Impact of alternative initiation, splicing, and termination on the diversity of the mRNA transcripts encoded by the mouse transcriptome

We analyzed the FANTOM2 clone set of 60,770 RIKEN full-length mouse cDNA sequences and 44,122 public mRNA sequences. We developed a new computational procedure to identify and classify the forms of splice variation evident in this data set and organized the results into a publicly accessible database that can be used for future expression array construction, structural genomics, and analyses of the mechanism and regulation of alternative splicing. Statistical analysis shows that at least 41% and possibly as much as 60% of multiexon genes in mouse have multiple splice forms. Of the transcription units with multiple splice forms, 49% contain transcripts in which the apparent use of an alternative transcription start (stop) is accompanied by alternative splicing of the initial (terminal) exon. This implies that alternative transcription may frequently induce alternative splicing. The fact that 73% of all exons with splice variation fall within the annotated coding region indicates that most splice variation is likely to affect the protein form. Finally, we compared the set of constitutive (present in all transcripts) exons with the set of cryptic (present only in some transcripts) exons and found statistically significant differences in their length distributions, the nucleoticle distributions around their splice junctions, and the frequencies of occurrence of several short sequence motifs.

Accessing chain length dependent termination rate coefficients of methyl methacrylate (MMA) via the reversible addition fragmentation chain transfer (RAFT) process

The RAFT-CLD-T methodology is demonstrated to be not only applicable to 1-substituted monomers such as styrene and acrylates, but also to 1,1-disubstituted monomers such as MMA. The chain length of the terminating macromolecules is controlled by CPDB in MMA bulk free radical polymerization at 80 degrees C. The evolution of the chain length dependent termination rate coefficient, k(t)(i,i), was constructed in a step-wise fashion, since the MMA/CPDB system displays hybrid behavior (between conventional and living free radical polymerization) resulting in initial high molecular weight polymers formed at low RAFT agent concentrations. The obtained CLD of k(t) in MMA polymerizations is compatible with the composite model for chain length dependent termination. For the initial chain-length regime, up to a degree of polymerization of 100, k(t) decreases with alpha (in the expression k(t)(i,i) = k(t)(0) . i(-alpha)) being close to 0.65 at 80 degrees C. At chain lengths exceeding 100, the decrease is less pronounced (affording an alpha of 0.15 at 80 degrees C). However, the data are best represented by a continuously decreasing nonlinear functionality implying a chain length dependent alpha.

Photoreceptor projection and termination pattern in the lamina of gonodactyloid stomatopods (mantis shrimp)

The apposition compound eyes of gonodactyloid stomatopods are divided into a ventral and a dorsal hemisphere by six equatorial rows of enlarged ommatidia, the mid-band (MB). Whereas the hemispheres are specialized for spatial vision, the MB consists of four dorsal rows of ommatidia specialized for colour vision and two ventral rows specialized for polarization vision. The eight retinula cell axons (RCAs) from each ommatidium project retinotopically onto one corresponding lamina cartridge, so that the three retinal data streams (spatial, colour and polarization) remain anatomically separated. This study investigates whether the retinal specializations are reflected in differences in the RCA arrangement within the corresponding lamina cartridges. We have found that, in all three eye regions, the seven short visual fibres (svfs) formed by retinula cells 1-7 (R1-R7) terminate at two distinct lamina levels, geometrically separating the terminals of photoreceptors sensitive to either orthogonal e-vector directions or different wavelengths of light. This arrangement is required for the establishment of spectral and polarization opponency mechanisms. The long visual fibres (lvfs) of the eighth retinula cells (R8) pass through the lamina and project retinotopically to the distal medulla externa. Differences between the three eye regions exist in the packing of svf terminals and in the branching patterns of the lvfs within the lamina. We hypothesize that the R8 cells of MB rows 1-4 are incorporated into the colour vision system formed by R1-R7, whereas the R8 cells of MB rows 5 and 6 form a separate neural channel from R1 to R7 for polarization processing.

Increasing the efficacy of Judas goats by sterilisation and pregnancy termination

The use of Judas goats to locate remnant animals is a potentially powerful tool for enhancing goat-eradication efforts, which are especially important to island conservation. However, current Judas goat methodology falls short of its potential efficacy. Female Judas goats are often pregnant at the time of deployment or become impregnated in the field; pregnant females leave associated goats to give birth, causing downtime of Judas goat operations. Further, male Judas goats may inseminate remnant females. Sterilising Judas goats prior to deployment removes these inefficiencies. Here, we describe two methods (epididymectomy for males and tubal occlusion for females) that sterilise Judas goats while still maintaining sexual motivation and other behaviours associated with intact animals. These surgeries are straightforward, time efficient, and may be conducted in the field by staff with minimal training. Given the widespread and deleterious impacts of non-native herbivores to ecosystems and the importance of Judas operations in detecting animals at low densities, sterilisation and termination of pregnancy should be applied routinely in Judas goat (and possibly other species) programs to increase the efficacy of low-density control operations and eradication campaigns.

Integration of ice-core, marine and terrestrial records for the Australian Last Glacial Maximum and Termination: a contribution from the OZ INTIMATE group

The degree to which Southern Hemisphere climatic changes during the end of the last glacial period and early Holocene (30-8 ka) were influenced or initiated by events occurring in the high latitudes of the Northern Hemisphere is a complex issue. There is conflicting evidence for the degree of hemispheric 'teleconnection' and an unresolved debate as to the principle forcing mechanism(s). The available hypotheses are difficult to test robustly, however, because the few detailed palaeoclimatic records in the Southern Hemisphere are widely dispersed and lack duplication. Here we present climatic and environmental reconstructions from across Australia, a key region of the Southern Hemisphere because of the range of environments it covers and the potentially important role regional atmospheric and oceanic controls play in global climate change. We identify a general scheme of events for the end of the last glacial period and early Holocene but a detailed reconstruction proved problematic. Significant progress in climate quantification and geochronological control is now urgently required to robustly investigate change through this period. Copyright (c) 2006 John Wiley & Sons, Ltd.

Climatic variability in the southwest Pacific during the Last Termination (20-10 kyr BP)

The degree to which palaeoclimatic changes in the Southern Hemisphere co-varied with events in the high latitude Northern Hemisphere during the Last Termination is a contentious issue, with conflicting evidence for the degree of 'teleconnection' between different regions of the Southern Hemisphere. The available hypotheses are difficult to test robustly, however, because there are few detailed palaeoclimatic records in the Southern Hemisphere. Here we present climatic reconstructions from the southwestern Pacific, a key region in the Southern Hemisphere because of the potentially important role it plays in global climate change. The reconstructions for the period 20-10 kyr BP were obtained from five sites along a transect from southern New Zealand, through Australia to Indonesia, supported by 125 calibrated C-14 ages. Two periods of significant climatic change can be identified across the region at around 17 and 14.2 cal kyr BP, most probably associated with the onset of warming in the West Pacific Warm Pool and the collapse of Antarctic ice during Meltwater Pulse-1A, respectively. The severe geochronological constraints that inherently afflict age models based on radiocarbon dating and the lack of quantified climatic parameters make more detailed interpretations problematic, however. There is an urgent need to address the geochronological limitations, and to develop more precise and quantified estimates of the pronounced climate variations that clearly affected this region during the Last Termination. (c) 2005 Elsevier Ltd. All rights reserved.

Termination of real-time programs: Definitely, definitely not, or maybe

Real-time control programs are often used in contexts where (conceptually) they run forever. Repetitions within such programs (or their specifications) may either (i) be guaranteed to terminate, (ii) be guaranteed to never terminate (loop forever), or (iii) may possibly terminate. In dealing with real-time programs and their specifications, we need to be able to represent these possibilities, and define suitable refinement orderings. A refinement ordering based on Dijkstra's weakest precondition only copes with the first alternative. Weakest liberal preconditions allow one to constrain behaviour provided the program terminates, which copes with the third alternative to some extent. However, neither of these handles the case when a program does not terminate. To handle this case a refinement ordering based on relational semantics can be used. In this paper we explore these issues and the definition of loops for real-time programs as well as corresponding refinement laws.