Design and evaluation of genome-wide libraries for RNA interference screens

RNA interference (RNAi) screens have enabled the systematic analysis of many biological processes in cultured cells and whole organisms. The success of such screens and the interpretation of the data depend on the stringent design of RNAi libraries. We describe and validate NEXT-RNAi, a software for the automated design and evaluation of RNAi sequences on a genome-wide scale. NEXT-RNAi is implemented as open-source software and is accessible at http://www.nextrnai.org/

High-resolution signal-in-space measurements of VHF omnidirectional ranges using UAS

In this paper, we describe measurement results of the signal-in-space of very high frequency (VHF) omnidirectional range (VOR) facilities. In aviation VOR are used to display the current course of the aircraft in the cockpit. To understand the influence of wind turbines (WT) on the signal integrity of terrestrial navigation and radar signals, the signal content and its changes, respectively, must be investigated. So far, only numerical simulations have been carried out on the frequency-modulation (FM) part of the Doppler-VOR (DVOR) signal to estimate the influence of WT on DVOR. Up to now, the amplitude-modulated (AM) part of the DVOR was not assessed at all. In 2016, we presented an unmanned aerial system (UAS) as a carrier for state-of-the-art radio-frequency (RF) measurement instrumentation (Schrader et al., 2016a, c; Bredemeyer et al., 2016), to measure and to record the true signal-in-space (both FM and AM signal) during the flight. The signal-in-space (which refers to time-resolved signal content and field strength, respectively) is measured and sampled without loss of information and, furthermore, synchronously stored with time stamp and with precise position in space, where the measurements were taken

Should NICE reconsider the 2016 UK guidelines on TB contact tracing? A cost-effectiveness analysis of contact investigations in London.

BACKGROUND: In January 2016, clinical TB guidance in the UK changed to no longer recommend screening contacts of non-pulmonary, non-laryngeal (ETB) index cases. However, no new evidence was cited for this change, and there is evidence that screening these contacts may be worthwhile. The objective of this study was to estimate the cost-effectiveness of screening contacts of adult ETB cases and adult pulmonary or laryngeal TB (PTB) cases in London, UK. METHODS: We carried out a cross-sectional analysis of data collected on TB index cases and contacts in the London TB register and an economic evaluation using a static model describing contact tracing outcomes. Incremental cost-effectiveness ratios (ICERs) were calculated using no screening as the baseline comparator. All adult TB cases (≥15 years old) in London from 2012 to 2015, and their contacts, were eligible (2465/5084 PTB and 2559/6090 ETB index cases were included). RESULTS: Assuming each contact with PTB infects one person/month, the ICER of screening contacts of ETB cases was £78 000/quality-adjusted life-years (QALY) (95% CI 39 000 to 140 000), and screening contacts of PTB cases was £30 000/QALY (95% CI 18 000 to 50 000). The ICER of screening contacts of ETB cases was £30 000/QALY if each contact with PTB infects 3.4 people/month. Limitations of this study include the use of self-reported symptomatic periods and lack of knowledge about onward transmission from PTB contacts. CONCLUSIONS: Screening contacts of ETB cases in London was almost certainly not cost-effective at any conventional willingness-to-pay threshold in England, supporting recent changes to National Institute for Health and Care Excellence national guidelines

Biomechanical comparison of menisci from different species and artificial constructs

Background: Loss of meniscal tissue is correlated with early osteoarthritis but few data exist regarding detailed biomechanical properties (e. g. viscoelastic behavior) of menisci in different species commonly used as animal models. The purpose of the current study was to biomechanically characterize bovine, ovine, and porcine menisci (each n = 6, midpart of the medial meniscus) and compare their properties to that of normal and degenerated human menisci (n = 6) and two commercially available artificial scaffolds (each n = 3). Methods: Samples were tested in a cyclic, minimally constraint compression-relaxation test with a universal testing machine allowing the characterization of the viscoelastic properties including stiffness, residual force and relative sample compression. T-tests were used to compare the biomechanical parameters of all samples. Significance level was set at p < 0.05. Results: Throughout cyclic testing stiffness, residual force and relative sample compression increased significantly (p < 0.05) in all tested meniscus samples. From the tested animal meniscus samples the ovine menisci showed the highest biomechanical similarity to human menisci in terms of stiffness (human: 8.54 N/mm +/- 1.87, cycle 1; ovine: 11.24 N/mm +/- 2.36, cycle 1, p = 0.0528), residual force (human: 2.99 N +/- 0.63, cycle 1 vs. ovine 3.24 N +/- 0.13, cycle 1, p = 0.364) and relative sample compression (human 19.92\% +/- 0.63, cycle 1 vs. 18.72\% +/- 1.84 in ovine samples at cycle 1, p = 0.162). The artificial constructs - as hypothesized- revealed statistically significant inferior biomechanical properties. Conclusions: For future research the use of ovine meniscus would be desirable showing the highest biomechanical similarities to human meniscus tissue. The significantly different biomechanical properties of the artificial scaffolds highlight the necessity of cellular ingrowth and formation of extracellular matrix to gain viscoelastic properties. As a consequence, a period of unloading (at least partial weight bearing) is necessary, until the remodeling process in the scaffold is sufficient to withstand forces during weight bearing

Growth factor release by vesicular phospholipid gels: in-vitro results and application for rotator cuff repair in a rat model

Background: Biological augmentation of rotator cuff repair is of growing interest to improve biomechanical properties and prevent re-tearing. But intraoperative single shot growth factor application appears not sufficient to provide healing support in the physiologic growth factor expression peaks. The purpose of this study was to establish a sustained release of granulocyte-colony stimulating factor (G-CSF) from injectable vesicular phospholipid gels (VPGs) in vitro and to examine biocompatibility and influence on histology and biomechanical behavior of G-CSF loaded VPGs in a chronic supraspinatus tear rat model. Methods: G-CSF loaded VPGs were produced by dual asymmetric centrifugation. In vitro the integrity, stability and release rate were analyzed. In vivo supraspinatus tendons of 60 rats were detached and after 3 weeks a transosseous refixation with G-CSF loaded VPGs augmentation (n = 15;control, placebo, 1 and 10 mu g G-CSF/d) was performed. 6 weeks postoperatively the healing site was analyzed histologically (n = 9;H&E by modified MOVIN score/Collagen I/III) and biomechanically (n = 6). Results: In vitro testing revealed stable proteins after centrifugation and a continuous G-CSF release of up to 4 weeks. Placebo VPGs showed histologically no negative side effects on the healing process. Histologically in vivo testing demonstrated significant advantages for G-CSF 1 mu g/d but not for G-CSF 10 mu g/d in Collagen III content (p = 0.035) and a higher Collagen I/III ratio compared to the other groups. Biomechanically G-CSF 1 mu g/d revealed a significant higher load to failure ratio (p = 0.020) compared to control but no significant differences in stiffness. Conclusions: By use of VPGs a continuous growth factor release could be obtained in vitro. The in vivo results demonstrate an improvement of immunohistology and biomechanical properties with a low dose G-CSF application via VPG. The VPG itself was well tolerated and had no negative influence on the healing behavior. Due to the favorable properties (highly adhesive, injectable, biocompatible) VPGs are a very interesting option for biologic augmentation. The study may serve as basis for further research in growth factor application models

Геоэкологическая характеристика и элементный состав листьев тополя территории г. Тюмень

Работа направлена на изучение элементного состава листьев тополя как биогеохимического индикатора состояния окружающей среды городов с выраженной специализацией. Исследование проведено на примере города Тюмень.The work is directed at studying the elemental composition of poplar leaves as a biogeochemical indicator of the state of the environment of cities with a pronounced specialization. The study was conducted on the example of the city of Tyumen

ETMR-05: Single-cell transcriptomics of ETMR reveals developmental cellular programs and tumor-pericyte communications in the microenvironment [Abstract]

BACKGROUND: Embryonal tumors with multilayered rosettes (ETMR) are pediatric brain tumors bearing a grim prognosis, despite intensive multimodal therapeutic approaches. Insights into cellular heterogeneity and cellular communication of tumor cells with cells of the tumor microenvironment (TME), by applying single-cell (sc) techniques, potentially identify mechanisms of therapy resistance and target-directed treatment approaches. MATERIAL AND METHODS: To explore ETMR cell diversity, we used single-cell RNA sequencing (scRNA-seq) in human (n=2) and murine ETMR (transgenic mode; n=4) samples, spatial transcriptomics, 2D and 3D cultures (including co-cultures with TME cells), multiplex immunohistochemistry and drug screens. RESULTS: ETMR microenvironment is composed of tumor and non-tumor cell types. The ETMR malignant compartment harbour cells representing distinct transcriptional metaprograms, (NSC-like, NProg-like and Neuroblast-like), mirroring embryonic neurogenic cell states and fuelled by neurogenic pathways (WNT, SHH, Hippo). The ETMR TME is composed of oligodendrocyte and neuronal progenitor cells, neuroblasts, microglia, and pericytes. Tumor-specific ligand-receptor interaction analysis showed enrichment of intercellular communication between NProg-like ETMR cells and pericytes (PC). Functional network analyses reveal ETMR-PC interactions related to stem-cell signalling and extracellular matrix (ECM) organization, involving factors of the WNT, BMP, and CxCl12 networks. Results from ETMR-PC co-culture and spatial transcriptomics pointed to a pivotal role of pericytes in keeping ETMR in a germinal neurogenic state, enriched in stem-cell signalling. Drug screening considering cellular heterogeneity and cellular communication suggested novel therapeutic approaches. CONCLUSION: ETMR demonstrated diversity in the microenvironment, with enrichment of cell-cell communications with pericytes, supporting stem-cell signalling and interfering in the organization of the tumor extracellular matrix. Targeting ETMR-PC interactions might bring new opportunities for target-directed therapy

Mondo-Mlx Mediates Organismal Sugar Sensing through the Gli-Similar Transcription Factor Sugarbabe

The ChREBP/Mondo-Mlx transcription factors are activated by sugars and are essential for sugar tolerance. They promote the conversion of sugars to lipids, but beyond this, their physiological roles are insufficiently understood. Here, we demonstrate that in an organism-wide setting in Drosophila, Mondo-Mlx controls the majority of sugar-regulated genes involved in nutrient digestion and transport as well as carbohydrate, amino acid, and lipid metabolism. Furthermore, human orthologs of the Mondo-Mlx targets display enrichment among gene variants associated with high circulating triglycerides. In addition to direct regulation of metabolic genes, Mondo-Mlx maintains metabolic homeostasis through downstream effectors, including the Activin ligand Dawdle and the Gli-similar transcription factor Sugarbabe. Sugarbabe controls a subset of Mondo-Mlx-dependent processes, including de novo lipogenesis and fatty acid desaturation. In sum, Mondo-Mlx is a master regulator of other sugar-responsive pathways essential for adaptation to a high-sugar diet.Peer reviewe

Dynamics of canopy development of Cunninghamia lanceolata mid-age plantation in relation to foliar nitrogen and soil quality influenced by stand density

It has been generally accepted that different silvicultural practices affect the forest canopy morphology and structure. During forest establishment, many natural sites were converted to coniferous plantations in southern China. Retention of the canopy during stand conversion may be desirable to promote ecological function and meet conservation objectives. We tested the impact of planting density, foliar nitrogen and soil chemical properties on the canopy development of Chinese fir (Cunninghamia lanceolata) mid-age monoculture stands. Low density (1450 trees hm−2 with planting spacing of 2.36 × 2.36 m), intermediate-density (2460 trees hm−2 with planting spacing of 1.83 × 1.83 m) and high density (3950 trees hm−2 with planting spacing of 1.44 × 1.44 m) stands were selected in Xinkou forest plantations in Sanming City, China. Canopy characteristics such as leaf area index (LAI), mean tilt angle of the leaf (MTA) and average canopy openness index (DIFN) were measured. Measurements were taken using LAI-2200 PCA. The results illustrated that stand density was the primal factor responsible in canopy structuring while soil chemical properties seem to play a secondary role for canopy dynamics. LAI increased from 3.974 m2 m-2 to 5.072 m2 m-2 and MTA increases from 34.8° to 48.7° as the stand density increased while the DIFN decreased from 0.1542 to 0.0902 with the increasing stand density but it was no significantly different in intermediate and high-density stands. Additionally, LAI and MTA were positively correlated to foliar nitrogen while the DIFN was negatively correlated. In general, soil available nitrogen, available phosphorus and soil pH were not significant to canopy parameters. The results presented provide guiding principles about the canopy dynamics distribution in varying stand densities from LICOR measurements in mid-age Chinese fir monoculture. Furthermore, this provides a base to study canopy dynamics at mature stage forests because of more senescence activities.This research was financially supported by the National Natural Science Foundation of China (31870614 and 30970451), the Forestry Peak Discipline Project of Fujian Agriculture and Forestry University, China (71201800716) and Postdoctoral research funding of Central South University of Forestry and Technology (70702-45200003)