A new species of recently extinct rice rat (Megalomys) from Barbados

Recently extinct insular populations of oryzomyine rice rats (Cricetidae: Sigmodontinae) are known from across the Lesser Antilles, but most remain undescribed. Historical records of a possible now-extinct endemic rodent from Barbados are supported by presence of oryzomyine remains in Late Quaternary sites on the island, including several pre-Columbian Holocene archaeological sites. The Barbados oryzomyine is described as Megalomys georginae sp. nov., and is most closely related to species from the nearby islands of Martinique and St. Lucia, M. desmarestii and M. luciae. These species all display a zygomatic plate with its posterior margin level with the alveolus of M1, a divided anterocone on M1, and distinct anterolophids and metaflexids on m2 and m3, and are recovered as a monophyletic clade in morphological-molecular and morphology-only analyses. The new species differs from other Megalomys species in having the labial accessory root of M1 absent, a reduced anteromedian flexus on M1, two roots on m2 and m3, a supratrochlear foramen on the humerus, and in its much smaller body size. Other extinct Caribbean oryzomyines are not recovered in a monophyletic clade with Megalomys.     

More than 400 million years of evolution and some plants still can't make it on their own: plant stress tolerance via fungal symbiosis

All plants in natural ecosystems are thought to be symbioticwith mycorrhizal and/or endophytic fungi. Collectively, thesefungi express different symbiotic lifestyles ranging from parasitismto mutualism. Analysis of Colletotrichum species indicates thatindividual isolates can express either parasitic or mutualisticlifestyles depending on the host genotype colonized. The endophytecolonization pattern and lifestyle expression indicate thatplants can be discerned as either disease, non-disease, or non-hosts.Fitness benefits conferred by fungi expressing mutualistic lifestylesinclude biotic and abiotic stress tolerance, growth enhancement,and increased reproductive success. Analysis of plant–endophyteassociations in high stress habitats revealed that at leastsome fungal endophytes confer habitat-specific stress toleranceto host plants. Without the habitat-adapted fungal endophytes,the plants are unable to survive in their native habitats. Moreover,the endophytes have a broad host range encompassing both monocotsand eudicots, and confer habitat-specific stress tolerance toboth plant groups. Key words: Colletotrichum, fungal endophytes, stress tolerance, symbiosis, symbiotic lifestyle Received 19 June 2007; Revised 25 November 2007 Accepted 30 November 2007     

Metabolic profiling of serum using Ultra Performance Liquid Chromatography and the LTQ-Orbitrap mass spectrometry system

Advances in analytical instrumentation can provide significant advantages to the volume and quality of biological knowledge acquired in metabolomic investigations. The interfacing of sub-2mum liquid chromatography (UPLC ACQUITY((R))) and LTQ-Orbitrap mass spectrometry systems provides many theoretical advantages. The applicability of the interfaced systems was investigated using a simple 11-component metabolite mix and a complex mammalian biofluid, serum. Metabolites were detected in the metabolite mix with signals that were linear with their concentration over 2.5-3.5 orders of magnitude, with correlation coefficients greater than 0.993 and limits of detection less than 1mumolL(-1). Reproducibility of retention time (RSD<3%) and chromatographic peak area (RSD<15%) and a high mass accuracy (<2ppm) were observed for 14 QC serum samples interdispersed with other serum samples, analysed over a period of 40h. The evaluation of a single deconvolution software package (XCMS) was performed and showed that two parameters (snthresh and bw) provided significant changes to the number of peaks detected and the peak area reproducibility for the dataset used. The data were used to indicate possible biomarkers of pre-eclampsia and showed both the instruments and XCMS to be applicable to the reproducible and valid detection of disease biomarkers present in serum.     

Phosphorylation regulates tau interactions with Src homology 3 domains of phosphatidylinositol 3-kinase, phospholipase Cgamma1, Grb2, and Src family kinases

The microtubule-associated protein tau can associate with various other proteins in addition to tubulin, including the SH3 domains of Src family tyrosine kinases. Tau is well known to aggregate to form hyperphosphorylated filamentous deposits in several neurodegenerative diseases (tauopathies) including Alzheimer disease. We now report that tau can bind to SH3 domains derived from the p85alpha subunit of phosphatidylinositol 3-kinase, phospholipase Cgamma1, and the N-terminal (but not the C-terminal) SH3 of Grb2 as well as to the kinases Fyn, cSrc, and Fgr. However, the short inserts found in neuron-specific isoforms of Src prevented the binding of tau. The experimentally determined binding of tau peptides is well accounted for when modeled into the peptide binding cleft in the SH3 domain of Fyn. After phosphorylation in vitro or in transfected cells, tau showed reduced binding to SH3 domains; no binding was detected with hyperphosphorylated tau isolated from Alzheimer brain, but SH3 binding was restored by phosphatase treatment. Tau mutants with serines and threonines replaced by glutamate, to mimic phosphorylation, showed reduced SH3 binding. These results strongly suggest that tau has a potential role in cell signaling in addition to its accepted role in cytoskeletal assembly, with regulation by phosphorylation that may be disrupted in the tauopathies including Alzheimer disease.     

Species Structure of Plankton Microalgae on the Coast of the Sea of Okhotsk on Sakhalin Island

The results of long-term studies of the species structure of microalgae plankton of the coast of the Sea of Okhotsk of Sakhalin Island were summarized. There were 227 species and 4 intraspecific taxa attributed to 8 divisions. The greatest number of species was represented by the divisions Bacillariophyta (112 species and 3 intraspecific taxa) and Dinophyta (96 and 1 respectively). For the first time 5 diatom, 4 dinoflagellate, and 1 euglenophyte species were recorded for the Sea of Okhotsk.     

Exploring the Gastrointestinal “Nemabiome”: Deep Amplicon Sequencing to Quantify the Species Composition of Parasitic Nematode Communities

Parasitic helminth infections have a considerable impact on global human health as well as animal welfare and production. Although co-infection with multiple parasite species within a host is common, there is a dearth of tools with which to study the composition of these complex parasite communities. Helminth species vary in their pathogenicity, epidemiology and drug sensitivity and the interactions that occur between co-infecting species and their hosts are poorly understood. We describe the first application of deep amplicon sequencing to study parasitic nematode communities as well as introduce the concept of the gastro-intestinal “nemabiome”. The approach is analogous to 16S rDNA deep sequencing used to explore microbial communities, but utilizes the nematode ITS-2 rDNA locus instead. Gastro-intestinal parasites of cattle were used to develop the concept, as this host has many well-defined gastro-intestinal nematode species that commonly occur as complex co-infections. Further, the availability of pure mono-parasite populations from experimentally infected cattle allowed us to prepare mock parasite communities to determine, and correct for, species representation biases in the sequence data. We demonstrate that, once these biases have been corrected, accurate relative quantitation of gastro-intestinal parasitic nematode communities in cattle fecal samples can be achieved. We have validated the accuracy of the method applied to field-samples by comparing the results of detailed morphological examination of L3 larvae populations with those of the sequencing assay. The results illustrate the insights that can be gained into the species composition of parasite communities, using grazing cattle in the mid-west USA as an example. However, both the technical approach and the concept of the ‘nemabiome’ have a wide range of potential applications in human and veterinary medicine. These include investigations of host-parasite and parasite-parasite interactions during co-infection, parasite epidemiology, parasite ecology and the response of parasite populations to both drug treatments and control programs.     

Taxonomy, phylogeny, biogeography, and ecology of Sabulodinium undulatum (Dinophyceae), including an emended description of the species

Samples of Sabulodinium undulatum Saunders et Dodge, the type species of the monospecific genus, were collected and characterized from Germany, Russia, Japan and Canada. This species has a laterally flattened, oval cell with a truncated apex and a dorsally pointing small episome. The dorsal margin of the hyposome has an undulating shape. A dorsal spine and/or antapical spine are sometimes present. The specimens of this heterotrophic species are 27.5–42.5 μm long and 18.5–36.0 μm wide, and have a theca with the plate arrangement apical pore complex (APC) 5′ 1a 6″ 5c 4s 6′′′ 1′′′′. The shape of the dorsal theca is variable. The species distribution seems to be restricted to northern temperate regions. Sabulodinium undulatum occurred in all sandy eulittoral areas throughout the year and was also present in sandy sublittoral and supralittoral (beach) samples. The species can tolerate a broad range of temperatures and salinities. Sabulodinium occurred from −2.0 to +24.3°C and 4–35 salinity. It is likely that the observed variability in morphology and habitat reflect several varieties. We propose to establish three varieties within the species, namely S. undulatum var. undulatum, S. undulatum var. glabromarginatum, and S. undulatum var. monospinum. The systematic position of Sabulodinium is discussed in the context of comparative morphological and molecular phylogenetic data.