Project description:Riboswitches that couple binding of ligands to conformational changes offer sensors and control elements for RNA synthetic biology and medical biotechnology. However, design of these riboswitches has required expert intuition or software specialized to transcription or translation outputs; design has been particularly challenging for applications in which the riboswitch output cannot be amplified by other molecular machinery. We present a fully automated design method called RiboLogic for such "stand-alone" riboswitches and test it via high-throughput experiments on 2875 molecules using RNA-MaP (RNA on a massively parallel array) technology. These molecules consistently modulate their affinity to the MS2 bacteriophage coat protein upon binding of flavin mononucleotide, tryptophan, theophylline, and microRNA miR-208a, achieving activation ratios of up to 20 and significantly better performance than control designs. By encompassing a wide diversity of stand-alone switches and highly quantitative data, the resulting ribologic-solves experimental data set provides a rich resource for further improvement of riboswitch models and design methods.
Project description:Two-dimensional CuFeSe2 nanosheets have been successfully obtained via solution-phase synthesis using a sacrificial template method. The high purity was confirmed by X-ray diffraction and the two-dimensional morphology was validated by transmission electron microscopy. The intense absorption in the 400-1400 nm region has been the basis for the CuFeSe2 nanosheets' photothermal capabilities testing. The colloidal CuFeSe2 (CFS) nanosheets capped with S2- short ligands (CFS-S) exhibit excellent biocompatibility in cell culture studies and strong photothermal effects upon 808 nm laser irradiation. The nanosheets were further loaded with the cancer drug doxorubicin and exposed to laser irradiation, which accelerated the release of doxorubicin, achieving synergy in the therapeutic effect.
Project description:Bioinformatics skills have become essential for many research areas; however, the availability of qualified researchers is usually lower than the demand and training to increase the number of able bioinformaticians is an important task for the bioinformatics community. When conducting training or hands-on tutorials, the lack of control over the analysis tools and repositories often results in undesirable situations during training, as unavailable online tools or version conflicts may delay, complicate, or even prevent the successful completion of a training event. The eBioKit is a stand-alone educational platform that hosts numerous tools and databases for bioinformatics research and allows training to take place in a controlled environment. A key advantage of the eBioKit over other existing teaching solutions is that all the required software and databases are locally installed on the system, significantly reducing the dependence on the internet. Furthermore, the architecture of the eBioKit has demonstrated itself to be an excellent balance between portability and performance, not only making the eBioKit an exceptional educational tool but also providing small research groups with a platform to incorporate bioinformatics analysis in their research. As a result, the eBioKit has formed an integral part of training and research performed by a wide variety of universities and organizations such as the Pan African Bioinformatics Network (H3ABioNet) as part of the initiative Human Heredity and Health in Africa (H3Africa), the Southern Africa Network for Biosciences (SAnBio) initiative, the Biosciences eastern and central Africa (BecA) hub, and the International Glossina Genome Initiative.
Project description:H1299 cells (p53-/-) were transfected with plasmid constructs expressing p53 alone, p47 alone or both, and gene expression profile was probed
Project description:This study, a randomized controlled trial, evaluated the effectiveness of free-standing air filters and window air conditioners (ACs) in 126 low-income households of children with asthma. Households were randomized into a control group, a group receiving a free-standing HEPA filter placed in the child's sleeping area, and a group receiving the filter and a window-mounted AC. Indoor air quality (IAQ) was monitored for week-long periods over three to four seasons. High concentrations of particulate matter (PM) and carbon dioxide were frequently seen. When IAQ was monitored, filters reduced PM levels in the child's bedroom by an average of 50%. Filter use varied greatly among households and declined over time, for example, during weeks when pollutants were monitored, filter use was initially high, averaging 84±27%, but dropped to 63±33% in subsequent seasons. In months when households were not visited, use averaged only 34±30%. Filter effectiveness did not vary in homes with central or room ACs. The study shows that measurements over multiple seasons are needed to characterize air quality and filter performance. The effectiveness of interventions using free-standing air filters depends on occupant behavior, and strategies to ensure filter use should be an integral part of interventions.Environmental tobacco smoke (ETS) increased particulate matter (PM) levels by about 14 ?g/m3 and was often detected using ETS-specific tracers despite restrictions on smoking in the house as reported on questionnaires administered to caregivers. PM concentrations depended on season, filter usage, relative humidity, air exchange ratios, number of children, outdoor PM levels, sweeping/dusting, and presence of a central air conditioner (AC). Free-standing air filters can be an effective intervention that provides substantial reductions in PM concentrations if the filters are used. However, filter use was variable across the study population and declined over the study duration, and thus strategies are needed to encourage and maintain use of filters. The variability in filter use suggests that exposure misclassification is a potential problem in intervention studies using filters. The installation of a room AC in the bedroom, intended to limit air exchange ratios, along with an air filter, did not lower PM levels more than the filter alone.
Project description:The Clinical Genome Resource (ClinGen) Sequence Variant Interpretation Working Group set out to refine the American College of Medical Genetics and Genomics and the Association of Molecular Pathologists (ACMG/AMP) variant pathogenicity recommendations for stand-alone rule BA1 (a variant with minor allele frequency [MAF] > 0.05 is benign), by clarifying how it should be used and specifying a set of variants that should be exempted from this rule. We cross-referenced ClinVar and Exome Aggregation Consortium data to identify variants for which there was a plausible argument for pathogenicity and the variant exists in one or more population data sets at MAF > 0.05. We identified nine such variants that were present in these data sets that may not be benign. The ACMG/AMP criteria were applied to these variants that resulted in four pathogenic and five variants of uncertain significance. We have refined benign rule BA1 by clarifying terms used to describe its use, which databases we recommend using, and assumptions made about this rule. We also recognized an initial list of nine variants for which there was some evidence of pathogenicity even though the MAF was high for these variants. We specify processes whereby individuals can petition ClinGen for amendments to our variant-specific assertions and the criteria experts should use when setting a numerically lower threshold for BA1 for specific genes.
Project description:AAA+ disaggregases solubilize aggregated proteins and confer heat tolerance to cells. Their disaggregation activities crucially depend on partner proteins, which target the AAA+ disaggregases to protein aggregates while concurrently stimulating their ATPase activities. Here, we report on two potent ClpG disaggregase homologs acquired through horizontal gene transfer by the species Pseudomonas aeruginosa and subsequently abundant P. aeruginosa clone C. ClpG exhibits high, stand-alone disaggregation potential without involving any partner cooperation. Specific molecular features, including high basal ATPase activity, a unique aggregate binding domain, and almost exclusive expression in stationary phase distinguish ClpG from other AAA+ disaggregases. Consequently, ClpG largely contributes to heat tolerance of P. aeruginosa primarily in stationary phase and boosts heat resistance 100-fold when expressed in Escherichia coli This qualifies ClpG as a potential persistence and virulence factor in P. aeruginosa.
Project description:Live-cell microscopy is crucial for biomedical studies and clinical tests. The technique is, however, limited to few laboratories due to its high cost and bulky size of the necessary culture equipment. In this study, we propose a portable microfluidic-cell-culture system, which is merely 15 cm×11 cm×9 cm in dimension, powered by a conventional alkali battery and costs less than USD 20. For long-term cell culture, a fresh culture medium exposed to 5% CO2 is programmed to be delivered to the culture chamber at defined time intervals. The 37 °C culture temperature is maintained by timely electrifying the ITO glass slide underneath the culture chamber. Our results demonstrate that 3T3 fibroblasts, HepG2 cells, MB-231 cells and tumor spheroids can be well-maintained for more than 48 h on top of the microscope stage and show physical characters (e.g., morphology and mobility) and growth rate on par with the commercial stage-top incubator and the widely adopted CO2 incubator. The proposed portable cell culture device is, therefore, suitable for simple live-cell studies in the lab and cell experiments in the field when samples cannot be shipped.
Project description:Diffusion-weighted magnetic resonance imaging (DW MRI) is a fast unenhanced technique that shows promise as a stand-alone modality for cancer screening and characterization. Currently, DW MRI may have lower sensitivity than that of dynamic contrast-enhanced MRI as a standalone modality for breast cancer detection but superior to that of mammography, which may provide a useful alternative for supplemental screening. Standardized acquisition and interpretation of DW MRI can improve the image quality and reduce the variability of the results. Furthermore, high-resolution DW MRI, with advanced techniques and postprocessing, will facilitate better detection and characterization of subcentimeter cancers and reduce false-negatives and false-positives. Future results from ongoing prospective multicenter clinical trials using standardized and optimized protocols will facilitate the use of DW MRI as a stand-alone modality.