Morphology and morphogenesis of a new marine hypotrichous ciliate (Protozoa,Ciliophora, Pseudoamphisiellidae), including a report on the small subunit rRNA gene sequence

The morphology and morphogenesis of a new marine hypotrichous ciliate Pseudoamphisiella elongata sp. nov. isolated from mussel‐farming waters near Qingdao, China, are described based on living and protargol‐impregnated specimens. Morphologically, the new species can be distinguished from its known congeners by its elongate body shape, narrow oral field, having fewer dorsal kineties and caudal cirri, more marginal cirri, and differentiated pretransverse cirri. The identification as a new species is firmly supported by the sequences of the small subunit ribosomal rRNA (SSU rRNA) gene, compared with other known Pseudoamphisiella species, and the phylogenetic analysis. The morphogenetic characteristics can be summarized as follows: (1) the parental adoral zone of membranelles and undulating membranes are entirely rebuilt by the oral primordium, which develops de novo in the outermost region of the cortex; (2) the oral primordium in the opisthe and the frontoventral–transverse (FVT) anlagen in both dividers are formed independently on the cell surface; (3) an ‘extra’ marginal anlage originates to the right of the right marginal anlage, and develops into two or three ‘extra’ marginal cirri; (4) the FVT anlagen develop in the primary mode, and the last FVT streak contributes two migratory cirri (frontoterminal cirri), which are probably resorbed; (5) the right marginal anlagen in both dividers occur close together, independent of the old structure. © 2010 The Linnean Society of London, Zoological Journal of the Linnean Society, 2010, 158 , 231–243.     

The genome sequence of the biocontrol fungus Metarhizium anisopliae and comparative genomics of Metarhizium species

Background

Metarhizium anisopliae is an important fungal biocontrol agent of insect pests of agricultural crops. Genomics can aid the successful commercialization of biopesticides by identification of key genes differentiating closely related species, selection of virulent microbial isolates which are amenable to industrial scale production and formulation and through the reduction of phenotypic variability. The genome of Metarhizium isolate ARSEF23 was recently published as a model for M. anisopliae, however phylogenetic analysis has since re-classified this isolate as M. robertsii. We present a new annotated genome sequence of M. anisopliae (isolate Ma69) and whole genome comparison to M. robertsii (ARSEF23) and M. acridum (CQMa 102).

Results

Whole genome analysis of M. anisopliae indicates significant macrosynteny with M. robertsii but with some large genomic inversions. In comparison to M. acridum, the genome of M. anisopliae shares lower sequence homology. While alignments overall are co-linear, the genome of M. acridum is not contiguous enough to conclusively observe macrosynteny. Mating type gene analysis revealed both MAT1-1 and MAT1-2 genes present in M. anisopliae suggesting putative homothallism, despite having no known teleomorph, in contrast with the putatively heterothallic M. acridum isolate CQMa 102 (MAT1-2) and M. robertsii isolate ARSEF23 (altered MAT1-1). Repetitive DNA and RIP analysis revealed M. acridum to have twice the repetitive content of the other two species and M. anisopliae to be five times more RIP affected than M. robertsii. We also present an initial bioinformatic survey of candidate pathogenicity genes in M. anisopliae.

Conclusions

The annotated genome of M. anisopliae is an important resource for the identification of virulence genes specific to M. anisopliae and development of species- and strain- specific assays. New insight into the possibility of homothallism and RIP affectedness has important implications for the development of M. anisopliae as a biopesticide as it may indicate the potential for greater inherent diversity in this species than the other species. This could present opportunities to select isolates with unique combinations of pathogenicity factors, or it may point to instability in the species, a negative attribute in a biopesticide.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-660) contains supplementary material, which is available to authorized users.     

Characterization of Two Novel α-Glucosidases from Bifidobacterium breve UCC2003

Two α-glucosidase-encoding genes (agl1 and agl2) from Bifidobacterium breve UCC2003 were identified and characterized. Based on their similarity to characterized carbohydrate hydrolases, the Agl1 and Agl2 enzymes are both assigned to a subgroup of the glycosyl hydrolase family 13, the α-1,6-glucosidases (EC 3.2.1.10). Recombinant Agl1 and Agl2 into which a His₁₂ sequence was incorporated (Agl1_His and Agl2_His, respectively) exhibited hydrolytic activity towards panose, isomaltose, isomaltotriose, and four sucrose isomers—palatinose, trehalulose, turanose, and maltulose—while also degrading trehalose and, to a lesser extent, nigerose. The preferred substrates for both enzymes were panose, isomaltose, and trehalulose. Furthermore, the pH and temperature optima for both enzymes were determined, showing that Agl1_His exhibits higher thermo and pH optima than Agl2_His. The two purified α-1,6-glucosidases were also shown to have transglycosylation activity, synthesizing oligosaccharides from palatinose, trehalulose, trehalose, panose, and isomaltotriose.The gastrointestinal tract is inhabited by a complex community of microorganisms, also referred to as the microbiota, which are believed to play an important role in human health and disease (39). This concept has been driving extensive attempts to positively influence the composition and/or activity of the intestinal microbiota through the use of so-called probiotics and/or prebiotics. A probiotic has been defined as “a preparation or a product containing viable, defined microorganisms in sufficient numbers, which alter the microflora (by implantation or colonization) in a compartment of the host and by that exert beneficial health effect in this host” (48). A prebiotic has recently been (re)defined as “a selectively fermented ingredient that allows specific changes, both in the composition and/or activity in the gastrointestinal microbiota that confers benefits upon host well-being and health” (42). Finally, a synbiotic is the combination of a probiotic and a prebiotic (16).One of the dominant bacteria of the intestinal microbiota of humans and animals (51) is bifidobacteria. These are gram-positive, pleomorphic, and anaerobic bacteria that have received increasing scientific attention in recent years due to their perceived probiotic activity (15, 27). The growth of gut-derived bifidobacteria has been shown to be selectively stimulated by various dietary carbohydrates that can thus be considered as prebiotics (30). In this context, it is interesting to note that more than 8% of the identified genes on bifidobacterial genomes are predicted to be involved in sugar metabolism, thus indicative of extensive carbon source-degrading abilities (55, 56).Carbohydrate degradation has been extensively studied in a variety of different Bifidobacterium species (reviewed in reference 53). For example, various α- and β-galactosidases have been characterized in Bifidobacterium breve 203 (60), Bifidobacterium adolescentis DSM20083 (20), Bifidobacterium bifidum NCIMB41171 (18), and Bifidobacterium longum MB219 (43). A number of studies have also shown that Bifidobacterium spp. produce various α- and β-glucosidase activities (reviewed in reference 53), while Bifidobacterium infantis ATCC 15697 (58), Bifidobacterium lactis DSM10140(T) (13), and B. breve UCC2003 (45) have been reported to produce β-fructofuranosidases during growth on fructooligosaccharides. Additionally, starch-, amylopectin-, and pullulan-degrading activities in bifidobacteria have been investigated (36, 44). Several β-glucosidases have been biochemically characterized from a number of strains of bifidobacteria, e.g., B. adolescentis Int-57 (8), B. breve clb (35,) and Bifidobacterium sp. strain SEN (59). To date, only two α-glucosidases (AglA and AglB) have been described from B. adolescentis DSM20083 (54). AglA was shown to preferentially hydrolyze isomaltotriose, while AglB exhibits a high preference to maltose. Both AglA and AglB were also demonstrated to have transglycosylation activity. Aside from this report, little is known about the biochemical characteristics of α-glucosidase enzymes from bifidobacteria, although it is a common activity observed among these bacteria (41).Carbohydrates other than the commercially exploited prebiotics, e.g., fructooligosaccharides (such as inulin) and trans-galactooligosaccharides (42), have received relatively little attention with regard to their possible prebiotic properties. Such potential prebiotics are, for example, honey oligosaccharides, some of which are also interesting because of their noncariogenic properties (14). One of the predominant fractions of noncariogenic sugars in honey is isomaltulose (5, 46), also called palatinose or 6-O-α-d-glucopyranosyl-d-fructose, which is a reducing disaccharide and a functional isomer of sucrose. Palatinose possesses approximately one-third of the sweetness of sucrose and is very resistant to acid and invertase hydrolysis (29, 32). The hydrolysis and adsorption of palatinose in the small intestine thus occurs at a much slower rate than does those of sucrose (17), which results in a reduction of the postprandial plasma glucose and insulin levels (3), which means that most palatinose passes through the small intestine to present a growth substrate for elements of the colonic microbiota.In this study, we describe the identification of two genes, agl1 and agl2, present in the genome of B. breve UCC2003 and responsible for the hydrolysis of α-glycosidic linkages, such as those present in palatinose.     

A structured overview of simultaneous component based data integration

Background  

Data integration is currently one of the main challenges in the biomedical sciences. Often different pieces of information are gathered on the same set of entities (e.g., tissues, culture samples, biomolecules) with the different pieces stemming, for example, from different measurement techniques. This implies that more and more data appear that consist of two or more data arrays that have a shared mode. An integrative analysis of such coupled data should be based on a simultaneous analysis of all data arrays. In this respect, the family of simultaneous component methods (e.g., SUM-PCA, unrestricted PCovR, MFA, STATIS, and SCA-P) is a natural choice. Yet, different simultaneous component methods may lead to quite different results.     

Morphology and Phylogeny of Two New Pleurostomatid Ciliates,Epiphyllum shenzhenense n. sp. and Loxophyllum spirellum n. sp. (Protozoa,Ciliophora) from A Mangrove Wetland,South China

ABSTRACT. The morphology, infraciliature, and small subunit (SSU) rRNA gene sequences of two new pleurostomatid ciliates, Epiphyllum shenzhenense n. sp. and Loxophyllum spirellum n. sp., isolated from a mangrove wetland near Shenzhen, South China, were investigated. Epiphyllum shenzhenense n. sp. is morphologically characterized by leaf‐shaped cell about 150 × 35 μm in vivo, usually with four contractile vacuoles, 20–29 right kineties and 10–26 left kineties, ca. four macronuclear nodules, and two types of extrusomes (i.e. short spindle‐shaped and long bar‐shaped). As a new species, L. spirellum n. sp. is distinguished from its congeners by its posterior dorsal margin twisted onto the left side, the distribution of extrusomes (evenly arranged along the oral slit, the posterior end, and clustered to 7–13 warts on dorsal margin), the subterminally positioned contractile vacuole, the number of kineties (8–10 on right side, 4–5 on left side), and its genetic distance from congeners. Phylogenetic trees based on the SSU rRNA gene sequence for both organisms were constructed, which indicate that Epiphyllum is a distinct genus and occupies a basal position in the Pleurostomatida clade; L. spirellum n. sp. falls well into the Loxophyllum clade, which has a close relationship with Litonotus and Spiroloxophyllum.     

Genome Sequence of Moraxella catarrhalis RH4, an Isolate of Seroresistant Lineage

Here we report the annotated genome sequence of Moraxella catarrhalis strain RH4, a seroresistant-lineage strain isolated from the blood of an infected patient. This genome sequence will allow us to gain further insight into the genetic diversity of clinical M. catarrhalis isolates and will facilitate study of M. catarrhalis pathogenesis.     

Accurate measurement of gene copy number for human alpha-defensin DEFA1A3

Background

Multi-allelic copy number variants include examples of extensive variation between individuals in the copy number of important genes, most notably genes involved in immune function. The definition of this variation, and analysis of its impact on function, has been hampered by the technical difficulty of large-scale but accurate typing of genomic copy number. The copy-variable alpha-defensin locus DEFA1A3 on human chromosome 8 commonly varies between 4 and 10 copies per diploid genome, and presents considerable challenges for accurate high-throughput typing.

Results

In this study, we developed two paralogue ratio tests and three allelic ratio measurements that, in combination, provide an accurate and scalable method for measurement of DEFA1A3 gene number. We combined information from different measurements in a maximum-likelihood framework which suggests that most samples can be assigned to an integer copy number with high confidence, and applied it to typing 589 unrelated European DNA samples. Typing the members of three-generation pedigrees provided further reassurance that correct integer copy numbers had been assigned. Our results have allowed us to discover that the SNP rs4300027 is strongly associated with DEFA1A3 gene copy number in European samples.

Conclusions

We have developed an accurate and robust method for measurement of DEFA1A3 copy number. Interrogation of rs4300027 and associated SNPs in Genome-Wide Association Study SNP data provides no evidence that alpha-defensin copy number is a strong risk factor for phenotypes such as Crohn’s disease, type I diabetes, HIV progression and multiple sclerosis.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-14-719) contains supplementary material, which is available to authorized users.     

Biodiversity of stream insects in the Malaysian Peninsula: spatial patterns and environmental constraints

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Viscoelastic Properties of a Mixed Culture Biofilm from Rheometer Creep Analysis

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