Genetic inhomogeneous Poisson processes describing the roles of an isolated mature tree in forest regeneration

The spatial distribution of genotyped adult plants and offspring can be modeled by genetic inhomogeneous Poisson processes. This paper reports the development of a previously proposed point process model to cover safe site conditions for sapling survival, unknown seed sources and wider ranges of dispersal kernels. Suppose that a species has limited seed dispersal and shade-tolerance, and that young trees are clustered around highly isolated adults. The clustering might be formed solely by dispersed seeds from adults. However, the survival of the offspring might be influenced by shading by the adults crowns. The new genetic processes are applicable to such cases, as demonstrated for a young population of Fagus crenata, a shade-tolerant canopy tree species, in a 55-year-old stand regenerated after shelterwood logging. Isozyme analysis revealed that the regenerating trees were genetically related to the nearest adults, but some were not their respective daughters. The maximum likelihood method has led us to the following regeneration: seeds were dispersed mostly within 20 m of their mothers; two residual adults in the plot had equal female reproductive success; about 10% of offspring even close to the adult were not their daughters; the adults crowns reduced the survival of offspring up to 20–25 m away. However, the degree of model fitting was unsatisfactory. Hence, our models, in principle, can quantify two roles of highly isolated adults: providing seed sources and safe sites, but the case study suggests that other, unknown factors influence F. crenata regeneration after shelterwood harvesting.     

Species diversity and functional assessment of macroinvertebrate communities in Austrian rivers

We applied an extensive data set from 211 locations along Austrian rivers to assess community structure and the ratios of functional feeding groups of benthic macroinvertebrates. A total of 569 taxa have been identified. At the catchment scale, the Enns, Salzach, and Traun Rivers exhibited the highest taxa richness whereas the Inn River showed the lowest richness. Beta-diversity was highest along the impounded and fragmented Enns and Drau Rivers. Consequently, high corridor diversity corresponded to a low degree of nestedness. Overall, scrapers and gathering-collectors dominated the benthic community. Further, the relationship between habitat conditions and metrics based on functional feeding groups were statistically analyzed to validate the potential of these metrics as indicators of ecosystem attributes. We examined four major ecosystem attributes: species diversity, material cycling, longitudinal material transport, and lateral material input. Multiple regression analyses for midorder rivers demonstrated that metrics were significantly related to habitat conditions. For example, the metric set indicating primary production was positively correlated with periphyton cover, dissolved oxygen, dominant sediment size, and average annual discharge. Overall, most metrics exhibited unique responses to habitat conditions, implying that they are useful proxies of ecosystem attributes. Thus, a function-based approach based on macroinvertebrates has the potential to become an effective tool for the assessment of river ecosystems.     

The CENP-H-I complex is required for the efficient incorporation of newly synthesized CENP-A into centromeres

In vertebrates, centromeres lack defined sequences and are thought to be propagated by epigenetic mechanisms involving the incorporation of specialized nucleosomes containing the histone H3 variant centromere protein (CENP)-A. However, the precise mechanisms that target CENP-A to centromeres remain poorly understood. Here, we isolated a multi-subunit complex, which includes the established inner kinetochore components CENP-H and CENP-I, and nine other proteins, from both human and chicken cells. Our analysis of these proteins demonstrates that the CENP-H-I complex can be divided into three functional sub-complexes, each of which is required for faithful chromosome segregation. Interestingly, newly expressed CENP-A is not efficiently incorporated into centromeres in knockout mutants of a subclass of CENP-H-I complex proteins, indicating that the CENP-H-I complex may function, in part, as a marker directing CENP-A deposition to centromeres.     

Increased level of DJ-1 in the cerebrospinal fluids of sporadic Parkinson's disease

DJ-1 is an antioxidant protein whose loss of function by gene mutations has been linked to familial Parkinson's disease (PD). The main objective of the present study was to determine if this molecule was also involved in the pathogenesis of sporadic PD. For this purpose, quantitative immunoblot assays were performed to evaluate DJ-1 in cerebrospinal fluids (CSF) collected from sporadic PD patients (n=40) and non-PD controls (n=38). The results showed that the CSF DJ-1 levels in PD were significantly higher than those in non-PD controls. Especially, upregulation of CSF DJ-1 in the early stage of PD (Yahr I-II) were distinct compared to those in the advanced stage of PD (Yahr III-IV) and non-PD controls (p<0.001 by ANOVA with post hoc Bonferroni's test), suggesting a protective role of DJ-1 against oxidative stress during the early stage. Thus, we propose that CSF DJ-1 could be a possible biomarker for early sporadic PD.     

Growth characteristic of anaerobic ammonium-oxidizing bacteria in an anaerobic biological filtrated reactor

The doubling time of anaerobic ammonium-oxidizing (anammox) bacteria in an anaerobic biological filtrated (ABF) reactor was determined. Fluorescence in situ hybridization analysis was used to detect and count anammox bacteria cells in anammox sludge. As a result, the populations of anammox bacteria at 14th and 21st days were 1.1×10⁶ and 1.7×10⁷ cells/ml reactor, respectively. From these results, the doubling time of anammox bacteria was calculated as 1.8 days, and the specific growth rate (μ) was 0.39 day⁻¹. This result indicated that the anammox bacteria have higher growth rate than the reported value (doubling time, 11 days). Furthermore, it was clearly demonstrated that nitrogen conversion rate was proportional to the population of anammox bacteria. Maintaining the ideal environment for the growth of anammox bacteria in the ABF reactor might lead to faster growth. This is the first report of the growth rate of anammox bacteria based on the direct counting of anammox bacteria.     

Construction of a Cloning System for the Mass Production of a Virus-Binding Protein Specific for Poliovirus Type 1

In our previous study, virus-binding proteins (VBPs) demonstrating the ability to strongly bind poliovirus type 1 (PV1) were recovered from a bacterial culture derived from activated sludge. The isolated VBPs would be useful as viral adsorbents for water and wastewater treatments. The VBP gene of activated sludge bacteria was isolated, and the cloning system of the VBP was established. The isolation of the VBP gene from DNA libraries for activated sludge bacteria was achieved with the colony hybridization technique. The sequence of the VBP gene consisted of 807 nucleotides encoding 268 amino acids. Fifteen amino acid sequences were retrieved from 2,137,877 sequences by a homology search using the BLAST server at the National Center for Biotechnology Information. The protein encoded in the isolated genome was considered to be a newly discovered protein from activated sludge culture, because any sequences in protein databases were not perfectly matched with the sequence of the VBP. It was confirmed that Escherichia coli BL21 transformed by pRSET carrying the isolated VBP gene could extensively produce the VBP clones. Enzyme-linked immunosorbent assay (ELISA) revealed that the VBP clone exhibited the binding ability with intact particles of PV1. The equilibrium binding constant between PV1 and VBP in the ELISA well was estimated to be 2.1 × 10⁷ (M⁻¹), which also indicated that the VBP clones have a high affinity with the PV1 particle. The VBP cloning system developed in this study would make it possible to produce a mass volume of VBPs and to utilize them as a new material of the specific adsorbent in several technologies, including virus removal, concentration, and detection.