Functional analysis of yeast snoRNA and snRNA 3' end formation mediated by uncoupling of cleavage and polyadenylation

Many nuclear and nucleolar small RNAs are accumulated as nonpolyadenylated species and require 3′-end processing for maturation. Here, we show that several genes coding for box C/D and H/ACA snoRNAs and for the U5 and U2 snRNAs contain sequences in their 3′ portions which direct cleavage of primary transcripts without being polyadenylated. Genetic analysis of yeasts with mutations in different components of the pre-mRNA cleavage and polyadenylation machinery suggests that this mechanism of 3"-end formation requires cleavage factor IA (CF IA) but not cleavage and polyadenylation factor activity. However, in vitro results indicate that other factors participate in the reaction besides CF IA. Sequence analysis of snoRNA genes indicated that they contain conserved motifs in their 3" noncoding regions, and mutational studies demonstrated their essential role in 3"-end formation. We propose a model in which CF IA functions in cleavage and polyadenylation of pre-mRNAs and, in combination with a different set of factors, in 3"-end formation of nonpolyadenylated polymerase II transcripts.

Resistance and resilience: Can the abrupt end of extreme drought reverse avifaunal collapse?

Aim: Climate change is expected to increase the frequency and intensity of extreme climatic events, such as severe droughts and intense rainfall periods. We explored how the avifauna of a highly modified region responded to a 13-year drought (the 'Big Dry'), followed by a two-year period of substantially higher than average rainfall (the 'Big Wet'). Location: Temperate woodlands in north central Victoria, Australia. Methods: We used two spatially extensive, long-term survey programmes, each of which was repeated three times: early and late in the Big Dry, and in the Big Wet. We compared species-specific changes in reporting rates between periods in both programmes to explore the resistance (the ability to persist during drought) and resilience (extent of recovery post-drought) of species to climate extremes. Results: There was a substantial decline in the reporting rates of 42-62% (depending on programme) of species between surveys conducted early and late in the Big Dry. In the Big Wet, there was some recovery, with 21-29% of species increasing substantially. However, more than half of species did not recover and 14-27% of species continued to decline in reporting rate compared with early on in the Big Dry. Species' responses were not strongly related to ecological traits. Species resistance to the drought was inversely related to resilience in the Big Wet for 20-35% of the species, while 76-78% of species with low resistance showed an overall decline across the study period. Conclusions: As declines occurred largely irrespective of ecological traits, this suggests a widespread mechanism is responsible. Species that declined the most during the Big Dry did not necessarily show the greatest recoveries. In already much modified regions, climate extremes such as extended drought will induce on-going changes in the biota. © 2014 John Wiley & Sons Ltd.

Sedimentology and ichnology of two lower Triassic sections in South China: implications for the biotic recovery following the end-Permian mass extinction

Biotic recovery following the end-Permian mass extinction was investigated using trace fossil and facies analysis of two Lower–Middle Triassic sections in South China. The Susong section (Lower Yangtze Sedimentary Province) comprises a range of carbonate and mudstone facies that record overall shallowing from offshore to intertidal settings. The Tianshengqiao section (Upper Yangtze Sedimentary Province) consists of mixed carbonate and siliciclastic facies deposited in shallow marine to offshore settings. Griesbachian to Dienerian ichnological records in both sections are characterized by low ichnodiversity, low ichnofabric indices (1–2) and low bedding plane bioturbation indices (1–2). Higher ichnofabric indices (3 and 4), corresponding to a dense population of diminutive ichnotaxon, in the Tianshengqiao section suggest opportunistic infaunal biotic activity during the earliest Triassic. Ichnological data from the Susong section show an increase in ichnodiversity during the late Smithian with 11 ichnogenera identified and increased ichnofabric indices of 4–5 and bedding plane bioturbation indices of 3–5. Although complex traces such as Rhizocorallium are present in Spathian-aged strata in this section, low ichnodiversity and ichnofabric indices and diminutive Planolites suggest a decline in recovery. In the Tianshengqiao section, ichnofabric indices are moderate to high (3–5) although only six ichnogenera are present and Planolites burrows are consistently small in Smithian and Spathian strata. Complex traces, such as large Rhizocorallium and Thalassinoides, and large Planolites, did not appear until the Anisian. Ichnological results from both sections record the response of organisms to unfavourable environmental conditions although the Susong section shows earlier recovery during the Smithian prior to latest Smithian–Spathian decline. This decline may have resulted from a resurgence of euxinic to anoxic marine environment in various regions of South China. Ichnological data from the Tianshengqiao section indicate protracted recovery throughout the Early Triassic as previously found elsewhere in South China. Comparison of the South China trace fossil records with global ichnological data show a diachronous pattern of recovery of trace makers and highlights the heterogeneous development of oxic facies on the marked variation in recovery rate.

Proliferation of MISS-related microbial mats following the end-Permian mass extinction in the northern Paleo-Tethys: evidence from southern Qilianshan region, western China

As a consequence of the end-Permian mass extinction, microbes proliferated in the post-extinction shallow marine ecosystems, in which they grew as various microbially induced sedimentary structures (MISSs) in siliciclastic settings. This paper reports, for the first time, the discovery of abundant MISSs from the lowest Triassic sandstones of shallow-water margin origin in the Zhihema sections of the southern Qilianshan region, West China. The sandstones are characterized by well-developed cross-beddings and ripple marks, and a Claraia-dominated bivalve assemblage of middle-late Griesbachian age. These sedimentary structures, together with the bivalves, suggest a high-energy peritidal zone of a shoreface setting in a clastic shallow sea environment. Seven types of MISSs are recognized and described here: pictograph-like sand cracks/crack-fills, polygonal sand crack-fills, erosional remnants, multidirectional linear grooves, sinuous crack-fills, fusiform sand cracks/crack-fills, and leveled ripple marks. Most of the newly found MISSs are morphologically comparable with their ancient and modern counterparts. Detailed optical microscope and scanning electron microscope (SEM) analyses reveal that thin clayey laminae and filamentous mica grains are aligned parallel to bedding plane, and that the matrix-supported quartz grains, overall, are oriented; both of which are interpreted to indicate biogenic origin. The biogenic origin of these MISSs is reinforced by the presence of copious putative nanoglobules and filamentous biofilm-like organic objects in the interspaces of clay minerals in laminated layers. These nanometer-scale objects are interpreted as bacterial bodies or remains that have been replaced with inorganic minerals upon fossilization. The presence of MISSs on the northern margins of Paleo-Tethys indicates that the post-extinction microbial mats had expanded their distributions from low-latitude to moderate-high latitude regions. Moreover, unlike some previously reported microbial mats that contain very rare body and trace fossils, the southern Qilianshan MISSs were found in association with abundant vertical burrows and bivalves, suggesting that the MISS-forming microbial mats may have served as oases for trace-making organisms and opportunistic bivalves to flourish in shallow-marine habitats immediately after the end-Permian mass extinction.