Redesigned and chemically-modified hammerhead ribozymes with improved activity and serum stability

BACKGROUND: Hammerhead ribozymes are RNA-based molecules which bind and cleave other RNAs specifically. As such they have potential as laboratory reagents, diagnostics and therapeutics. Despite having been extensively studied for 15 years or so, their wide application is hampered by their instability in biological media, and by the poor translation of cleavage studies on short substrates to long RNA molecules. This work describes a systematic study aimed at addressing these two issues. RESULTS: A series of hammerhead ribozyme derivatives, varying in their hybridising arm length and size of helix II, were tested in vitro for cleavage of RNA derived from the carbamoyl phosphate synthetase II gene of Plasmodium falciparum. Against a 550-nt transcript the most efficient (t(1/2 )= 26 seconds) was a miniribozyme with helix II reduced to a single G-C base pair and with twelve nucleotides in each hybridising arm. Miniribozymes of this general design were targeted to three further sites, and they demonstrated exceptional cleavage activity. A series of chemically modified derivatives was prepared and examined for cleavage activity and stability in human serum. One derivative showed a 10(3)-fold increase in serum stability and a doubling in cleavage efficiency compared to the unmodified miniribozyme. A second was almost 10(4)-fold more stable and only 7-fold less active than the unmodified parent. CONCLUSION: Hammerhead ribozyme derivatives in which helix II is reduced to a single G-C base pair cleave long RNA substrates very efficiently in vitro. Using commonly available phosphoramidites and reagents, two patterns of nucleotide substitution in this derivative were identified which conferred both good cleavage activity against long RNA targets and good stability in human serum

Vocalization Induced CFos Expression in Marmoset Cortex

All non-human primates communicate with conspecifics using vocalizations, a system involving both the production and perception of species-specific vocal signals. Much of the work on the neural basis of primate vocal communication in cortex has focused on the sensory processing of vocalizations, while relatively little data are available for vocal production. Earlier physiological studies in squirrel monkeys had shed doubts on the involvement of primate cortex in vocal behaviors. The aim of the present study was to identify areas of common marmoset (Callithrix jacchus) cortex that are potentially involved in vocal communication. In this study, we quantified cFos expression in three areas of marmoset cortex – frontal, temporal (auditory), and medial temporal – under various vocal conditions. Specifically, we examined cFos expression in these cortical areas during the sensory, motor (vocal production), and sensory–motor components of vocal communication. Our results showed an increase in cFos expression in ventrolateral prefrontal cortex as well as the medial and lateral belt areas of auditory cortex in the vocal perception condition. In contrast, subjects in the vocal production condition resulted in increased cFos expression only in dorsal premotor cortex. During the sensory–motor condition (antiphonal calling), subjects exhibited cFos expression in each of the above areas, as well as increased expression in perirhinal cortex. Overall, these results suggest that various cortical areas outside primary auditory cortex are involved in primate vocal communication. These findings pave the way for further physiological studies of the neural basis of primate vocal communication

Stylasterid corals: a new paleotemperature archive

Stylasterids are a ubiquitous deep-sea coral taxon that build their skeletons from either calcite, aragonite, or both. Yet, robust geochemical proxy data from these corals are limited. In this study, 95 modern stylasterids, spanning a wide range of depths (63 to 2894 m) and ambient seawater temperatures (0 to 17 °C), were tested for their potential use as paleoceanographic archives. Stable oxygen and carbon isotopic composition (O and C) were measured from the main trunk of all specimens and five specimens were further sub-sampled to assess internal chemical variability. The isotope data show non-equilibrium precipitation from seawater for both O and C, with the growing tips of colonies yielding the isotopically lowest values. Overall, the calcitic corals showed lower isotope values for O and C than aragonitic specimens. Within the aragonite corals, we present a O:temperature calibration that exhibits a significant linear relationship with the equation Ocoral-seawater = −0.22(°C) + 3.33(±0.06) across a temperature range of 0 to 30 °C, using samples from this study and published data. This work highlights the potential application of stylasterid coral O data to reconstruct paleo seawater temperature

Who is our cohort: Recruitment, representativeness, baseline risk and retention in the "Watch Me Grow" study?

Background: The "Watch Me Grow" (WMG) study examines the current developmental surveillance system in South West Sydney. This paper describes the establishment of the study birth cohort, including the recruitment processes, representativeness, follow-up and participants' baseline risk for future developmental risk. Methods: Newborn infants and their parents were recruited from two public hospital postnatal wards and through child health nurses during the years 2011-2013. Data was obtained through a detailed participant questionnaire and linked with the participant's electronic medical record (EMR). Representativeness was determined by Chi-square analyses of the available clinical, psychosocial and sociodemographic EMR data, comparing the WMG participants to eligible non-participants. Reasons for non-participation were also elicited. Participant characteristics were examined in six, 12, and 18-month follow-ups. Results: The number of infants recruited totalled 2,025, with 50 % of those approached agreeing to participate. Reasons for parents not participating included: lack of interest, being too busy, having plans to relocate, language barriers, participation in other research projects, and privacy concerns. The WMG cohort was broadly representative of the culturally diverse and socially disadvantaged local population from which it was sampled. Of the original 2025 participants enrolled at birth, participants with PEDS outcome data available at follow-up were: 792 (39 %) at six months, 649 (32 %) at 12 months, and 565 (28 %) at 18 months. Participants with greater psychosocial risk were less likely to have follow-up outcome data. Almost 40 % of infants in the baseline cohort were exposed to at least two risk factors known to be associated with developmental risk. Conclusions: The WMG study birth cohort is a valuable resource for health services due to the inclusion of participants from vulnerable populations, despite there being challenges in being able to actively follow-up this populatio

Potential responses to climate change in organisms with complex life histories: evolution and plasticity in Pacific salmon

Salmon life histories are finely tuned to local environmental conditions, which are intimately linked to climate. We summarize the likely impacts of climate change on the physical environment of salmon in the Pacific Northwest and discuss the potential evolutionary consequences of these changes, with particular reference to Columbia River Basin spring/summer Chinook (Oncorhynchus tshawytscha) and sockeye (Oncorhynchus nerka) salmon. We discuss the possible evolutionary responses in migration and spawning date egg and juvenile growth and development rates, thermal tolerance, and disease resistance. We know little about ocean migration pathways, so cannot confidently suggest the potential changes in this life stage. Climate change might produce conflicting selection pressures in different life stages, which will interact with plastic (i.e. nongenetic) changes in various ways. To clarify these interactions, we present a conceptual model of how changing environmental conditions shift phenotypic optima and, through plastic responses, phenotype distributions, affecting the force of selection. Our predictions are tentative because we lack data on the strength of selection, heritability, and ecological and genetic linkages among many of the traits discussed here. Despite the challenges involved in experimental manipulation of species with complex life histories, such research is essential for full appreciation of the biological effects of climate change

Real world outcomes of biopsy-proven oncocytic neoplasm of the kidney managed by surveillance.

OBJECTIVES: To evaluate outcomes of patients diagnosed with oncocytic renal neoplasms on routine renal mass biopsy and to describe the natural history of these tumours when managed with surveillance as opposed to immediate intervention. To report disease-specific survival. PATIENTS AND METHODS: Patients were identified from a retrospective review of pathology databases from three tertiary referral centres that utilise renal mass biopsy in routine clinical practice. All patients with biopsy-proven oncocytic tumours were included and a retrospective review of online patient records was undertaken. RESULTS: There were 184 biopsy-proven oncocytic renal neoplasms identified in 172 patients. There were two biopsy complications (both pneumothorax, Clavien-Dindo Grade I). Of these lesions, 135 were reported as oncocytomas or oncocytic renal neoplasms that were not further classified and 37 were reported as chromophobe carcinoma (ChRCC). The median age at diagnosis was 70 (33-88). The average tumour diameter at diagnosis was 33 mm. One hundred seven tumours were initially managed with surveillance (including 13 ChRCC) with a minimum follow-up of 6 months and a median of 39 months (6-144) whereas 49 patients underwent immediate treatment. The mean growth rate across all oncocytic renal neoplasms managed by surveillance was 3 mm/year. There was no statistically significant difference in growth rates between oncocytic renal neoplasms and ChRCC. Thirteen patients with oncocytic renal neoplasms initially managed by surveillance moved on to an active management strategy during follow-up. The clinical indication given for a change from surveillance was tumour growth in 12 cases and patient choice in 1 case. Where definitive pathology was available, there was 85% concordance with the biopsy. There were no cases of development of metastatic disease or disease-related morbidity or mortality during the study. CONCLUSIONS: This multicentre retrospective cohort study supports the hypothesis that selected biopsy-proven oncocytic renal neoplasms can be safely managed with surveillance in the medium term. Routine renal mass biopsy may reduce surgery for benign or indolent renal tumours and the potential associated morbidity for these patients

Single nucleotide polymorphisms unravel hierarchical divergence and signatures of selection among Alaskan sockeye salmon (Oncorhynchus nerka) populations

<p>Abstract</p> <p>Background</p> <p>Disentangling the roles of geography and ecology driving population divergence and distinguishing adaptive from neutral evolution at the molecular level have been common goals among evolutionary and conservation biologists. Using single nucleotide polymorphism (SNP) multilocus genotypes for 31 sockeye salmon (<it>Oncorhynchus nerka</it>) populations from the Kvichak River, Alaska, we assessed the relative roles of geography (discrete boundaries or continuous distance) and ecology (spawning habitat and timing) driving genetic divergence in this species at varying spatial scales within the drainage. We also evaluated two outlier detection methods to characterize candidate SNPs responding to environmental selection, emphasizing which mechanism(s) may maintain the genetic variation of outlier loci.</p> <p>Results</p> <p>For the entire drainage, Mantel tests suggested a greater role of geographic distance on population divergence than differences in spawn timing when each variable was correlated with pairwise genetic distances. Clustering and hierarchical analyses of molecular variance indicated that the largest genetic differentiation occurred between populations from distinct lakes or subdrainages. Within one population-rich lake, however, Mantel tests suggested a greater role of spawn timing than geographic distance on population divergence when each variable was correlated with pairwise genetic distances. Variable spawn timing among populations was linked to specific spawning habitats as revealed by principal coordinate analyses. We additionally identified two outlier SNPs located in the major histocompatibility complex (MHC) class II that appeared robust to violations of demographic assumptions from an initial pool of eight candidates for selection.</p> <p>Conclusions</p> <p>First, our results suggest that geography and ecology have influenced genetic divergence between Alaskan sockeye salmon populations in a hierarchical manner depending on the spatial scale. Second, we found consistent evidence for diversifying selection in two loci located in the MHC class II by means of outlier detection methods; yet, alternative scenarios for the evolution of these loci were also evaluated. Both conclusions argue that historical contingency and contemporary adaptation have likely driven differentiation between Kvichak River sockeye salmon populations, as revealed by a suite of SNPs. Our findings highlight the need for conservation of complex population structure, because it provides resilience in the face of environmental change, both natural and anthropogenic.</p

Adaptation, extinction and global change

We discuss three interlinked issues: the natural pace of environmental change and adaptation, the likelihood that a population will adapt to a potentially lethal change, and adaptation to elevated CO2, the prime mover of global change