Plasma cell-free DNA promise monitoring and tissue injury assessment of COVID-19.

Coronavirus 2019 (COVID-19) is a complex disease that affects billions of people worldwide. Currently, effective etiological treatment of COVID-19 is still lacking; COVID-19 also causes damages to various organs that affects therapeutics and mortality of the patients. Surveillance of the treatment responses and organ injury assessment of COVID-19 patients are of high clinical value. In this study, we investigated the characteristic fragmentation patterns and explored the potential in tissue injury assessment of plasma cell-free DNA in COVID-19 patients. Through recruitment of 37 COVID-19 patients, 32 controls and analysis of 208 blood samples upon diagnosis and during treatment, we report gross abnormalities in cfDNA of COVID-19 patients, including elevated GC content, altered molecule size and end motif patterns. More importantly, such cfDNA fragmentation characteristics reflect patient-specific physiological changes during treatment. Further analysis on cfDNA tissue-of-origin tracing reveals frequent tissue injuries in COVID-19 patients, which is supported by clinical diagnoses. Hence, our work demonstrates and extends the translational merit of cfDNA fragmentation pattern as valuable analyte for effective treatment monitoring, as well as tissue injury assessment in COVID-19.

Functional gene assessment of bread wheat: breeding implications in Ningxia Province.

BACKGROUND: The overall genetic distribution and divergence of cloned genes among bread wheat varieties that have occurred during the breeding process over the past few decades in Ningxia Province, China, are poorly understood. Here, we report the genetic diversities of 44 important genes related to grain yield, quality, adaptation and resistance in 121 Ningxia and 86 introduced wheat cultivars and advanced lines. RESULTS: The population structure indicated characteristics of genetic components of Ningxia wheat, including landraces of particular genetic resources, introduced varieties with rich genetic diversities and modern cultivars in different periods. Analysis of allele frequencies showed that the dwarfing alleles Rht-B1b at Rht-B1 and Rht-D1b at Rht-D1, 1BL/1RS translocation, Hap-1 at GW2-6B and Hap-H at Sus2-2B are very frequently present in modern Ningxia cultivars and in introduced varieties from other regions but absent in landraces. This indicates that the introduced wheat germplasm with numerous beneficial genes is vital for broadening the genetic diversity of Ningxia wheat varieties. Large population differentiation between modern cultivars and landraces has occurred in adaptation genes. Founder parents carry excellent allele combinations of important genes, with a higher number of favorable alleles than modern cultivars. Gene flow analysis showed that six founder parents have greatly contributed to breeding improvement in Ningxia Province, particularly Zhou 8425B, for yield-related genes. CONCLUSIONS: Varieties introduced from other regions with rich genetic diversity and landraces with well-adapted genetic resources have been applied to improve modern cultivars. Founder parents, particularly Zhou 8425B, for yield-related genes have contributed greatly to wheat breeding improvement in Ningxia Province. These findings will greatly benefit bread wheat breeding in Ningxia Province as well as other areas with similar ecological environments.

Effects of bacterial-feeding nematodes on soil microbial activity and the microbial community in oil-contaminated soil.

Rapid economic development has caused an increase in serious pollution problems due to the ever-increasing use of oil and its products, thus making oil pollution control an urgent task. Studies have shown that large amounts of bacterial-feeding nematodes are present in oil-contaminated soil; their function is as yet unclear. In this experiment, different densities of Caenorhabditis elegans (C. elegans) were inoculated into artificially simulated oil-contaminated soil to examine their effects on microbial activity and the microbial community in oil-contaminated soil. Six treatments were investigated: sterilized oil-contaminated soil as control 1 (FSP), nematode-free soil as control 2 (S), oil-contaminated soil (SP), oil-contaminated soil + 5, 10 or 20 individual C. elegans per gram of dry soil (i.e., SPN5, SPN10, SPN20). Results showed that oil pollution significantly increased the soil basal respiration. However, C. elegans weakened the soil basal respiration to different degrees and soil microbial respiration entropy essentially changed in line with the soil basal respiration. Oil pollution and C. elegans boosted catalase activity in contaminated soil by approximately 64.2-145.1%. Soil urease activity of SPN5, SPN10 and SPN20 was 88.5%, 126.7% and 109.0% stronger, respectively, than that of SP. The inoculation of C. elegans changed the microbial phospholipid fatty acid content in the oil-contaminated soil, including soil bacteria, fungi, actinomycetes, Gram-positive bacteria (G+) and Gram-negative bacteria (G-). Therefore, this research demonstrates that C. elegans can stimulate microbial reproduction in oil-contaminated soil, enhance related soil enzyme activities and regulate soil microbial community structure and diversity, thereby improving the contaminated soil environment and promoting oil degradation.

Assessment of tissue polarimetric properties using Stokes polarimetric imaging with circularly polarized illumination.

Tissue-depolarization and linear-retardance are the main polarization characteristics of interest for bulk tissue characterization, and are normally interpreted from Mueller polarimetry. Stokes polarimetry can be conducted using simpler instrumentation and in a shorter time. Here, we use Stokes polarimetric imaging with circularly polarized illumination to assess the circular-depolarization and linear-retardance properties of tissue. Results obtained were compared with Mueller polarimetry in transmission and reflection geometry, respectively. It is found that circular-depolarization obtained from these 2 methods is very similar in both geometries, and that linear-retardance is highly quantitatively similar for transmission geometry and qualitatively similar for reflection geometry. The majority of tissue circular-depolarization and linear-retardance image information (represented by local image contrast features) obtained from Mueller polarimetry is well preserved from Stokes polarimetry in both geometries. These findings can be referred to for further understanding tissue Stokes polarimetric data, and for further application of Stokes polarimetry under the circumstances where short acquisition time or low optical system complexity is a priority, such as polarimetric endoscopy and microscopy.

Study of optical clearing in polarization measurements by Monte Carlo simulations with anisotropic tissue-mimicking models.

We conducted Monte Carlo simulations based on anisotropic sclera-mimicking models to examine the polarization features in Mueller matrix polar decomposition (MMPD) parameters during the refractive index matching process, which is one of the major mechanisms of optical clearing. In a preliminary attempt, by changing the parameters of the models, wavelengths, and detection geometries, we demonstrate how the depolarization coefficient and retardance vary during the refractive index matching process and explain the polarization features using the average value and standard deviation of scattering numbers of the detected photons. We also study the depth-resolved polarization features during the gradual progression of the refractive index matching process. The results above indicate that the refractive index matching process increases the depth of polarization measurements and may lead to higher contrast between tissues of different anisotropies in deeper layers. MMPD-derived polarization parameters can characterize the refractive index matching process qualitatively.

Study on the validity of 3 × 3 Mueller matrix decomposition.

Using Monte Carlo simulations based on previously developed scattering models consisting of spherical and cylindrical scatterers imbedded in birefringent interstitial medium, we compare the polarization parameters extracted from the 3×3 and 4×4 Mueller matrix decomposition methods in forward and backward scattering directions. The results show that the parameters derived from the 3×3 Mueller matrix decomposition are usually not the same as those from the 4×4 Mueller matrix decomposition but display similar qualitative relations to changes in the microstructure of the sample, such as the density, size, and orientation distributions of the scatterers, and birefringence of the interstitial medium. The simulations are backed up by experiments when suitable samples are available.