The anammox case-a new experimental manifesto for microbiological eco-physiology

The anaerobic ammonium oxidation process is a new process for ammonia removal from wastewater. It is also a new microbial physiology that was previously believed to be impossible. The identification of Candidatus Brocadia anammoxidans and its relatives as the responsible bacteria was only possible with the development of a new experimental approach. That approach is the focus of this paper. The approach is a modernisation of the Winogradsky/Beyerinck strategy of selective enrichment and is based on the introduction of the molecular toolbox and modern bioreactor engineering to microbial ecology. It consists of five steps: (1) postulation of an ecological niche based on thermodynamic considerations and macro-ecological field data; (2) engineering of this niche into a laboratory bioreactor for enrichment culture; (3) black-box physiological characterisation of the enrichment culture as a whole; (4) phylogenetic characterisation of the enriched community using molecular tools; (5) physical separation of the dominant members of the enrichment culture using gradient centrifugation and the identification of the species of interest in accordance with Koch's postulates; (6) verification of the in situ importance of these species in the actual ecosystems. The power of this approach is illustrated with a case study: the identification of the planctomycetes responsible for anaerobic ammonium oxidation. We argue that this was impossible using molecular ecology or conventional ‘cultivation based techniques’ alone. We suggest that the approach might also be used for the microbiological study of many interesting microbes such as anaerobic methane oxidisers. This revised version was published online in August 2006 with corrections to the Cover Date.     

Electron and nuclear dynamics in many-electron atoms, molecules and chlorophyll-protein complexes: A review

It has been shown [V.A. Shuvalov, Quantum dynamics of electrons in many-electron atoms of biologically important compounds, Biochemistry (Mosc.) 68 (2003) 1333-1354; V.A. Shuvalov, Quantum dynamics of electrons in atoms of biologically important molecules, Uspekhi biologicheskoi khimii, (Pushchino) 44 (2004) 79-108] that the orbit angular momentum L of each electron in many-electron atoms is L = mVr = n? and similar to L for one-electron atom suggested by N. Bohr. It has been found that for an atom with N electrons the total electron energy equation E = −(Z^eff)²e⁴m/(2n²?²N) is more appropriate for energy calculation than standard quantum mechanical expressions. It means that the value of L of each electron is independent of the presence of other electrons in an atom and correlates well to the properties of virtual photons emitted by the nucleus and creating a trap for electrons. The energies for elements of the 1st up to the 5th rows and their ions (total amount 240) of Mendeleev' Periodical table were calculated consistent with the experimental data (deviations in average were 5 × 10^− 3). The obtained equations can be used for electron dynamics calculations in molecules. For H₂ and H₂⁺ the interference of electron-photon orbits between the atoms determines the distances between the nuclei which are in agreement with the experimental values. The formation of resonance electron-photon orbit in molecules with the conjugated bonds, including chlorophyll-like molecules, appears to form a resonance trap for an electron with E values close to experimental data. Two mechanisms were suggested for non-barrier primary charge separation in reaction centers (RCs) of photosynthetic bacteria and green plants by using the idea of electron-photon orbit interference between the two molecules. Both mechanisms are connected to formation of the exciplexes of chlorophyll-like molecules. The first one includes some nuclear motion before exciplex formation, the second one is related to the optical transition to a charge transfer state.     

Changes in proteomics profile during maturation of marrow-derived dendritic cells treated with oxidized low-density lipoprotein

Increasing evidence suggests that dendritic cells (DCs) and oxidized low-density lipoprotein (ox-LDL) participate in atherosclerosis. However, few data on the molecular mechanisms of this process are available. To address this question, we used iTRAQ labeling followed by LC-MS/MS analysis to identify many proteins that changed markedly during the maturation of dendritic cells stimulated with ox-LDL. Among a total of 781 identified proteins, 93 were upregulated and 100 were downregulated. The major and significant changes in upregulated proteins were that ox-LDL not only affected the levels of intracellular cathepsins G, Z, D and S, but also significantly enhanced cathepsin S secretion by the treated cells. Our results may provide clues for a more comprehensive understanding the pathogenesis of atherosclerosis.     

Current controversies in cholangiocarcinoma

Cholangiocarcinoma represents 10% of primary liver malignancies and accounts for less than 3% of all gastrointestinal malignant tumors, with an enormous geographical variation. This neoplasia can arise from the biliary tract epithelium or hepatic progenitor cells. Depending on the anatomic localization, it is classified into three subtypes: intrahepatic, perihilar and distal. This fact is one of the main difficulties, because there are many studies that indistinctly include the results in the management of these different types of cholangiocarcinoma, without differentiating its location and even including gallbladder cancer.There are many controversial points in epidemiology, liver transplantation as a treatment, limitations of different results by group and type of treatment, histological testing and chemotherapy. This is a narrative review about topics in cholangiocarcinoma. This article is part of a Special Issue entitled: Cholangiocytes in Health and Disease edited by Jesus Banales, Marco Marzioni, Nicholas LaRusso and Peter Jansen.     

Wood density as a proxy of drought-induced forest dieback in silver fir

Drought-induced dieback is a matter of global concern. It has been widely reported and could compromise the climate warming mitigation potential of forests. That is why we need reliable early-warning proxies to achieve better forecasts of forest dieback and tree death. Tree-ring data can provide some of these needed proxies. Here I propose considering minimum (MND) and maximum (MXD) wood density values as proxies of tree vulnerability against drought. This hypothesis is evaluated in silver fir (Abies alba) forests from the western Spanish Pyrenees showing ongoing dieback processes after the severe 1985 drought. MXD increased in response to warm summer conditions in 1985 whereas MND increased in response to growing-season water deficit in 1986. The average between prior MXD (MXD_t-1) and subsequent MND (MND_t) could be used to detect severe drought impacts and forecast dieback.     

华山松吸收光谱及叶绿素荧光特性的地理变异

利用分离的叶绿体作实验材料,发现华山松(Pinus armandi Franch.)南方种源的4阶导数吸收光谱在680nm处峰值较大,在670nm处峰值较小,而北方种源中出现了在680nm处峰值较在670nm峰值小的类群,推断北方种群反应中心活力有下降趋势。南、北种源之间的低温(77K)荧光发射光谱有明显差异,PSⅠ、PSⅡ发射峰位置出现地理变动。低温荧光激发光谱分析表明,地理变异主要发生在叶绿素a的分子状态上。研究还表明,完整的针叶因为有角质层、松脂等物质干扰,检测不出光谱的差异,不是理想的实验材料。     

A technique for estimating maximum harvesting effort in a stochastic fishery model

Exploitation of biological resources and the harvest of population species are commonly practiced in fisheries, forestry and wild life management. Estimation of maximum harvesting effort has a great impact on the economics of fisheries and other bio-resources. The present paper deals with the problem of a bioeconomic fishery model under environmental variability. A technique for finding the maximum harvesting effort in fluctuating environment has been developed in a two-species competitive system, which shows that under realistic environmental variability the maximum harvesting effort is less than what is estimated in the deterministic model. This method also enables us to find out the safe regions in the parametric space for which the chance of extinction of the species is minimized. A real life fishery problem has been considered to obtain the inaccessible parameters of the system in a systematic way. Such studies may help resource managers to get an idea for controlling the system.     

Activation of human B lymphocytes. XVII. Synergy between nonspecific and specific signals in the antigen-specific responses of human B cells

The incubation of human peripheral blood lymphocytes (PBL) with the natural killer (NK)-sensitive MOLT-4 cell line results in PBL-target cell conjugate formation by certain lymphocyte subpopulations. Following velocity sedimentation, the PBL depleted of these conjugate-forming subpopulations are markedly diminished in the ability to mediate either antibody-dependent cellular cytotoxicity (ADCC) or NK activity. The immediate testing of highly pure PBL subpopulations isolated from the NK target conjugates does not reveal the expected recovery of augmented ADCC or NK levels. Following in vitro incubation, however, the PBL NK target-binding subpopulations do manifest augmented levels of both NK and ADCC, whereas the depleted PBL continue to display diminished NK and ADCC levels. In addition, the degree of augmented NK and ADCC levels recovered by the NK target-binding PBL subpopulations appears dependent on both the time and the temperature of in vitro incubation. Moreover, the ADCC recovery patterns are identical to those observed for NK activity regardless of the time and temperature of in vitro incubation. These results directly demonstrate that the PBL subpopulations isolated from certain NK target cells are functionally enriched in the ability to mediate from ADCC and NK activity.     

Sustained biological control of the cassava mealybugPhenacoccus manihoti [Hom.: Pseudococcidae] byEpidinocarsis lopezi [Hym.: Encyrtidae] in Nigeria

Following the successful introduction ofEpidinocarsis lopezi (De Santis) for biological control of the cassava mealybug (CM)Phenacoccus manihoti Mat.-Ferr. in southwestern Nigeria in 1981 and 1982, 11 groups of cassava fields were sampled every 2 weeks up to 1988 for impact assessment. After 1984, CM populations remained mostly below 10 per tip despite the presence of native hyperparasitoids, demonstrating the long-term success of biological control byE. lopezi in the region. Indigenous polyphagous coccinellids were found only during peak host densities, whereas the specificE. lopezi was common throughout the year. During some periods, percentage parasitism indicated delayed density dependence. Since 89% of all sampled cassava tips had no CM at all and the parasitisme is very mobile, parasitization rates were also calculated for individual infested tips (N=4,878). Parasitism increased slightly with host density on tips having between 1 and 10 CM of the 3^rd and 4^th instars, indicating positive density dependence. Such tips comprised 64% of all infested tips. At higher host densities, parasitism rates fell rapidly. The results are discussed in view of different theories on population regulation by biological control agents.