L-galactonate dehydratase is part of the fungal path for D-galacturonic acid catabolism

An L-galactonate dehydratase and the corresponding gene were identified from the mould Hypocrea jecorina (Trichoderma reesei). This novel enzyme converts L-galactonate to L-threo-3-deoxy-hexulosonate (2-keto-3-deoxy-L-galactonate). The enzyme is part of the fungal pathway for D-galacturonic acid catabolism, a pathway which is only partly known. It is the second enzyme of this pathway after the D-galacturonic acid reductase. L-galactonate dehydratase activity is present in H. jecorina cells grown on D-galacturonic acid but absent when other carbon sources are used for growth. A deletion of the L-galactonate dehydratase gene in H. jecorina results in a strain with no growth on D-galacturonic acid. The active enzyme was produced in the heterologous host Saccharomyces cerevisiae and characterized. It exhibited activity with L-galactonate and D-arabonate where the hydroxyl group of the C2 is in L- and the hydroxyl group of the C3 is in D-configuration in the Fischer projection. However, it did not exhibit activity with D-galactonate, D-gluconate, L-gulonate or D-xylonate where the hydroxyl groups of the C2 and C3 are in different configuration.     

Characterization of a Novel Flavivirus from Mosquitoes in Northern Europe That Is Related to Mosquito-Borne Flaviviruses of the Tropics

A novel flavivirus was isolated from mosquitoes in Finland, representing the first mosquito-borne flavivirus from Northern Europe. The isolate, designated Lammi virus (LAMV), was antigenically cross-reactive with other flaviviruses and exhibited typical flavivirus morphology as determined by electron microscopy. The genomic sequence of LAMV was highly divergent from the recognized flaviviruses, and yet the polyprotein properties resembled those of mosquito-borne flaviviruses. Phylogenetic analysis of the complete coding sequence showed that LAMV represented a distinct lineage related to the Aedes sp.-transmitted human pathogenic flaviviruses, similarly to the newly described Nounané virus (NOUV), a flavivirus from Africa (S. Junglen et al., J. Virol. 83:4462-4468, 2009). Despite the low sequence homology, LAMV and NOUV were phylogenetically grouped closely, likely representing separate species of a novel group of flaviviruses. Despite the biological properties preferring replication in mosquito cells, the genetic relatedness of LAMV to viruses associated with vertebrate hosts warrants a search for disease associations.The genus Flavivirus in the family Flaviviridae consists of 53 recognized virus species that are enveloped, positive-sense single-stranded RNA viruses. The virion consists of three structural proteins: capsid (C), membrane (M), and envelope (E). In addition, seven nonstructural proteins are present in infected cells (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5). Based on their antigenic properties and vector associations, flaviviruses have been grouped into mosquito-borne, tick-borne, and no-known-vector viruses and have been isolated from vertebrates, bats, and rodents (15, 25). The grouping of flaviviruses according to their transmission mode is strongly supported by phylogenetic analyses of their genomic sequences (9, 18, 31).Mosquito-borne flaviviruses are a large and divergent group of viruses that can be differentiated phylogenetically into those associated either with encephalitic disease and transmission by Culex spp. mosquitoes or with diseases with hemorrhagic complications and transmission by Aedes spp. (18). Seven groups of mosquito-borne flaviviruses, namely, the Aroa, dengue, Japanese encephalitis, Kokobera, Ntaya, Spondweni, and yellow fever virus groups are recognized (15, 25). These groups include important animal and human pathogens such as dengue virus (DENV), West Nile virus (WNV), Japanese encephalitis virus (JEV), and yellow fever virus (YFV).Unclassified insect flaviviruses that have no recognized association with vertebrates have been isolated from a variety of mosquito species and also from mosquito cell lines. These insect flaviviruses do not appear to infect vertebrate cells and are not associated with human or animal disease. The cell fusing agent virus (CFAV), a tentative species in the genus Flavivirus, was the first of these insect viruses to be characterized (5, 40), Although CFAV was originally identified in cultured mosquito cells, it was later isolated from mosquitoes collected in Puerto Rico (7). This as-yet-unclassified insect flavivirus group now also includes Kamiti river virus (KRV) isolated in Kenya (10, 38) and a virus isolated from Culex spp. in Japan, designated culex flavivirus (22). In addition, related viral sequences or isolates have been recently reported from mosquitoes in Spain (1), the United States and Trinidad (26), and Mexico (14). Moreover, the identification of flaviviruslike sequences integrated within the genomes of Aedes mosquitoes further complicates the evolutionary history of the flaviviruses. These sequences, currently referred to as cell silent agent are genetically most closely related to CFAV and possibly share common evolutionary origin (11). Phylogenetically, the insect viruses form a divergent outgroup that may represent a primordial flavivirus lineage. Apart from the insect flaviviruses, the other recently discovered novel flaviviruses represent highly divergent lineages, such as Tamana bat virus (13), and Ngoye virus (20). Recently, a novel flavivirus, Nounané virus (NOUV) was isolated from a novel mosquito vector species, Uranotaenia mashonaensis in Côte d''Ivoire (23), and was shown to be phylogenetically related to the human pathogenic mosquito-borne flaviviruses.Several arboviruses have been reported from Northern Europe including the flavivirus tick-borne encephalitis virus (24, 36) but, to date, no mosquito-borne flaviviruses have been isolated. Our aim was to screen for arboviruses in Finland by studying mosquitoes using virus isolation and subsequent arbovirus antigen detection, which resulted in the identification of a novel flavivirus. We present here the isolation and characterization of this isolate, designated Lammi virus (LAMV), and discuss the implications of our findings.     

Seasonal fluctuations in macrophyte cover and water transparency of four brown-water lakes: implications for crustacean zooplankton in littoral and pelagic habitats

The dynamics of crustacean zooplankton in the littoral and pelagic zones of four forest lakes having variable water qualities (colour range 130–340 mg Pt l⁻¹, Secchi depth 70–160 cm) were studied. The biomass of zooplankton was higher in the littoral zone than in the pelagic zone only in the lake having the highest transparency. In the three other lakes, biomass was significantly higher in the pelagic zone than in the littoral zone. In the two lakes with highest transparency, the littoral biomass of cladocerans significantly followed the development of macrophyte vegetation, and cladoceran biomass reached the maximum value at the time of highest macrophyte coverage. In lakes with lowest transparency, littoral zooplankton biomass developed independently of macrophyte density and decreased when macrophyte beds were densest. The seasonal development of the littoral copepod biomass did not follow the development of macrophytes in any of the lakes. The mean size of cladocerans in the pelagic zone decreased with increasing Secchi depth of the lake, whereas in the littoral zone no such phenomenon was detected. Seasonally, when water transparency increased temporarily in two of the lakes, the mean size of cladocerans in the pelagic zone decreased steeply. For copepods, no relationship between water transparency and body size was observed. The results suggested that in humic lakes the importance of the littoral zone as a refuge decreases with decreasing transparency of the water and that low water transparency protects cladocerans from fish predation. All the observed between-lake differences could not be explained by fish predation, but were probably attributed to the presence of chaoborid larvae with variable densities. Feeding efficiency of chaoborids is not affected by visibility and thus they can obscure the relationship between water quality, fish density, and the structure of crustacean zooplankton assemblages. Handling editor: S. I. Dodson     

Geographical patterns of micro‐organismal community structure: are diatoms ubiquitously distributed across boreal streams?

A topic under intensive study in community ecology and biogeography is the degree to which microscopic, as well as macroscopic organisms, show spatially-structured variation in community characteristics. In general, unicellular microscopic organisms are regarded as ubiquitously distributed and, therefore, without a clear biogeographic signal. This view was summarized 75  years ago by Baas-Becking, who stated "everything is everywhere, but, the environment selects". Within the context of metacommunity theory, this hypothesis is congruent with the species sorting model. By using a broad-scale dataset on stream diatom communities and environmental predictor variables across most of Finland, our main aim was to test this hypothesis. Patterns of spatial autocorrelation were evaluated by Moran's I based correlograms, whereas partial regression analysis and partial redundancy analysis were used to quantify the relative importance of environmental and spatial factors on total species richness and on community composition, respectively. Significant patterns of spatial autocorrelation were found for all environmental variables, which also varied widely. Our main results were clear-cut. In general, pure spatial effects clearly overcame those of environmental effects, with the former explaining much more variation in species richness and community composition. Most likely, missing environmental variables cannot explain the higher predictive power of spatial variables, because we measured key factors that have previously been found to be the most important variables (e.g. pH, conductivity, colour, phosphorus, nitrogen) shaping the structure of diatom communities. Therefore, our results provided only limited support for the Baas-Becking hypothesis and the species sorting perspective of metacommunity theory.     

Bioconversion of D-galacturonate to keto-deoxy-L-galactonate (3-deoxy-L-<Emphasis Type="Italic">threo</Emphasis>-hex-2-ulosonate) using filamentous fungi

Background  

The D-galacturonic acid derived from plant pectin can be converted into a variety of other chemicals which have potential use as chelators, clarifiers, preservatives and plastic precursors. Among these is the deoxy-keto acid derived from L-galactonic acid, keto-deoxy-L-galactonic acid or 3-deoxy-L- threo -hex-2-ulosonic acid. The keto-deoxy sugars have been found to be useful precursors for producing further derivatives. Keto-deoxy-L-galactonate is a natural intermediate in the fungal D-galacturonate metabolic pathway, and thus keto-deoxy-L-galactonate can be produced in a simple biological conversion.     

Small intestinal permeability and serum folate and cobalamin absorption after surgical construction of permanent jejunal fistulas in laboratory beagle dogs

Permanent jejunal fistulas enable easy, noninjurious, repeated and direct administration to and collection from the small intestines of conscious laboratory dogs. This study aimed at identifying potential alterations in the small intestinal morphology and function of this canine model after the surgery required to establish the fistulas. Assays of serum folate and cobalamin and (51)Cr-EDTA permeability tests were performed before and 4 wk after experimental jejunoplasties in 14 laboratory beagle dogs. Serum folate concentrations (mean ± SD) before (12.22 ± 1.80 μg/L) and after (14.14 ± 1.70 μg/L) jejunal surgery were within reference ranges for healthy dogs, although folate concentrations were higher after surgery. The cobalamin concentrations and the 6-h urinary excretion of (51)Cr-EDTA before (573.50 ± 150.04 ng/L and 6.75 ± 1.56%, respectively) and after (496.71 ± 164.22 ng/L and 6.41 ± 1.10%) were normal for healthy dogs, and no significant differences between pre- and postsurgical values were detected. The findings of the present study indicate that the small intestinal vitamin absorption and permeability of laboratory beagle dogs with jejunal fistulas remains unimpaired.     

Actin depolymerizing factors cofilin1 and destrin are required for ureteric bud branching morphogenesis

The actin depolymerizing factors (ADFs) play important roles in several cellular processes that require cytoskeletal rearrangements, such as cell migration, but little is known about the in vivo functions of ADFs in developmental events like branching morphogenesis. While the molecular control of ureteric bud (UB) branching during kidney development has been extensively studied, the detailed cellular events underlying this process remain poorly understood. To gain insight into the role of actin cytoskeletal dynamics during renal branching morphogenesis, we studied the functional requirements for the closely related ADFs cofilin1 (Cfl1) and destrin (Dstn) during mouse development. Either deletion of Cfl1 in UB epithelium or an inactivating mutation in Dstn has no effect on renal morphogenesis, but simultaneous lack of both genes arrests branching morphogenesis at an early stage, revealing considerable functional overlap between cofilin1 and destrin. Lack of Cfl1 and Dstn in the UB causes accumulation of filamentous actin, disruption of normal epithelial organization, and defects in cell migration. Animals with less severe combinations of mutant Cfl1 and Dstn alleles, which retain one wild-type Cfl1 or Dstn allele, display abnormalities including ureter duplication, renal hypoplasia, and abnormal kidney shape. The results indicate that ADF activity, provided by either cofilin1 or destrin, is essential in UB epithelial cells for normal growth and branching.     

Human and bovine lactoferrins in the milk of recombinant human lactoferrin-transgenic dairy cows during lactation

Seven Friesian human lactoferrin (hLf)-transgenic primiparous dairy cows expressing recombinant hLf (rhLf) in their milk were included in the study. After calving, concentrations of rhLf and bovine LF (bLf) in the milk, somatic cell count and milk yield were determined. The concentration of rhLf was found to be constant, about 2.9 mg/mL, throughout the early lactation period of 3 months. The concentration of bLf in colostrum was higher after calving, but decreased rapidly during the first days of lactation. The mean concentration of bLf was 0.15 mg/mL, but concentrations varied between cows from 0.07 mg/mL to 0.26 mg/mL. Based on that, it may be possible to improve the non-specific host defence mechanism in the mammary gland of dairy cows by enhancing the content of rhLf in the milk.     

Identification of preferred protein interactions by phage-display of the human Src homology-3 proteome

We have determined the human genome to contain 296 different Src homology-3 (SH3) domains and cloned them into a phage-display vector. This provided a powerful and unbiased system for simultaneous assaying of the complete human SH3 proteome for the strongest binding to target proteins of interest, without the limitations posed by short linear peptide ligands or confounding variables of more indirect methods for protein interaction screening. Studies involving three ligand proteins, human immunodeficiency virus-1 Nef, p21-activated kinase (PAK)2 and ADAM15, showed previously reported as well as novel SH3 partners with nanomolar affinities specific for them. This argues that SH3 domains may have a more dominant role in directing cellular protein interactions than has been assumed. Besides showing potentially important new SH3-directed interactions, these studies also led to the discovery of novel signalling proteins, such as the PAK2-binding adaptor protein POSH2 and the ADAM15-binding sorting nexin family member SNX30.     

New real-time quantitative PCR procedure for quantification of bifidobacteria in human fecal samples

The application of a real-time quantitative PCR method (5' nuclease assay), based on the use of a probe labeled at its 5' end with a stable, fluorescent lanthanide chelate, for the quantification of human fecal bifidobacteria was evaluated. The specificities of the primers and the primer-probe combination were evaluated by conventional PCR and real-time PCR, respectively. The results obtained by real-time PCR were compared with those obtained by fluorescent in situ hybridization, the current gold standard for intestinal microbiota quantification. In general, a good correlation between the two methods was observed. In order to determine the detection limit and the accuracy of the real-time PCR procedure, germfree rat feces were spiked with known amounts of bifidobacteria and analyzed by both methods. The detection limit of the method used in this study was found to be about 5 x 10(4) cells per g of feces. Both methods, real-time PCR and fluorescent in situ hybridization, led to an accurate quantification of the spiked samples with high levels of bifidobacteria, but real-time PCR was more accurate for samples with low levels. We conclude that the real-time PCR procedure described here is a specific, accurate, rapid, and easy method for the quantification of bifidobacteria in feces.