraperitoneally injected Tβ4 into 1‐day‐old mice on daily basis and then apical resection was performed on the mice 7 days later. Twenty one days after the resection, morphological analysis revealed that the Tβ4‐treated mice regenerated the resected ventricular apex, while the mice in PBS control group developed significant fibrosis without apical regeneration. The Tβ4‐treated mice had significantly better ventricular ejection fraction and fractional shortening than controls. During the process of regeneration, Wt1⁺ EPDCs migrated into myocardial region and some of them expressed Islet1 and the markers for mature cardiomyocytes, such as cTnT and SαA. These characteristics of Wt1⁺ EPDCs were also seen in the heart regeneration of mice subjected to apical resection 1 day after birth. Tβ4 has no essential effect on cell cycle activity as no disruption of actin filaments was observed in Tβ4‐treated hearts. These results revealed that the cardiac regeneration potential of neonatal mice could be extended to the 7th post‐natal day by Tβ4 and Wt1⁺ EPDCs mobilization might play an important role in the extension.     

Measuring cell forces by a photoelastic method

A new method for measuring the mechanical forces exerted by cells on the substratum and through the substratum to act on other cells is described. This method depends upon the growth of cells on a photoelastic substratum, polydimethylsiloxane coated with a near monolayer of fibronectin. Changes in the forces applied by the cells to the substratum lead to changes in birefringence, which can be measured and recorded by the Polscope computer-controlled polarizing microscope. The changes in azimuth and retardance can be measured. A method for calibrating the stress is described. The method is sensitive down to forces of 1 pN per square microns. Fairly rapid changes with time can be recorded with a time resolution of approximately 1 s. The observations show that both isolated adhering, spread cells and also cells close to contact exert stresses on the substratum and that the stresses are those that would be produced by forces of 10-1000 pN per cell. The forces are almost certainly exerted on nearby cells since movement of one cell causes strains to appear around other nearby cells. The method has the defect that strains under the cells, though detectable in principle, are unclear due to birefringence of the components of the cytoplasm and nucleus. It is of special interest that the strains on the substratum can change in the time course of a few seconds and appear to be concentrated near the base of the lamellopodium of the cell as though they originated there. As well as exerting forces on the substratum in the direction of the long axis of the cell, appreciable forces are exerted from the lateral sides of the cell. The observations and measurements tend to argue that microtopography and embedded beads can concentrate the forces.     

Measuring gene expression by quantitative proteome analysis

Proteome analysis is most commonly accomplished by the combination of two-dimensional gel electrophoresis for protein separation, visualization, and quantification and mass spectrometry for protein identification. Over the past year, exceptional progress has been made towards developing a new technology base for the precise quantification and identification of proteins in complex mixtures, that is, quantitative proteomics.