Structural insights into catalysis and dimerization enhanced exonuclease activity of RNase?J

RNase J is a conserved ribonuclease that belongs to the β-CASP family of nucleases. It possesses both endo- and exo-ribonuclease activities, which play a key role in pre-rRNA maturation and mRNA decay. Here we report high-resolution crystal structures of Deinococcus radiodurans RNase J complexed with RNA or uridine 5′-monophosphate in the presence of manganese ions. Biochemical and structural studies revealed that RNase J uses zinc ions for two-metal-ion catalysis. One residue conserved among RNase J orthologues (motif B) forms specific electrostatic interactions with the scissile phosphate of the RNA that is critical for the catalysis and product stabilization. The additional manganese ion, which is coordinated by conserved residues at the dimer interface, is critical for RNase J dimerization and exonuclease activity. The structures may also shed light on the mechanism of RNase J exo- and endonucleolytic activity switch.     

Bacillus subtilis RNase J1 endonuclease and 5′ exonuclease activities in the turnover of ΔermC mRNA

RNase J1, a ribonuclease with 5′ exonuclease and endonuclease activities, is an important factor in Bacillus subtilis mRNA decay. A model for RNase J1 endonuclease activity in mRNA turnover has RNase J1 binding to the 5′ end and tracking to a target site downstream, where it makes a decay-initiating cleavage. The upstream fragment from this cleavage is degraded by 3′ exonucleases; the downstream fragment is degraded by RNase J1 5′ exonuclease activity. Previously, ΔermC mRNA was used to show 5′-end dependence of mRNA turnover. Here we used ΔermC mRNA to probe RNase J1-dependent degradation, and the results were consistent with aspects of the model. ΔermC mRNA showed increased stability in a mutant strain that contained a reduced level of RNase J1. In agreement with the tracking concept, insertion of a strong stem–loop structure at +65 resulted in increased stability. Weakening this stem–loop structure resulted in reversion to wild-type stability. RNA fragments containing the 3′ end were detected in a strain with reduced RNase J1 expression, but were undetectable in the wild type. The 5′ ends of these fragments mapped to the upstream side of predicted stem–loop structures, consistent with an impediment to RNase J1 5′ exonuclease processivity. A ΔermC mRNA deletion analysis suggested that decay-initiating endonuclease cleavage could occur at several sites near the 3′ end. However, even in the absence of these sites, stability was further increased in a strain with reduced RNase J1, suggesting alternate pathways for decay that could include exonucleolytic decay from the 5′ end.     

Distinct Requirements for 5′-Monophosphate-assisted RNA Cleavage by Escherichia coli RNase E and RNase G

RNase E and RNase G are homologous endonucleases that play important roles in RNA processing and decay in Escherichia coli and related bacterial species. Rapid mRNA degradation is facilitated by the preference of both enzymes for decay intermediates whose 5′ end is monophosphorylated. In this report we identify key characteristics of RNA that influence the rate of 5′-monophosphate-assisted cleavage by these two ribonucleases. In vitro, both require at least two and prefer three or more unpaired 5′-terminal nucleotides for such cleavage; however, RNase G is impeded more than RNase E when fewer than four unpaired nucleotides are present at the 5′ end. Each can tolerate any unpaired nucleotide (A, G, C, or U) at either of the first two positions, with only modest biases. The optimal spacing between the 5′ end and the scissile phosphate appears to be eight nucleotides for RNase E but only six for RNase G. 5′-Monophosphate-assisted cleavage also occurs, albeit more slowly, when that spacing is greater or at most one nucleotide shorter than the optimum, but there is no simple inverse relationship between increased spacing and the rate of cleavage. These properties are also manifested during 5′-end-dependent mRNA degradation in E. coli.     

Serological identification and molecular characterization of B (A) 02 subtype in patients and blood donors from Eastern China

This study was designed to identify the rare?type?ABO?blood?groups, B(A) 02, from Eastern China. Three samples with discordant serological results during routine blood type identification and four samples from one sample’ family were selected. All of them were detected by serological method. The exon 6 and 7 of the ABO genes were amplified by PCR and sequenced. They were typed as AsubB by serology and as BO by genotype. In AsubB samples, nt 700C>G mutation was detected in B gene, which was previously defined as B(A)02 alleles. In these seven samples, six showed B(A)02/O01 and one showed B(A)02/O02.B(A)02 allele was found to be more common in this study than B(A)04 which is considered to be more frequent than B(A)02. The careful identification of rare blood types is important for the safety of clinical blood transfusion.     

黄芪多糖对RNase和RNase抑制因子的作用

黄芪多糖-Ⅱ(简称APS-2)系葡萄糖聚合体,分子量12,300,其作用与黄芪多糖(APS)相似。小鼠和大鼠皆腹腔注射200mg/kg/day×3J小鼠实验表明APS-2有显著抑制肝、脾碱性RNase活力的作用,对血清RNase活力无作用,对酸性RNase无明显抑制。大鼠实验表明对肝碱性RNase只有104,000×g部分有显著抑制作用,而对10,000×g部分无影响。对肝碱性RNase的抑制因子具显著性增强作用。因此黄芪多糖的作用是通过增强RNase抑制因子和抑制RNase活力,使RNA的分解代谢降低,从而引起RNA累积和合成速率的降低。     

Environmental Fluctuations and Level of Density-Compensation Strongly Affects the Probability of Fixation and Fixation Times

The probability of, and time to, fixation of a mutation in a population has traditionally been studied by the classic Wright–Fisher model where population size is constant. Recent theoretical expansions have covered fluctuating populations in various ways but have not incorporated models of how the environment fluctuates in combination with different levels of density-compensation affecting fecundity. We tested the hypothesis that the probability of, and time to, fixation of neutral, advantageous and deleterious mutations is dependent on how the environment fluctuates over time, and on the level of density-compensation. We found that fixation probabilities and times were dependent on the pattern of autocorrelation of carrying capacity over time and interacted with density-compensation. The pattern found was most pronounced at small population sizes. The patterns differed greatly depending on whether the mutation was neutral, advantageous, or disadvantageous. The results indicate that the degree of mismatch between carrying capacity and population size is a key factor, rather than population size per se, and that effective population sizes can be very low also when the census population size is far above the carrying capacity. This study highlights the need for explicit population dynamic models and models for environmental fluctuations for the understanding of the dynamics of genes in populations.     

Modeling and Estimation of Kinetic Parameters and Replicative Fitness of HIV-1 from Flow-Cytometry-Based Growth Competition Experiments

Growth competition assays have been developed to quantify the relative fitness of HIV-1 mutants. In this article, we develop mathematical models to describe viral/cellular dynamic interactions in the assay system from which the competitive fitness indices or parameters are defined. In our previous HIV-viral fitness experiments, the concentration of uninfected target cells was assumed to be constant (Wu et al. 2006). But this may not be true in some experiments. In addition, dual infection may frequently occur in viral fitness experiments and may not be ignorable. Here, we relax these two assumptions and extend our earlier viral fitness model (Wu et al. 2006). The resulting models then become nonlinear ODE systems for which closed-form solutions are not achievable. In the new model, the viral relative fitness is a function of time since it depends on the target cell concentration. First, we studied the structure identifiability of the nonlinear ODE models. The identifiability analysis showed that all parameters in the proposed models are identifiable from the flow-cytometry-based experimental data that we collected. We then employed a global optimization approach (the differential evolution algorithm) to directly estimate the kinetic parameters as well as the relative fitness index in the nonlinear ODE models using nonlinear least square regression based on the experimental data. Practical identifiability was investigated via Monte Carlo simulations.     

Cytochrome c and superoxide

Wegerich et al. (J. Biol. Inorg. Chem. 18:429–440, 2013), working with singly modified human cytochromes c, claim to have found a new mechanism for the reduction of iron(III) cytochrome c by superoxide. I show that electron transfer by way of the solvent-accessible haem edge—a mechanism not considered by Wegerich et al.—is still the correct mechanism. Furthermore, several deficiencies in this work preclude any comparisons with other publications on this topic.     

Thidiazuron-induced morphogenetic response in petiole cultures of Pelargonium × hortorum and Pelargonium × domesticum and its histological analysis

The possibility of inducing somatic embryogenesis in petiole cultures of two cultivars of Pelargonium × hortorum and of one cultivar of Pelargonium × domesticum using thidiazuron (TDZ) was investigated. Petioles were cultivated on a modified Murashige and Skoog medium with different concentrations and application periods of TDZ. Regeneration was achieved with all TDZ treatments for all cultivars and was highly variable. Shoots of different shapes and somatic embryo-like structures were observed. Histological examination revealed that no somatic embryos were formed, and regenerants had to be classified as shoots and shoot-like or leaf-like structures. The importance of these results on the classification of regeneration induced by TDZ in these species and on the propagation of these pelargoniums is discussed.     

固相RNasin亲和层析RNase

大鼠肝RNasin与溴化氰活化的Sepharose 4B反应制备了固相大鼠肝RNasin。用固相大鼠肝RNasin亲和层析大鼠肝中性RNase,可以将其分为两部分。固相大鼠肝RNasin可以亲和层析牛胰RNase的结果说明,牛胰和大鼠肝RNase在二级和三级结构上都非常相似。这为大鼠肝RNase来源于胰脏的观点提供了一个新证据。固相RNasin可以亲和吸附大肠杆菌RNase说明原核细胞RNase与真核细胞RNase在分子起源方面有一定的亲缘关系。固相RNasin柱层析为纯化RNase提供了一个简便的新方法。     

The Final Size of an Epidemic and Its Relation to the Basic Reproduction Number

We study the final size equation for an epidemic in a subdivided population with general mixing patterns among subgroups. The equation is determined by a matrix with the same spectrum as the next generation matrix and it exhibits a threshold controlled by the common dominant eigenvalue, the basic reproduction number R₀{\mathcal{R}_{0}}: There is a unique positive solution giving the size of the epidemic if and only if R₀{\mathcal{R}_{0}} exceeds unity. When mixing heterogeneities arise only from variation in contact rates and proportionate mixing, the final size of the epidemic in a heterogeneously mixing population is always smaller than that in a homogeneously mixing population with the same basic reproduction number R₀{\mathcal{R}_{0}}. For other mixing patterns, the relation may be reversed.     

Microenvironmental influences of apoptosis in vivo and in vitro

The apoptosis program of physiological cell death elicits a range of non-phlogistic homeostatic mechanisms—“recognition, response and removal”—that regulate the microenvironments of normal and diseased tissues via multiple modalities operating over short and long distances. The molecular mechanisms mediate intercellular signaling through direct contact with neighboring cells, release of soluble factors and production of membrane-delimited fragments (apoptotic bodies, blebs and microparticles) that allow for interaction with host cells over long distances. These processes effect the selective recruitment of mononuclear phagocytes and the specific activation of both phagocytic and non-phagocytic cells. While much evidence is available concerning the mechanisms underlying the recognition and responses of phagocytes that culminate in the engulfment and removal of apoptotic cell bodies, relatively little is yet known about the non-phagocytic cellular responses to the apoptosis program. These responses regulate inflammatory and immune cell activation as well as cell fate decisions of proliferation, differentiation and death. Here, we review current knowledge of these processes, considering especially how apoptotic cells condition the microenvironments of normal and malignant tissues. We also discuss how apoptotic cells that persist in the absence of phagocytic clearance exert inhibitory effects over their viable neighbors, paying particular attention to the specific case of cell cultures and highlighting how new cell-corpse-clearance devices—Dead-Cert^® Nanoparticles—can significantly improve the efficacy of cell cultures through effective removal of non-viable cells in the absence of phagocytes in vitro.     

Workload characterization in a high-energy data grid and impact on resource management

The analysis of data usage in a large set of real traces from a high-energy physics collaboration revealed the existence of an emergent grouping of files that we coined “filecules”. This paper presents the benefits of using this file grouping for prestaging data and compares it with previously proposed file grouping techniques along a range of performance metrics. Our experiments with real workloads demonstrate that filecule grouping is a reliable and useful abstraction for data management in science Grids; that preserving time locality for data prestaging is highly recommended; that job reordering with respect to data availability has significant impact on throughput; and finally, that a relatively short history of traces is a good predictor for filecule grouping. Our experimental results provide lessons for workload modeling and suggest design guidelines for data management in data-intensive resource-sharing environments.