Showing papers by "Brett J. Baker published in 2010"

Enigmatic, ultrasmall, uncultivated Archaea

Abstract: Metagenomics has provided access to genomes of as yet uncultivated microorganisms in natural environments, yet there are gaps in our knowledge-particularly for Archaea-that occur at relatively low abundance and in extreme environments. Ultrasmall cells (<500 nm in diameter) from lineages without cultivated representatives that branch near the crenarchaeal/euryarchaeal divide have been detected in a variety of acidic ecosystems. We reconstructed composite, near-complete approximately 1-Mb genomes for three lineages, referred to as ARMAN (archaeal Richmond Mine acidophilic nanoorganisms), from environmental samples and a biofilm filtrate. Genes of two lineages are among the smallest yet described, enabling a 10% higher coding density than found genomes of the same size, and there are noncontiguous genes. No biological function could be inferred for up to 45% of genes and no more than 63% of the predicted proteins could be assigned to a revised set of archaeal clusters of orthologous groups. Some core metabolic genes are more common in Crenarchaeota than Euryarchaeota, up to 21% of genes have the highest sequence identity to bacterial genes, and 12 belong to clusters of orthologous groups that were previously exclusive to bacteria. A small subset of 3D cryo-electron tomographic reconstructions clearly show penetration of the ARMAN cell wall and cytoplasmic membranes by protuberances extended from cells of the archaeal order Thermoplasmatales. Interspecies interactions, the presence of a unique internal tubular organelle [Comolli, et al. (2009) ISME J 3:159-167], and many genes previously only affiliated with Crenarchaea or Bacteria indicate extensive unique physiology in organisms that branched close to the time that Cren- and Euryarchaeotal lineages diverged.

Proteogenomic basis for ecological divergence of closely related bacteria in natural acidophilic microbial communities

Abstract: Bacterial species concepts are controversial. More widely accepted is the need to understand how differences in gene content and sequence lead to ecological divergence. To address this relationship in ecosystem context, we investigated links between genotype and ecology of two genotypic groups of Leptospirillum group II bacteria in comprehensively characterized, natural acidophilic biofilm communities. These groups share 99.7% 16S rRNA gene sequence identity and 95% average amino acid identity between their orthologs. One genotypic group predominates during early colonization, and the other group typically proliferates in later successional stages, forming distinct patches tens to hundreds of micrometers in diameter. Among early colonizing populations, we observed dominance of five genotypes that differed from each other by the extent of recombination with the late colonizing type. Our analyses suggest that the specific recombinant variant within the early colonizing group is selected for by environmental parameters such as temperature, consistent with recombination as a mechanism for ecological fine tuning. Evolutionary signatures, and strain-resolved expression patterns measured via mass spectrometry–based proteomics, indicate increased cobalamin biosynthesis, (de)methylation, and glycine cleavage in the late colonizer. This may suggest environmental changes within the biofilm during development, accompanied by redirection of compatible solutes from osmoprotectants toward metabolism. Across 27 communities, comparative proteogenomic analyses show that differential regulation of shared genes and expression of a small subset of the ∼15% of genes unique to each genotype are involved in niche partitioning. In summary, the results show how subtle genetic variations can lead to distinct ecological strategies.

Complex predicate formation

Abstract: Introduction The term ‘complex predicate’ has a wide usage, including, for example, serial verb constructions, light verb constructions, and particle + verb constructions, among others. An examination of the data provided by analysts in their discussions of complex predicates shows that monoclausality is the critical factor in determining whether a construction involves a complex predicate or not. Complex predicates are monoclausal structures involving two or more predicating morphemes. Butt (this volume) is explicit on this point. [T]he term complex predicate is used to designate a construction that involves two or more predicational elements (such as nouns, verbs, and adjectives) which predicate as a single element, i.e. their arguments map onto a monoclausal syntactic structure. We show that monoclausality as a criterion does not determine a unitary set of predicate structures. Rather, we show that there are two quite distinct ways of combining predicate information within monoclausal structures. We call one method ‘merger’ because the predicate information from the contributing constituents merges where they have common conceptual structure. This method produces predicate structures whose range classes with the range of predicate structures found in monomorphemic predicates. We propose that there are constraints on the conceptual structure of monomorphemic predicates which also apply to merger constructions. We discuss the constraints on monomorphemic predicates in Section 2.4. We call the other method ‘coindexation’ because relations among the contributing predicates are constrained only by a requirement that some of their arguments must be coindexed. This method produces multi-predicate structures whose range classes with multi-clausal structures.

Putting it All Together: Agreement, Incorporation, Coordination and External Possession in Wubuy (Australia)

Abstract: In this paper we examine the interaction of a number of grammatical phenomena in Wubuy, a polysynthetic language from northern Australia, and show how they can be given a comprehensive analysis within the framework of LFG. While each of these phenomena ? noun incorporation, verbal agreement, coordination and external possession ? has received various treatments within the LFG literature, no one study has addressed the compatibility of these analyses under interaction, despite the fact that they frequently co-occur in the world?s languages. We use data from Wubuy to showcase the effects of this interaction, and investigate the implications for LFG and for LFG analyses of polysynthetic languages more generally.

Indigenous language and social identity : papers in honour of Michael Walsh

Abstract: For almost 40 years, Michael Walsh has been working alongside Indigenous people: documenting language, music and other traditional knowledge, acting on behalf of claimants to land in the Northern Territory, and making crucial contributions to the revitalisation of Aboriginal languages in NSW. This volume, with contributions from his colleagues and students, celebrates his abiding interest in and commitment to Indigenous society with papers in two broad themes. 'Language, identity and country' addresses the often complex relations between Aboriginal social groups and countries, and linguistic identity. In 'Language, identity and social action' authors discuss the role that language plays in maintaining social identities in the realms of conversation, story-telling, music, language games, and in education. 'Language and Social Identity in Australian Indigenous Communities' will be of interest to students of linguistics, Indigenous studies, anthropology, and sociology.

A kinematic analysis of temporal differentiation of the four-way coronal stop contrast in Wubuy (Australia)

Abstract: Coronal stop contrast series are rare in the world’s languages, and are often reported to be articulatorily, perceptually, and phonologically fragile, in particular in an /iCi/ context. We present electromagnetic articulometry (EMA) data on the temporal differentiation of the four-way coronal stop series in the Australian Aboriginal language of Wubuy. The results show that the articulation of the stop series (at least for the laminal versus apical distinction) is temporally differentiated. Importantly, the EMA data also show that the reportedly ‘fragile’ alveolar-retroflex contrast is temporally distinct, even in the context of high-front vowel /i/. The latter finding suggests that the articulation of the Wubuy retroflex is not incompatible with /i/, as has previously been proposed, though it may indeed be more effortful to achieve than in other vowel contexts.