Molecular principles underlying dual RNA specificity in the Drosophila SNF protein

The first RNA recognition motif of the Drosophila SNF protein is an example of an RNA binding protein with multi-specificity. It binds different RNA hairpin loops in spliceosomal U1 or U2 small nuclear RNAs, and only in the latter case requires the auxiliary U2A′ protein. Here we investigate its functions by crystal structures of SNF alone and bound to U1 stem-loop II, U2A′ or U2 stem-loop IV and U2A′, SNF dynamics from NMR spectroscopy, and structure-guided mutagenesis in binding studies. We find that different loop-closing base pairs and a nucleotide exchange at the tips of the loops contribute to differential SNF affinity for the RNAs. U2A′ immobilizes SNF and RNA residues to restore U2 stem-loop IV binding affinity, while U1 stem-loop II binding does not require such adjustments. Our findings show how U2A′ can modulate RNA specificity of SNF without changing SNF conformation or relying on direct RNA contacts

Intrinsic flexibility of snRNA hairpin loops facilitates protein binding

Stem–loop II of U1 snRNA and Stem–loop IV of U2 snRNA typically have 10 or 11 nucleotides in their loops. The fluorescent nucleobase 2-aminopurine was used as a substitute for the adenines in each loop to probe the local and global structures and dynamics of these unusually long loops. Using steady-state and time-resolved fluorescence, we find that, while the bases in the loops are stacked, they are able to undergo significant local motion on the picosecond/nanosecond timescale. In addition, the loops have a global conformational change at low temperatures that occurs on the microsecond timescale, as determined using laser T-jump experiments. Nucleobase and loop motions are present at temperatures far below the melting temperature of the hairpin stem, which may facilitate the conformational change required for specific protein binding to these RNA loops

There is No Free Lunch: Tradeoffs in the Utility of Learned Knowledge

With the recent introduction of learning in integrated systems, there is a need to measure the utility of learned knowledge for these more complex systems. A difficulty arrises when there are multiple, possibly conflicting, utility metrics to be measured. In this paper, we present schemes which trade off conflicting utility metrics in order to achieve some global performance objectives. In particular, we present a case study of a multi-strategy machine learning system, mutual theory refinement, which refines world models for an integrated reactive system, the Entropy Reduction Engine. We provide experimental results on the utility of learned knowledge in two conflicting metrics - improved accuracy and degraded efficiency. We then demonstrate two ways to trade off these metrics. In each, some learned knowledge is either approximated or dynamically 'forgotten' so as to improve efficiency while degrading accuracy only slightly

What Can Hydrography Between the New England Slope, Bermuda and Africa Tell us About the Strength of the AMOC Over the Last 90 years?

The Gulf Stream is the only pathway in the subtropical North Atlantic by which warm water flows poleward. This transport of warm water and return of cold water at depth is called the Atlantic Meridional Overturning Circulation (AMOC). The dynamic method is applied to hydrocasts collected since the 1930s to estimate upper-ocean transport (0–1,000 m) between the U.S. Continental Slope and Bermuda and separately to Africa with focus on the longest directly observable timescale. Calculating transport between the Slope and Bermuda eliminates the Gulf Stream\u27s northern and southern recirculation gyres, while calculations between the Slope and Africa remove all other recirculating geostrophic flow. The net Slope-Bermuda upper-ocean transport is estimated to be 41.1 ± 0.4 Sv, decreasing by 2.0 ± 0.8 Sv between 1930 and 2020. The AMOC contribution is 18.4 ± 0.6 Sv, decreasing by 0.4 ± 0.6 Sv between 1930 and 2020

Who should participate in clinical trials and who not? Can clinical trials be made more efficient and effective?

Clinical trials objectives Although it may seem self-evident, it is important when establishing a clinical trial that there is an important question to be answered. Once such a question has been posed and an appropriate design established to answer that question, all efforts should be made to enrol as many patients into the trial as expeditiously as possible. The design of the trial should support that aim. Eligibility criteria Eligibility criteria should not be too elaborate or complex. For example, in an adjuvant breast cancer trial, specific details of the exact handling of tumour margins, exact doses of radiation therapy or number of nodes dissected may not be particularly important in comparison with entering a wide variety of patients from the adjuvant setting. Broader entr

Adipose Tissue Distribution and Survival Among Women with Nonmetastatic Breast Cancer.

ObjectivePrevious studies of breast cancer survival have not considered specific depots of adipose tissue such as subcutaneous adipose tissue (SAT) and visceral adipose tissue (VAT).MethodsThis study assessed these relationships among 3,235 women with stage II and III breast cancer diagnosed between 2005 and 2013 at Kaiser Permanente Northern California and between 2000 and 2012 at Dana Farber Cancer Institute. SAT and VAT areas (in centimeters squared) were calculated from routine computed tomography scans within 6 (median: 1.2) months of diagnosis, covariates were collected from electronic health records, and vital status was assessed by death records. Hazard ratios (HRs) and 95% CIs were estimated using Cox regression.ResultsSAT and VAT ranged from 19.0 to 891 cm2 and from 0.484 to 454 cm2 , respectively. SAT was related to increased risk of death (127-cm2 increase; HR [95% CI]: 1.13 [1.02-1.26]), but no relationship was found with VAT (78.18-cm2 increase; HR [95% CI]: 1.02 [0.91-1.14]). An association with VAT was noted among women with stage II cancer (stage II: HR: 1.17 [95% CI: 0.99-1.39]; stage III: HR: 0.90 [95% CI: 0.76-1.07]; P interaction < 0.01). Joint increases in SAT and VAT were associated with mortality above either alone (simultaneous 1-SD increase: HR 1.19 [95% CI: 1.05-1.34]).ConclusionsSAT may be an underappreciated risk factor for breast cancer-related death

Alteration of the hypothalamic-pituitary-gonadal axis in estrogen- and androgen-treated adult male leopard frog, Rana pipiens

BACKGROUND: Gonadal steroids, in particular 5 alpha-dihydrotestosterone (DHT) and 17 beta-estradiol (E2), have been shown to feed back on the hypothalamic-pituitary-gonadal (HPG) axis of the ranid frog. However, questions still remain on how DHT and E2 impact two of the less-studied components of the ranid HPG axis, the hypothalamus and the gonad, and if the feedback effects are consistently negative. Thus, the goal of the study was to examine the effects of DHT and E2 upon the HPG axis of the gonadally-intact, sexually mature male leopard frogs, Rana pipiens. METHODS: R. pipiens were implanted with silastic capsules containing either cholesterol (Ch, a control), DHT, or E2 for 10 or 30 days. At each time point, steroid-induced changes in hypothalamic GnRH and pituitary LH concentrations, circulating luteinizing hormone (LH), and testicular histology were examined. RESULTS: Frogs implanted with DHT or E2 for 10 days did not show significant alterations in the HPG axis. In contrast, frogs implanted with hormones for 30 days had significantly lower circulating LH (for both DHT and E2), decreased pituitary LH concentration (for E2 only), and disrupted spermatogenesis (for both DHT and E2). The disruption of spermatogenesis was qualitatively similar between DHT and E2, although the effects of E2 were consistently more potent. In both DHT and E2-treated animals, a marked loss of all pre-meiotic germ cells was observed, although the loss of secondary spermatogonia appeared to be the primary cause of disrupted spermatogenesis. Unexpectedly, the presence of post-meiotic germ cells was either unaffected or enhanced by DHT or E2 treatment. CONCLUSIONS: Overall, these results showed that both DHT and E2 inhibited circulating LH and disrupted spermatogenesis progressively in a time-dependent manner, with the longer duration of treatment producing the more pronounced effects. Further, the feedback effects exerted by both steroid hormones upon the HPG axis were largely negative, although the possibility exists for a stimulatory effect upon the post-meiotic germ cells

Analyzing Pili Nut Value Chains in Sorsogon Province, Philippines

The importance of the pili nut (Canarium ovatum Engl.) industry cannot be discounted due to its immense domestic potential in Sorsogon Province, Philippines, where 62% out of the total volume of canarium nut production in the Bicol Region is concentrated. This paper examined the pili nut value chain network in the study area. Supplemented by secondary data sources, primary data gathering was conducted involving interviews with 15 pili farmers, 30 processors, and 20 traders located in Sorsogon City and 5 other pili-growing towns in Sorsogon Province. Analytical tools such as descriptive and net margin analyses were used. Results showed that farmers, processors, processor-wholesaler-retailers, processor-retailers, wholesaler-retailers, and retailers comprised the value chain. Four pili pulp and shelled pili chains where processors were not participants were identified while 12 dried kernel chains were mapped out. Selling dried kernel pili during the lean season gives farmers the highest value at PhP147.94 per kilogram rather than selling raw or shelled pili where returns are only one-fifth of this value. Traders refrain from buying dried kernel pili from farmers since they prefer buying pili with pulp and shelled pili so they can do the processing themselves. Chain problems include the lack of technical, financial, and information support; scattered location of pili farms; and low levels of product innovation. Recommendations offered include forming a cooperative or consolidating group to assemble all harvests, justify the purchase of depulping and other processing equipment, hasten production and processing technology transfer, and increase competitiveness