DNA and RNA oligomers are used in a myriad of diverse biological and biochemical experiments. These oligonucleotides are designed to have unique biophysical, chemical and hybridization properties. We have created an integrated set of bioinformatics tools that predict the properties of native and chemically modified nucleic acids and assist in their design. Researchers can select PCR primers, probes and antisense oligonucleotides, find the most suitable sequences for RNA interference, calculate stable secondary structures, and evaluate the potential for two sequences to interact. The latest, most accurate thermodynamic algorithms and models are implemented. This free software is available at http://www.idtdna.com/SciTools/SciTools.aspx.

This paper is organised as follows. §1 examines the phonological and phonetic aspects of syllable structure, vowel deletion, CL and stress in Piro, and identifies the problems to be solved. After specifying the theoretical assumptions in §2, I present a proposal to account for Piro's prosodic structure, segment deletion and CL (§3). §4 compares the proposal with several conceivable alternatives, and touches on issues regarding prosodic licensing and stray erasure. A brief conclusion is given in §5. Syllabic and morale structures in Piro 405 (2) a. CV te.no 'tall' ki.ni.ma 'bead bracelet' b. CCV slo.ta 'clam' tla.hwa 'toad' c. CCCV nkno.ya.te 'my turtle' ra.su.ka.mtna 'they ran' The distribution of three-consonant clusters is limited, however: they result only from morphological concatenations that involve monoconsonantal affixes (Lin 1987, 1997a): (3) a. n-knoyate->nkno.ya.te'my turtle' my-turtle b. hasuka + m + ta + kaka-»ha.su.ka.mtka.ka 'cause to run' (79) to flee-TRANSITORY-THEME CLOSURE-CAUSATIVE As noted in Lin (1987, 1993), one important aspect of Piro syllable structure is that no sonority constraints are placed on the combinations of consonants. The examples in (4) show that any two consonants can occur in either order. Word-initial geminate clusters are also allowed, as shown in (4g). All permissible consonant clusters occur in both word-initial and word-medial positions. (4) a. b. c. d. e. f. g. tpa mwenutu wyoptota ksu tmennu smota nnika curve 'cheap' 'we receive' 'tube' 'flaw' 'blunt point' 'I eat' pto wmahatya ywalitxa skota mtenotu msa wwuhene ... s group 'we lack' 'hip' ' lower abdomen' 'short' ' empty corn cob' 'our child' The only exceptions to such considerable freedom of consonant clustering are certain combinations of obstruents that are similar in place and/or manner of articulation : 4 (5) a.

The availability of genome sequences makes it possible to develop microarrays that can be used for profiling gene expression over developmental time, as organisms respond to environmental challenges, and for comparison between wild-type and mutant strains under various conditions. The desired characteristics of microarrays (intense signals, hybridization specificity and extensive coverage of the transcriptome) were not fully met by the previous Chlamydomonas reinhardtii microarray: probes derived from cDNA sequences (approximately 300 bp) were prone to some nonspecific cross-hybridization and coverage of the transcriptome was only approximately 20%. The near completion of the C. reinhardtii nuclear genome sequence and the availability of extensive cDNA information have made it feasible to improve upon these aspects. After developing a protocol for selecting a high-quality unigene set representing all known expressed sequences, oligonucleotides were designed and a microarray with approximately 10,000 unique array elements (approximately 70 bp) covering 87% of the known transcriptome was developed. This microarray will enable researchers to generate a global view of gene expression in C. reinhardtii. Furthermore, the detailed description of the protocol for selecting a unigene set and the design of oligonucleotides may be of interest for laboratories interested in developing microarrays for organisms whose genome sequences are not yet completed (but are nearing completion).

No abstract

Primary productivity in the nutrient-poor subtropical ocean gyres depends on new nitrogen inputs from nitrogen fixers that convert inert dinitrogen gas into bioavailable forms. Temperature and iron (Fe) availability constrain marine nitrogen fixation, and both are changing due to anthropogenic ocean warming. We examined the physiological responses of the globally important marine nitrogen fixer, Crocosphaera watsonii across its full thermal range as a function of iron availability. At the lower end of its thermal range, from 22 to 27°C, Crocosphaera growth, nitrogen fixation, and Nitrogen-specific Iron Use Efficiencies (N-IUEs, mol N fixed hour–1 mol Fe–1) increased with temperature. At an optimal growth temperature of 27°C, N-IUEs were 66% higher under iron-limited conditions than iron-replete conditions, indicating that low-iron availability increases metabolic efficiency. However, Crocosphaera growth and function decrease from 27 to 32°C, temperatures that are predicted for an increasing fraction of tropical oceans in the future. Altogether, this suggests that Crocosphaera are well adapted to iron-limited, warm waters, within prescribed limits. A model incorporating these results under the IPCC RCP 8.5 warming scenario predicts that Crocosphaera N-IUEs could increase by a net 47% by 2100, particularly in higher-latitude waters. These results contrast with published responses of another dominant nitrogen fixer (Trichodesmium), with predicted N-IUEs that increase most in low-latitude, tropical waters. These models project that differing responses of Crocosphaera and Trichodesmium N-IUEs to future warming of iron-limited oceans could enhance their current contributions to global marine nitrogen fixation with rates increasing by ∼91 and ∼22%, respectively, thereby shifting their relative importance to marine new production and also intensifying their regional divergence. Thus, interactive temperature and iron effects may profoundly transform existing paradigms of nitrogen biogeochemistry and primary productivity in open ocean regimes.