Ammonia‐oxidizing archaea: important players in paddy rhizosphere soil?

The diversity (richness and community composition) of ammonia-oxidizing archaea (AOA) and bacteria (AOB) in paddy soil with different nitrogen (N) fertilizer amendments for 5 weeks were investigated using quantitative real-time polymerase chain reaction, denaturing gradient gel electrophoresis (DGGE) jand clone library analysis based on the ammonia monooxygenase α-subunit ( amoA ) gene. Ammonia-oxidizing archaea predominated among ammonia-oxidizing prokaryotes in the paddy soil, and the AOA:AOB DNA-targeted amoA gene ratios ranged from 1.2 to 69.3. Ammonia-oxidizing archaea were more abundant in the rhizosphere than in bulk soil. Rice cultivation led to greater abundance of AOA than AOB amoA gene copies and to differences in AOA and AOB community composition. These results show that AOA is dominant in the rhizosphere paddy soil in this study, and we assume that AOA were influenced more by exudation from rice root (e.g. oxygen, carbon dioxide) than AOB.     

Catalytic residues of gamma delta resolvase act in cis.

The resolvase protein of the gamma delta transposon is a site-specific recombinase that acts by a concerted break-and-join mechanism. To analyse the role of individual resolvase subunits in DNA strand cleavage, we have directed the binding of catalytic mutants to specific recombination crossover sites or half-sites. Our results demonstrate that the resolvase subunit bound at the half-site proximal to each scissile phosphodiester bond provides the Ser10 nucleophile and Arg8, Arg68 and Arg71 residues essential for cleavage and covalent attachment to the DNA. Several other residues near the presumptive active site are also shown to act in cis. Double-strand cleavage at one crossover site can proceed independently of cleavage at the other site, although interactions between the resolvase dimers bound at the two crossover sites remain essential. An appropriately oriented heterodimer of active and inactive protomers can in most cases mediate either a 'top' or 'bottom' single-strand cleavage, suggesting that there is no obligatory order of strand cleavages. Top-strand cleavage is associated with the topoisomerase I activity of resolvase, suggesting that a functional asymmetry may be imposed on the crossover site by the structure of the active synapse.     

A specific PCR assay for the diagnosis of Clonorchis sinensis infection in humans, cats and fishes

Clonorchiasis caused by Clonorchis sinensis is a fish-borne parasitic disease which is endemic in a number of countries. Using the sequences of the internal transcribed spacers (ITS-1 and ITS-2) of nuclear ribosomal DNA (rDNA) of C. sinensis as genetic markers, a pair of C. sinensis-specific primers was designed and used to establish a specific PCR assay for the diagnosis of C. sinensis infection in humans, cats and fish. This approach allowed the specific identification of C. sinensis after optimizing amplification conditions, with no amplicons being amplified from related heterogeneous DNA samples, and sequencing of amplicons confirmed the identity of the sequences amplified. The detection limit of this assay was 1.03 pg of adult C. sinensis, 1.1 metacercariae per gram of fish filet, and a single egg in human and cat feces. The PCR assay should provide a useful tool for the diagnosis and molecular epidemiological investigation of clonorchiasis in humans and animals.     

Identification of cross-linked peptides from complex samples

We have developed pLink, software for data analysis of cross-linked proteins coupled with mass-spectrometry analysis. pLink reliably estimates false discovery rate in cross-link identification and is compatible with multiple homo- or hetero-bifunctional cross-linkers. We validated the program with proteins of known structures, and we further tested it on protein complexes, crude immunoprecipitates and whole-cell lysates. We show that it is a robust tool for protein-structure and protein-protein-interaction studies.     

Ferric ion (hydr)oxo clusters in the “Venus flytrap” cleft of FbpA: M?ssbauer, calorimetric and mass spectrometric studies

Isothermal calorimetric studies of the binding of iron(III) citrate to ferric ion binding protein from Neisseria gonorrhoeae suggested the complexation of a tetranuclear iron(III) cluster as a single step binding event (apparent binding constant K(app) (ITC) = 6.0(5) × 10(5) M(-1)). High-resolution Fourier transform ion cyclotron resonance mass spectrometric data supported the binding of a tetranuclear oxo(hydroxo) iron(III) cluster of formula [Fe(4)O(2)(OH)(4)(H(2)O)(cit)](+) in the interdomain binding cleft of FbpA. The mutant H9Y-nFbpA showed a twofold increase in the apparent binding constant [K(app) (ITC) = 1.1(7) × 10(6) M(-1)] for the tetranuclear iron(III) cluster compared to the wild-type protein. M?ssbauer spectra of Escherichia coli cells overexpressing FbpA and cultured in the presence of added (57)Fe citrate were indicative of the presence of dinuclear and polynuclear clusters. FbpA therefore appears to have a strong affinity for iron clusters in iron-rich environments, a property which might endow the protein with new biological functions.     

Role of small conductance calcium-activated potassium channels expressed in PVN in regulating sympathetic nerve activity and arterial blood pressure in rats

Small conductance Ca(2+)-activated K(+) (SK) channels regulate membrane properties of rostral ventrolateral medulla (RVLM) projecting hypothalamic paraventricular nucleus (PVN) neurons and inhibition of SK channels increases in vitro excitability. Here, we determined in vivo the role of PVN SK channels in regulating sympathetic nerve activity (SNA) and mean arterial pressure (MAP). In anesthetized rats, bilateral PVN microinjection of SK channel blocker with peptide apamin (0, 0.125, 1.25, 3.75, 12.5, and 25 pmol) increased splanchnic SNA (SSNA), renal SNA (RSNA), MAP, and heart rate (HR) in a dose-dependent manner. Maximum increases in SSNA, RSNA, MAP, and HR elicited by apamin (12.5 pmol, n = 7) were 330 ± 40% (P < 0.01), 271 ± 40% (P < 0.01), 29 ± 4 mmHg (P < 0.01), and 34 ± 9 beats/min (P < 0.01), respectively. PVN injection of the nonpeptide SK channel blocker UCL1684 (250 pmol, n = 7) significantly increased SSNA (P < 0.05), RSNA (P < 0.05), MAP (P < 0.05), and HR (P < 0.05). Neither apamin injected outside the PVN (12.5 pmol, n = 6) nor peripheral administration of the same dose of apamin (12.5 pmol, n = 5) evoked any significant changes in the recorded variables. PVN-injected SK channel enhancer 5,6-dichloro-1-ethyl-1,3-dihydro-2H-benzimidazol-2-one (DCEBIO, 5 nmol, n = 4) or N-cyclohexyl-N-[2-(3,5-dimethyl-pyrazol-1-yl)-6-methyl-4-pyrimidin]amine (CyPPA, 5 nmol, n = 6) did not significantly alter the SSNA, RSNA, MAP, and HR. Western blot and RT-PCR analysis of punched PVN tissue showed abundant expression of SK1-3 channels. We conclude that SK channels expressed in the PVN play an important role in the regulation of sympathetic outflow and cardiovascular function.     

Selecting Biological Meaningful Environmental Dimensions of Low Discrepancy among Ranges to Predict Potential Distribution of Bean Plataspid Invasion

Background

The Bean plataspid (Megacopta cribraria) (Hemiptera: Pentatomidae), native to Asia, is becoming an invasive species in North America; its potential spread to soybean producing areas in the US is of great concern. Ecological niche modelling (ENM) has been used increasingly in predicting invasive species'' potential distribution; however, poor niche model transferability was sometimes reported, leading to the artifactual conclusion of niche differentiation during species'' invasion.

Methodology/Principals

We aim to improve the geographical transferability of ENM via environmental variable selection to predict the potential distribution of Bean plataspid invasion. Sixteen environmental dimensions between native and introduced Bean plataspid populations were compared, and classified into two datasets with different degrees of discrepancy by the interquartile range (IQR) overlap in boxplot. Niche models based on these two datasets were compared in native model prediction and invading model projection. Classical niche model approaches (i.e., model calibrated on native range and transferred outside) were used to anticipate the potential distribution of Bean plataspid invasion.

Conclusions/Significance

Niche models based on the two datasets showed little difference in native model predictions; however, when projecting onto the introduced area, models based on the environmental datasets showing low discrepancy among ranges recovered good model transferability in predicting the newly established population of Bean plataspid in the US. Recommendations were made for selecting biological meaningful environmental dimensions of low discrepancy among ranges to improve niche model transferability among these geographically separated areas. Outside of its native range, areas with invasion potential include the southeastern US in North America, southwestern Europe, southeastern South America, southern Africa, and the eastern coastal Australia.     

亚硝基胍诱变选育林肯霉素高产菌株

以林肯链霉菌９４７－８（Ｓｔｒｅｐｔｏｍｙｃｅｓｌｉｎｃｏｌｎｅｎｓｉｓ９４７－８）为出发菌株（产林肯霉素９４０γ／ｍｌ）。采用孢子热处理方法处理出发菌株孢子,得到变异株９４７－８ｓ,产林肯霉素１０８０γ／ｍｌ。对９４７－８ｓ菌株进行ＮＴＧ诱变处理,得变异株９４７－８ｘ,产林肯霉素为１２１８γ／ｍｌ,且生产能力稳定。