Utility and Outcomes of the 2019 American College of Medical Genetics and Genomics-Clinical Genome Resource Guidelines for Interpretation of Copy Number Variants with Borderline Classifications at an Academic Clinical Diagnostic Laboratory.

In 2019, the American College of Medical Genetics and Genomics and the Clinical Genome Resource published updated technical standards for the interpretation and reporting of copy number variants (CNVs), introducing a semiquantitative classification system to improve standardization and consistency between laboratories. Evaluation of these guidelines' performance will inform laboratories about the impact of their implementation into clinical practice. A total of 145 difficult-to-classify CNVs, originally assessed by an academic molecular diagnostic laboratory, were re-interpreted/classified according to the American College of Medical Genetics and Genomics-Clinical Genome Resource guidelines. Classifications between interpretation systems were then compared. The concordance rate was 60.7%, and significantly more variants of uncertain significance were obtained when using the guidelines (n = 98) versus the laboratory's classification system (n = 49; P < 0.001). The concordance rate was presumably impacted by the intentionally unclear nature of the selected variants. The difference in variant of uncertain significance rate was largely due to laboratory-specific practices for variant interpretation and reporting and differences in utilization of general population data. Laboratory-specific policies and practices may need to be addressed for true standardization. Challenges to consistent guideline utilization are centered around the general lack of high-quality curated data available for CNV interpretations and the inherent subjectivity in the selection of evidence criteria and application of evidence points. Multiple aspects of the guidelines were highlighted to further improve classification standardization.

Total nitrogen is the main soil property associated with soil fungal community in karst rocky desertification regions in southwest China.

Karst rocky desertification (KRD) is a type of land deterioration, resulting in the degraded soil and a delicate ecosystem. Previous studies focused on the influence of KRD on the animals and plants, the impact of KRD on microorganisms, especially soil fungi remains to be discovered. This study reveals the change in the soil fungal community in response to KRD progression in southwest China. Illumina HiSeq was used to survey the soil fungal community. Results showed that the soil fungal community in the severe KRD (SKRD) was noticeably different from that in other KRD areas. Statistical analyses suggested that soil TN was the primary factor associated with the fungal community, followed by pH. Phylum Ascomycota was significantly abundant in non-degraded soils; whereas Basidiomycota predominated in SKRD. The ratio of Ascomycota/Basidiomycota significantly decreased along with KRD progression, which might be used as an indicator of KRD severity. Phylum Basidiomycota was sensitive to changes in all the soil properties but AP. Genus Sebacina might have the potential to promote vegetation and land restoration in KRD areas. This study fills a gap of knowledge on changes in soil fungal communities in accordance with KRD progression.

Development of a Cell-Based High-Throughput Screening Assay to Identify Porcine Host Defense Peptide-Inducing Compounds.

Novel alternatives to antibiotics are needed for the swine industry, given increasing restrictions on subtherapeutic use of antibiotics. Augmenting the synthesis of endogenous host defense peptides (HDPs) has emerged as a promising antibiotic-alternative approach to disease control and prevention. To facilitate the identification of HDP inducers for swine use, we developed a stable luciferase reporter cell line, IPEC-J2/PBD3-luc, through permanent integration of a luciferase reporter gene driven by a 1.1 kb porcine ß-defensin 3 (PBD3) gene promoter in porcine IPEC-J2 intestinal epithelial cells. Such a stable reporter cell line was employed in a high-throughput screening of 148 epigenetic compounds and 584 natural products, resulting in the identification of 41 unique hits with a minimum strictly standardized mean difference (SSMD) value of 3.0. Among them, 13 compounds were further confirmed to give at least a 5-fold increase in the luciferase activity in the stable reporter cell line, with 12 being histone deacetylase (HDAC) inhibitors. Eight compounds were subsequently observed to be comparable to sodium butyrate in inducing PBD3 mRNA expression in parental IPEC-J2 cells in the low micromolar range. Six HDAC inhibitors including suberoylanilide hydroxamine (SAHA), HC toxin, apicidin, panobinostat, SB939, and LAQ824 were additionally found to be highly effective HDP inducers in a porcine 3D4/31 macrophage cell line. Besides PBD3, other HDP genes such as PBD2 and cathelicidins (PG1-5) were concentration-dependently induced by those compounds in both IPEC-J2 and 3D4/31 cells. Furthermore, the antibacterial activities of 3D4/31 cells were augmented following 24 h exposure to HDAC inhibitors. In conclusion, a cell-based high-throughput screening assay was developed for the discovery of porcine HDP inducers, and newly identified HDP-inducing compounds may have potential to be developed as alternatives to antibiotics for applications in swine and possibly other animal species.

Soil pH Is the Primary Factor Correlating With Soil Microbiome in Karst Rocky Desertification Regions in the Wushan County, Chongqing, China.

Karst rocky desertification (KRD) is a process of land degradation, which causes desert-like landscapes, deconstruction of endemic biomass, and declined soil quality. The relationship of KRD progression with above-ground communities (e.g. vegetation and animal) is well-studied. Interaction of soil desertification with underground communities, such as soil microbiome, however, is vastly unknown. This study characterizes change in soil bacterial community in response to KRD progression. Soil bacterial communities were surveyed by deep sequencing of 16S amplicons. Eight soil properties, pH, soil organic matter (SOM), total and available nitrogen (TN and AN), total and available phosphorus (TP and AP), and total and available potassium (TK and AK), were measured to assess soil quality. We find that the overall soil quality decreases along with KRD progressive gradient. Soil bacterial community compositions are distinguishingly different in KRD stages. The richness and diversity in bacterial community do not significantly change with KRD progression although a slight increase in diversity was observed. A slight decrease in richness was seen in SKRD areas. Soil pH primarily correlates with bacterial community composition. We identified a core microbiome for KRD soils consisting of; Acidobacteria, Alpha-Proteobacteria, Planctomycetes, Beta-Proteobacteria, Actinobacteria, Firmicutes, Delta-Proteobacteria, Chloroflexi, Bacteroidetes, Nitrospirae, and Gemmatimonadetes in this study. Phylum Cyanobacteria is significantly abundant in non-degraded soils, suggesting that Cyanobacterial activities might be correlated to soil quality. Our results suggest that Proteobacteria are sensitive to changes in soil properties caused by the KRD progression. Alpha- and beta-Proteobacteria significantly predominated in SKRD compared to NKRD, suggesting that Proteobacteria, along with many others in the core microbiome (Acidobacteria, Actinobacteria, Firmicutes, and Nitrospirae), were active in nutrient limiting degraded soils. This study demonstrates the relationship of soil properties with bacterial community in KRD areas. Our results fill the gap of knowledge on change in soil bacterial community during KRD progression.