THERPA: A small molecule database related to prion protein regulation and prion diseases progression

<p>Prion diseases are fatal neurodegenerative disorders that affect humans and animals. Although various small molecules have been evaluated for application in the treatment of prion diseases, none have been shown to be efficacious. Expanding our knowledge of these molecules is important for understanding of the complex mechanisms of prion diseases. To improve access to the scattered information on small molecules related to prion diseases, we built a database of therapeutic molecules associated with prion diseases (THERPA, therpa.pythonanywhere.com). THERPA includes 119 small molecules and their 283 relationships with prion diseases. THERPA is an interactive visual database and useful for improving search efficiency which can help researchers identify intrinsic small molecules that can be used for developing therapeutics for prion diseases.</p

Cancer-Microenvironment-Sensitive Activatable Quantum Dot Probe in the Second Near-Infrared Window

Recent technological advances have expanded fluorescence (FL) imaging into the second near-infrared region (NIR-II; wavelength = 1000–1700 nm), providing high spatial resolution through deep tissues. However, bright and compact fluorophores are rare in this region, and sophisticated control over NIR-II probes has not been fully achieved yet. Herein, we report an enzyme-activatable NIR-II probe that exhibits FL upon matrix metalloprotease activity in tumor microenvironment. Bright and stable PbS/CdS/ZnS core/shell/shell quantum dots (QDs) were synthesized as a model NIR-II fluorophore, and activatable modulators were attached to exploit photoexcited electron transfer (PET) quenching. The quasi type-II QD band alignment allowed rapid and effective FL modulations with the compact surface ligand modulator that contains methylene blue PET quencher. The modulator was optimized to afford full enzyme accessibility and high activation signal surge upon the enzyme activity. Using a colon cancer mouse model, the probe demonstrated selective FL activation at tumor sites with 3-fold signal enhancement in 10 min. Optical phantom experiments confirmed the advantages of the NIR-II probe over conventional dyes in the first near-infrared region

Additional file 3: Table S3. of Whole genome scan reveals the genetic signature of African Ankole cattle breed and potential for higher quality beef

Summary of genes common for both XP-EHH and XP-CLR test statistics. (XLS 45 kb

Additional file 6: Table S5. of Whole genome scan reveals the genetic signature of African Ankole cattle breed and potential for higher quality beef

Names and descriptions of major candidate meat quality related genes. All gene names and descriptions are based on RefSeq. (DOCX 24 kb

Additional file 5: Figure S1. of Whole genome scan reveals the genetic signature of African Ankole cattle breed and potential for higher quality beef

Tajima’s D and FST plot of positively selected gene regions in Sanga and indicus cattle populations. The Tajima’s D plot for each gene region (upper plot for each gene) is the Tajima’s D value within 50 kb window plotted for both populations. The smaller (negative) Tajima’s D value in Sanga population shows that the gene region considered is under positive selection. The FST plot (lower plot for each gene) is the FST values within 50 kb windows separated by 5 kb steps. (DOCX 300 kb

Additional file 4: Table S4. of Whole genome scan reveals the genetic signature of African Ankole cattle breed and potential for higher quality beef

Gene Ontology Biological Process terms obtained from DAVID gene ontology analysis using all XP-EHH and XP-CLR gene lists. (XLS 47 kb