Further reading in geomicrobiology

In the wetland rhizosphere, high densities of lithotrophic Fe(II)-oxidizing bacteria (FeOB) and a favorable environment (i.e., high Fe(II) availability and microaerobic conditions) suggest that these organisms are actively contributing to the formation of Fe plaque on plant roots. We manipulated the presence/absence of an Fe(II)-oxidizing bacterium (Sideroxydans paludicola, strain BrT) in axenic hydroponic microcosms containing the roots of intact Juncus effusus (soft rush) plants to determine if FeOB affected total rates of rhizosphere Fe(II) oxidation and Fe plaque accumulation. Our experimental data highlight the importance of both FeOB and plants in influencing short-term rates of rhizosphere Fe oxidation. Over time scales ca. 1 wk, the FeOB increased Fe(II) oxidation rates by 1.3 to 1.7 times relative to FeOB-free microcosms. Across multiple experimental trials, Fe(II) oxidation rates were significantly correlated with root biomass, reflecting the importance of radial O ₂ loss in supporting rhizosphere Fe(II) oxidation. Rates of root Fe(III) plaque accumulation (time scales: 3 to 6 wk) were ～ 70 to 83% lower than expected based on the short-term Fe(II) oxidation rates and were unaffected by the presence/absence of FeOB. Decreasing rates of Fe(II) oxidation and Fe(III) plaque accumulation with increasing time scales indicate changes in rates of Fe(II) diffusion and radial O ₂ loss, shifts in the location of Fe oxide accumulation, or temporal changes in the microbial community within the microcosms. The microcosms used herein replicated many of the environmental characteristics of wetland systems and allowed us to demonstrate that FeOB can stimulate rates of Fe(II) oxidation in the wetland rhizosphere, a finding that has implications for the biogeochemical cycling of carbon, metals, and nutrients in wetland ecosystems.     

Vector field statistical analysis of kinematic and force trajectories

When investigating the dynamics of three-dimensional multi-body biomechanical systems it is often difficult to derive spatiotemporally directed predictions regarding experimentally induced effects. A paradigm of ‘non-directed’ hypothesis testing has emerged in the literature as a result. Non-directed analyses typically consist of ad hoc scalar extraction, an approach which substantially simplifies the original, highly multivariate datasets (many time points, many vector components). This paper describes a commensurately multivariate method as an alternative to scalar extraction. The method, called ‘statistical parametric mapping’ (SPM), uses random field theory to objectively identify field regions which co-vary significantly with the experimental design. We compared SPM to scalar extraction by re-analyzing three publicly available datasets: 3D knee kinematics, a ten-muscle force system, and 3D ground reaction forces. Scalar extraction was found to bias the analyses of all three datasets by failing to consider sufficient portions of the dataset, and/or by failing to consider covariance amongst vector components. SPM overcame both problems by conducting hypothesis testing at the (massively multivariate) vector trajectory level, with random field corrections simultaneously accounting for temporal correlation and vector covariance. While SPM has been widely demonstrated to be effective for analyzing 3D scalar fields, the current results are the first to demonstrate its effectiveness for 1D vector field analysis. It was concluded that SPM offers a generalized, statistically comprehensive solution to scalar extraction's over-simplification of vector trajectories, thereby making it useful for objectively guiding analyses of complex biomechanical systems.     

GENETIC ANALYSIS OF MATE DISCRIMINATION IN DROSOPHILA SIMULANS

Courtship is an elaborate behavior that conveys information about the identity of animal species and suitability of individual males as mates. In Drosophila, there is extensive evidence that females are capable of evaluating and comparing male courtships, and accepting or rejecting males as mates. These relatively simple responses minimize random sexual encounters involving subpar conspecific males and heterospecific males, and over generations can potentially select novel physical and behavioral traits. Despite its evolutionary and behavioral significance, little is still known about the genes involved in mating choice and how choices for novel males and females arise during evolution. Drosophila simulans and Drosophila sechellia are two recently diverged species of Drosophila in which females have a preference for conspecific males. Here we analyzed a total of 1748 F2 hybrid females between these two species and found a small number of dominant genes controlling the preference for D. simulans males. We also mapped two redundant X‐linked loci of mating choice, Macho‐XA and Macho‐XB, and show that neither one is required for female attractiveness. Together, our results reveal part of the genetic architecture that allows D. simulans females to recognize, mate, and successfully generate progenies with D. simulans males.     

基于BP神经网络与ETM+遥感数据的盐城滨海自然湿地覆被分类

高效而精确的湿地遥感分类是大范围湿地资源动态监测与管理的必要保障。本研究使用ETM 遥感数据,借助Matlab神经网络工具箱,构建了基于BP神经网络的滨海湿地覆被分类模型,并将其应用于江苏盐城沿海湿地珍禽国家级自然保护区的核心区的自然湿地覆被分类研究中。本研究选择3、4、7、8波段作为输入层变量,单隐藏层设为10个节点,输出层变量对应待划分的8种覆被类型,构建三层式BP神经网络滨海湿地覆被分类模型。结果显示,BP分类总精度为85.91%,Kappa系数为0.8328,与最小距离法和极大似然法的分类总精度相比,分别提高了7.99%和6.08%,Kappa系数也相比提高。研究结果表明,BP神经网络分类法是一种较为有效的湿地遥感影像分类技术,能够提高分类精度。     

QTL Mapping of Downy Mildew Resistance in an Introgression Line Derived from Interspecific Hybridization Between Cucumber and Cucumis hystrix

Downy mildew (DM), caused by Pseudoperonospora cubensis (Berk. & M.A. Curtis) Rostovzev, is a worldwide major disease of cucumbers (Cucumis sativus L.). By screening 10 introgression lines (ILs) derived from interspecific hybridization between cucumber and the wild Cucumis, C. hystrix, through a whole plant assay, one introgression line (IL52) was identified with high DM‐resistance. IL52 was further used as a resistant parent to make an F₂ population with ‘changchunmici’ (susceptible parent). The F₂ population (300 plants) was investigated for DM‐yellowing, DM‐necrosis and DM‐resistance in the adult stage. A genetic map spanning 642.5 cM with 104 markers was constructed and used for QTL analysis from the population. Three QTL regions were identified on chromosome 5 and chromosome 6. By interval mapping analysis, two QTLs for DM‐resistance were determined on chromosome 5 (DM_5.1 and DM_5.2), which explained 17.9% and 14.2% of the variation, respectively. QTLs for DM‐yellowing were in the same regions as DM‐resistance. For DM‐necrosis, by interval mapping analysis, one QTL was determined on chromosome 5 (Necr_5.1) that explained 18.3% of the variation and one on chromosome 6 (Necr_6.1) that explained 13.9% of the variation. Our results indicated that the identification of molecular markers linked to the QTLs could be further applied for marker‐assisted selection (MAS) of downy mildew resistance in cucumber.     

Some Effects of Ethanolic Extracts of Potatoes on Phosphorylase Activity

Effects of materials extracted from potatoes with hot 80% ethanol on the course of phosphorylase reactions were examined. These materials had no effect on phosphorylase activities as determined by the rate of liberation of inorganic phosphate from glucose-1-phosphate in the presence of a large amount of primer; however, in the presence of a small amount of primer or in its absence, these materials had significant effects on the liberation of inorganic phosphate and starch formation. These results suggested the presence of a small amount of primers in these materials. Evidence was presented against the participation of d-enzyme on the formation of starch when partially purified preparations of potato phosphorylase or crude extracts from potatoes were used as the enzyme.     

Inhibition of CD73 AMP hydrolysis by a therapeutic antibody with a dual,non-competitive mechanism of action

CD73 (ecto-5′-nucleotidase) has recently been established as a promising immuno-oncology target. Given its role in activating purinergic signaling pathways to elicit immune suppression, antagonizing CD73 (i.e., releasing the brake) offers a complimentary pathway to inducing anti-tumor immune responses. Here, we describe the mechanistic activity of a new clinical therapeutic, MEDI9447, a human monoclonal antibody that non-competitively inhibits CD73 activity. Epitope mapping, structural, and mechanistic studies revealed that MEDI9447 antagonizes CD73 through dual mechanisms of inter-CD73 dimer crosslinking and/or steric blocking that prevent CD73 from adopting a catalytically active conformation. To our knowledge, this is the first report of an antibody that inhibits an enzyme's function through 2 distinct modes of action. These results provide a finely mapped epitope that can be targeted for selective, potent, and non-competitive inhibition of CD73, as well as establish a strategy for inhibiting enzymes that function in both membrane-bound and soluble states.     

Molecular basis for the mechanism of action of an anti-TACE antibody

Inhibitors of tumor necrosis factor-α converting enzyme (TACE) have potential as therapeutics for various diseases. Many small molecule inhibitors, however, exhibit poor specificity profiles because they target the highly conserved catalytic cleft of TACE. We report for the first time the molecular interaction of a highly specific anti-TACE antagonistic antibody (MEDI3622). We characterized the binding of MEDI3622 using mutagenesis, as well as structural modeling and docking approaches. We show that MEDI3622 recognizes a unique surface loop of sIVa-sIVb β-hairpin on TACE M-domain, but does not interact with the conserved catalytic cleft or its nearby regions. The exquisite specificity of MEDI3622 is mediated by this distinct structural feature on the TACE M-domain. These findings may aid the design of antibody therapies against TACE.     

In-depth structural characterization of Kadcyla® (ado-trastuzumab emtansine) and its biosimilar candidate

The biopharmaceutical industry has become increasingly focused on developing biosimilars as less expensive therapeutic products. As a consequence, the regulatory approval of 2 antibody-drug conjugates (ADCs), Kadcyla® and Adcetris® has led to the development of biosimilar versions by companies located worldwide. Because of the increased complexity of ADC samples that results from the heterogeneity of conjugation, it is imperative that close attention be paid to the critical quality attributes (CQAs) that stem from the conjugation process during ADC biosimilar development process. A combination of physicochemical, immunological, and biological methods are warranted in order to demonstrate the identity, purity, concentration, and activity (potency or strength) of ADC samples. As described here, we performed extensive characterization of a lysine conjugated ADC, ado-trastuzumab emtansine, and compared its CQAs between the reference product (Kadcyla®) and a candidate biosimilar. Primary amino acid sequences, drug-to-antibody ratios (DARs), conjugation sites and site occupancy data were acquired and compared by LC/MS methods. Furthermore, thermal stability, free drug content, and impurities were analyzed to further determine the comparability of the 2 ADCs. Finally, biological activities were compared between Kadcyla® and biosimilar ADCs using a cytotoxic activity assay and a HER2 binding assay. The in-depth characterization helps to establish product CQAs, and is vital for ADC biosimilars development to ensure their comparability with the reference product, as well as product safety.