Zheng, C.-J. | Search bioRxiv

bioRxiv2023

The Natural Products Discovery Center: Release of the First 8490 Sequenced Strains for Exploring Actinobacteria Biosynthetic Diversity

Actinobacteria, the bacterial phylum most renowned for natural product discovery, has been established as a valuable source for drug discovery and biotechnology but is underrepresented within accessible genome and strain collections. Herein, we introduce the Natural Products Discovery Center (NPDC), featuring 122,449 strains assembled over eight decades, the genomes of the first 8490 NPDC strains (7142 Actinobacteria), and the online NPDC Portal making both strains and genomes publicly available. A comparative survey of RefSeq and NPDC Actinobacteria highlights the taxonomic and biosynthetic diversity within the NPDC collection, including three new genera, hundreds of new species, and [~]7000 new gene cluster families. Selected examples demonstrate how the NPDC Portals strain metadata, genomes, and biosynthetic gene clusters can be leveraged using genome mining approaches. Our findings underscore the ongoing significance of Actinobacteria in natural product discovery, and the NPDC serves as an unparalleled resource for both Actinobacteria strains and genomes.

microbiology↗

bioRxiv2020

Age and gender dependence of liver diffusion parameters and the evidence of intravoxel incoherent motion modelling of perfusion component is constrained by diffusion component.

ObjectivesTo establish reference values for middle aged subjects and investigate age and gender dependence of liver diffusion MRI parameters. MethodsThe IVIM type of liver diffusion scan was based on a single-shot spin-echo type echo-planar sequence using a 1.5-T magnet with 16 b-values. DDVD (diffusion-derived vessel density) was the signal difference between b=0 and b=2 s/mm2 images after removing visible vessels. IVIM analysis was performed with full-fitting and segmented-fitting, and with threshold b-value of 60 or 200 s/mm2, and fitting started from b=2 s/mm2. 32 men (age range: 25-71 years) and 26 men (age: 22-69 years) had DDVD and IVIM analysis respectively, while 36 women (age: 20-71 years) had DDVD and IVIM analysis. ResultsDDVD had an age-related reduction noted for women. IVIM results of full fitting had good agreement with segmented fitting with threshold b of 60 s/mm2 results, but less so with results of threshold b of 200 s/mm2. As age increases, female subjects Dslow measure had significant reduction, and PF and Dfast measure had significant increase. For the age group of 40-55 years, DDVD, Dslow, PF, and Dfast were 12.27{+/-}3.90, 1.072{+/-}0.067 (10-3mm2/s), 0.141{+/-}0.025, 61.0{+/-}14.0 (10-3mm2/s), and 13.4{+/-}3.6, 1.069{+/-}0.074 mm2/s, 0.119{+/-}0.014, 57.1{+/-}13.2 mm2/s, for men and women, respectively. ConclusionDDVD measure suggest that aging may be associated with reduction in liver perfusion. Lower Dslow measurement can lead to artificial higher PF and Dfast measurement, providing the evidence of IVIM modeling of perfusion component is constrained by diffusion component.

biophysics↗