Isolation of the exoelectrogenic bacterium Ochrobactrum anthropi YZ-1 by using a U-tube microbial fuel cell

Exoelectrogenic bacteria have potential for many different biotechnology applications due to their ability to transfer electrons outside the cell to insoluble electron acceptors, such as metal oxides or the anodes of microbial fuel cells (MFCs). Very few exoelectrogens have been directly isolated from MFCs, and all of these organisms have been obtained by techniques that potentially restrict the diversity of exoelectrogenic bacteria. A special U-tube-shaped MFC was therefore developed to enrich exoelectrogenic bacteria with isolation based on dilution-to-extinction methods. Using this device, we obtained a pure culture identified as Ochrobactrum anthropi YZ-1 based on 16S rRNA gene sequencing and physiological and biochemical characterization. Strain YZ-1 was unable to respire using hydrous Fe(III) oxide but produced 89 mW/m(2) using acetate as the electron donor in the U-tube MFC. Strain YZ-1 produced current using a wide range of substrates, including acetate, lactate, propionate, butyrate, glucose, sucrose, cellobiose, glycerol, and ethanol. Like another exoelectrogenic bacterium (Pseudomonas aeruginosa), O. anthropi is an opportunistic pathogen, suggesting that electrogenesis should be explored as a characteristic that confers advantages to these types of pathogenic bacteria. Further applications of this new U-tube MFC system should provide a method for obtaining additional exoelectrogenic microorganisms that do not necessarily require metal oxides for cell respiration.     

Two ZnF-UBP domains in isopeptidase T (USP5)

Human ubiquitin-specific cysteine protease 5 (USP5, also known as ISOT and isopeptidase T), an 835-residue multidomain enzyme, recycles ubiquitin by hydrolyzing isopeptide bonds in a variety of unanchored polyubiquitin substrates. Activation of the enzyme's hydrolytic activity toward ubiquitin-AMC (7-amino-4-methylcoumarin), a fluorogenic substrate, by the addition of free, unanchored monoubiquitin suggested an allosteric mechanism of activation by the ZnF-UBP domain (residues 163-291), which binds the substrate's unanchored diglycine carboxyl tail. By determining the structure of full-length USP5, we discovered the existence of a cryptic ZnF-UBP domain (residues 1-156), which was tightly bound to the catalytic core and was indispensable for catalytic activity. In contrast, the previously characterized ZnF-UBP domain did not contribute directly to the active site; a paucity of interactions suggested flexibility between these two domains consistent with an ability by the enzyme to hydrolyze a variety of different polyubiquitin chain linkages. Deletion of the known ZnF-UBP domain did not significantly affect rate of hydrolysis of ubiquitin-AMC and suggested that it is likely associated mainly with substrate targeting and specificity. Together, our findings show that USP5 uses multiple ZnF-UBP domains for substrate targeting and core catalytic function.     

A novel approach to sequence validating protein expression clones with automated decision making

Background  

Whereas the molecular assembly of protein expression clones is readily automated and routinely accomplished in high throughput, sequence verification of these clones is still largely performed manually, an arduous and time consuming process. The ultimate goal of validation is to determine if a given plasmid clone matches its reference sequence sufficiently to be "acceptable" for use in protein expression experiments. Given the accelerating increase in availability of tens of thousands of unverified clones, there is a strong demand for rapid, efficient and accurate software that automates clone validation.     

Contrasting effects of plant inter‐ and intraspecific variation on community trait responses to restoration of a sandy grassland ecosystem

Changes in plant community traits along an environmental gradient are caused by interspecific and intraspecific trait variation. However, little is known about the role of interspecific and intraspecific trait variation in plant community responses to the restoration of a sandy grassland ecosystem. We measured five functional traits of 34 species along a restoration gradient of sandy grassland (mobile dune, semi‐fixed dune, fixed dune, and grassland) in Horqin Sand Land, northern China. We examined how community‐level traits varied with habitat changes and soil gradients using both abundance‐weighted and non‐weighted averages of trait values. We quantified the relative contribution of inter‐ and intraspecific trait variation in specific leaf area (SLA), leaf dry matter content (LDMC), leaf carbon content (LCC), leaf nitrogen content (LNC), and plant height to the community response to habitat changes in the restoration of sandy grassland. We found that five weighted community‐average traits varied significantly with habitat changes. Along the soil gradient in the restoration of sandy grassland, plant height, SLA, LDMC, and LCC increased, while LNC decreased. For all traits, there was a greater contribution of interspecific variation to community response in regard to habitat changes relative to that of intraspecific variation. The relative contribution of the interspecific variation effect of an abundance‐weighted trait was greater than that of a non‐weighted trait with regard to all traits except LDMC. A community‐level trait response to habitat changes was due largely to species turnover. Though the intraspecific shift plays a small role in community trait response to habitat changes, it has an effect on plant coexistence and the maintenance of herbaceous plants in sandy grassland habitats. The context dependency of positive and negative covariation between inter‐ and intraspecific variation further suggests that both effects of inter‐ and intraspecific variation on a community trait should be considered when understanding a plant community response to environmental changes in sandy grassland ecosystems.     

Eliminating accidental deviations to minimize generalization error and maximize replicability: Applications in connectomics and genomics

Replicability, the ability to replicate scientific findings, is a prerequisite for scientific discovery and clinical utility. Troublingly, we are in the midst of a replicability crisis. A key to replicability is that multiple measurements of the same item (e.g., experimental sample or clinical participant) under fixed experimental constraints are relatively similar to one another. Thus, statistics that quantify the relative contributions of accidental deviations—such as measurement error—as compared to systematic deviations—such as individual differences—are critical. We demonstrate that existing replicability statistics, such as intra-class correlation coefficient and fingerprinting, fail to adequately differentiate between accidental and systematic deviations in very simple settings. We therefore propose a novel statistic, discriminability, which quantifies the degree to which an individual’s samples are relatively similar to one another, without restricting the data to be univariate, Gaussian, or even Euclidean. Using this statistic, we introduce the possibility of optimizing experimental design via increasing discriminability and prove that optimizing discriminability improves performance bounds in subsequent inference tasks. In extensive simulated and real datasets (focusing on brain imaging and demonstrating on genomics), only optimizing data discriminability improves performance on all subsequent inference tasks for each dataset. We therefore suggest that designing experiments and analyses to optimize discriminability may be a crucial step in solving the replicability crisis, and more generally, mitigating accidental measurement error.     

Identification of the ryanodine receptor mutation I4743M and its contribution to diamide insecticide resistance in Spodoptera exigua (Lepidoptera: Noctuidae)

Insect ryanodine receptors (RyRs) are the targets of diamide insecticides. Two point mutations G4946E and I4790M (numbering according to Plutella xylostella, PxRyR) in the transmembrane domain of the insect RyRs associated with diamide resistance have so far been identified in three lepidopteran pests, P. xylostella, Tuta absoluta and Chilo suppressalis. In this study, we identified one of the known RyR target site resistance mutations (I4790M) in a field‐collected population of Spodoptera exigua. The field‐collected WF population of S. exigua exhibited 154 fold resistance to chlorantraniliprole when compared with the susceptible WH‐S strain. Sequencing the transmembrane domains of S. exigua RyR (SeRyR) revealed that the resistant WF strain was homozygous for the I4743M mutation (corresponding to I4790M in PxRyR), whereas the G4900E allele (corresponding to G4946E of PxRyR) was not detected. The 4743M allele was introgressed into the susceptible WH‐S strain by crossing WF with WH‐S, followed by three rounds of backcrossing with WH‐S. The introgressed strain 4743M was homozygous for the mutant 4743M allele and shared about 94% of its genetic background with that of the recipient WH‐S strain. Compared with WH‐S, the near‐isogenic 4743M strain showed moderate levels of resistance to chlorantraniliprole (21 fold), cyantraniliprole (25 fold) and flubendiamide (22 fold), suggesting that the I4743M mutation confers medium levels of resistance to all three diamides. Genetic analysis showed diamide resistance in the 4743M strain was inherited as an autosomal and recessive trait. Results from this study have direct implications for the design of appropriate resistance monitoring and management practices to sustainably control S. exigua.     

Two new compounds from Trigonostemon heterophyllus

Phytochemical investigation on the stems of Trigonostemon heterophyllus led to the isolation of a new diterpene, trigonoheterene (1), and a new naphthoquinone, trigonoheterone (2), together with two known compounds, 3,4-seco-sonderianol, (3) and trigonochinene E, (4). Their structures were determined by spectroscopic techniques (UV, IR, MS, 1D and 2D NMR). All compounds were evaluated for cytotoxic activities and antibacterial activities.     

中国种子植物区系定量化研究 V．区系相似性

本文总结了应用相似系数即关联系数进行植物区系相似性分析的现状,指出了存在的问题．然后,从集合论角度讨论了区系相似性、相似关系及其相似系数的实质．作者以为在区系相似性分析中应用Ｒ．Ｒ．Ｓｏｋａｌ和Ｃ．Ｄ．Ｍｉｃｈｅｎｅｒ（１９５８）提出的简单匹配系数比较适宜,同时亦能避免以往区系相似性分析中缺乏可比性及某些“表相”相似等问题．最后,还提出了总体相似系数和类型相似系数二个新概念,以便按照吴征镒教授关于中国植物区系研究的学术思想统一研究各个不同地区植物区系的相似性．对此,作者用了６个区系实例进行了演算说明．     

Determinants of 14-3-3σ Protein Dimerization and Function in Drug and Radiation Resistance

Many proteins exist and function as homodimers. Understanding the detailed mechanism driving the homodimerization is important and will impact future studies targeting the “undruggable” oncogenic protein dimers. In this study, we used 14-3-3σ as a model homodimeric protein and performed a systematic investigation of the potential roles of amino acid residues in the interface for homodimerization. Unlike other members of the conserved 14-3-3 protein family, 14-3-3σ prefers to form a homodimer with two subareas in the dimeric interface that has 180° symmetry. We found that both subareas of the dimeric interface are required to maintain full dimerization activity. Although the interfacial hydrophobic core residues Leu¹² and Tyr⁸⁴ play important roles in 14-3-3σ dimerization, the non-core residue Phe²⁵ appears to be more important in controlling 14-3-3σ dimerization activity. Interestingly, a similar non-core residue (Val⁸¹) is less important than Phe²⁵ in contributing to 14-3-3σ dimerization. Furthermore, dissociating dimeric 14-3-3σ into monomers by mutating the Leu¹², Phe²⁵, or Tyr⁸⁴ dimerization residue individually diminished the function of 14-3-3σ in resisting drug-induced apoptosis and in arresting cells at G₂/M phase in response to DNA-damaging treatment. Thus, dimerization appears to be required for the function of 14-3-3σ.