Ultra Deep Sequencing Reveals the Mutational Landscape of Classical Hodgkin Lymphoma

The malignant Hodgkin and Reed Sternberg (HRS) cells of classical Hodgkin lymphoma (cHL) are scarce in affected lymph nodes, creating a challenge to detect driver somatic mutations. As an alternative to cell purification techniques, we hypothesized that ultra-deep exome sequencing would allow genomic study of HRS cells, thereby streamlining analysis and avoiding technical pitfalls. To test this, 31 cHL tumor/normal pairs were exome sequenced to ~1000x median depth of coverage. An orthogonal error-corrected sequencing approach verified >95% of the discovered mutations. We identified mutations in genes novel to cHL including: CDH5 and PCDH7; novel mutations in IL4R, and a novel pattern of recurrent mutations in pathways regulating Hippo signaling. This study provides proof-of-principle that ultra-deep exome sequencing can be utilized to identify recurrent mutations in HRS cells, allowing for the analysis for clinically relevant genomic variants in large cohorts of cHL patients.

Recovery of Valuable Materials from the Waste Crystalline-Silicon Photovoltaic Cell and Ribbon

With the dramatic increase of photovoltaic (PV) module installation in solar energy-based industries, the methods for recovering waste solar generators should be emphasized as the backup of the PV market for environmental protection. Crystalline-silicon accounts for most of the worldwide PV market and it contains valuable materials such as high purity of silicon (Si), silver (Ag), copper (Cu), tin (Sn), and lead (Pb). This study can provide an efficient recycling process for valuable materials resourced from waste crystalline-silicon PV module, including Si in the PV cell, and Ag, Cu, Pb, Sn, in PV ribbon. As tempered glass and Ethylene Vinyl Acetate (EVA) resin were removed, the module was separated into two materials, PV ribbon and PV cell. For PV cell purification, Si with purity at 99.84% was recovered by removing impurities such as aluminum (Al) and Ag by two-step leaching and dissolving the impurities. For PV ribbon recovering, purified metal or metal oxide was obtained through the processes of leaching/polishing, extraction, and chemical precipitation. In the polishing process, 99.5% of copper wire was collected. The purities of final products are 99.7% for CuO, 99.47% for PbO, 99.68% for SnO2, and 98.85% for Ag respectively.

Estimating and Correcting for Off-Target Cellular Contamination in Brain Cell Type Specific RNA-Seq Data

Transcriptionally profiling minor cellular populations remains an ongoing challenge in molecular genomics. Single-cell RNA sequencing has provided valuable insights into a number of hypotheses, but practical and analytical challenges have limited its widespread adoption. A similar approach, which we term single-cell type RNA sequencing (sctRNA-seq), involves the enrichment and sequencing of a pool of cells, yielding cell type-level resolution transcriptomes. While this approach offers benefits in terms of mRNA sampling from targeted cell types, it is potentially affected by off-target contamination from surrounding cell types. Here, we leveraged single-cell sequencing datasets to apply a computational approach for estimating and controlling the amount of off-target cell type contamination in sctRNA-seq datasets. In datasets obtained using a number of technologies for cell purification, we found that most sctRNA-seq datasets tended to show some amount of off-target mRNA contamination from surrounding cells. However, using covariates for cellular contamination in downstream differential expression analyses increased the quality of our models for differential expression analysis in case/control comparisons and typically resulted in the discovery of more differentially expressed genes. In general, our method provides a flexible approach for detecting and controlling off-target cell type contamination in sctRNA-seq datasets.

Ten years of clinical observation of olfactory ensheathing cell transplantation in patients with spinal cord injury

Objective:To evaluate the long-term curative efficacy and safety of olfactory ensheathing cell (OEC) transplantation by 10 years of follow-up investigation.Methods:A follow-up observation was done on 13 patients with allograft olfactory bulb-derived OEC transplantation from September 2005 to September 2007 at the Second Affiliated Hospital of Xi’an Jiaotong University. After cell purification, amplification, and identification, a 2 × 107/mL cell suspension was prepared for transplantation. In the posterior horn of the spinal cord 0.5 cm distal and proximal to the spinal cord injury zone, 4 needle points were selected to avoid the blood vessels. The needle depth was 3 mm, and the injection volume per point was 10 μL. Postoperatively and at 1 week, 4 weeks, 12 weeks, 24 weeks, 1 year, 3 years, 5 years, and 10 years after the surgery, the patient’s American Spinal Injury Association (ASIA) score, adverse reactions, and other minor observations were assessed.Results:All the patients did not have serious complications. No gliomas or other new organisms formed during the 10-year observation period. Eight of 13 patients had improvement in sensory function, and 5 patients showed improvement in motor function. The ASIA acupuncture, light touch, and exercise scores improved significantly 1 year after the surgery, and this improvement continued until the 10-year follow-up period. Three of 13 patients had improvement in defecation and urination, and 1 patient had improved neuralgia after spinal cord injury.Conclusion:OEC transplantation is safe and effective in treating spinal cord injury. The observation period of OEC transplantation is 1 to 3 years.

Polycyclic Aromatic Hydrocarbon (PAHs) Analyses in Marine Tissues Using Accelerated Solvent Extraction (ASE) in Tandem with In-Cell Purification and GC‑MS

The aim of this research was the replacement of conventional sample extraction techniques for polycyclic aromatic hydrocarbons (PAH) in tissue samples for a reliable, fast and ecofriendly procedure. The method was developed using a pressurized solvent extraction method and assessing two different standard reference materials (fish and mussel) and freeze-dried and fortified sardine samples (Sardinella sp.). Five different extraction procedures were evaluated and the best performance comprised 1 g of lyophilized tissue, 5 g of deactivated (5%) silica, a dichloromethane:methanol (4:1 v/v) mixture, a temperature of 80 °C, three cycles, 10 min of static time and 90 s of purge time. The method selected following these tests was further validated through the analysis of nine replicates of the National Institute of Standard and Technology (NIST) reference material No. 2976, resulting in an effective recovery of 83 ± 14%. The means and uncertainties attained for each PAH were equivalent to those of the reference material, corroborating the reliability of the developed method. A shorter processing time, less use of solvents and reagents and lower extract manipulation produced an effective method aligned with green-chemistry guidelines.

A portable sperm cell purification instrument based on continuous flow acoustophoretic separation of sperm cells for on-site forensic sample pretreatment

Obtaining purified male sperm specimen from the original forensic sample mixtures is a critical procedure in identifying criminal suspect in the forensic analysis of sexual assult crimes. Differential extraction (DE)...

The Effect of Sonication on Plant Stomatal Movement

The primary goal of this study was to determine the effect of sonication on stomatal movement. A minor goal was to determine the best time interval at which sonication is the most effective at removing mesophyll cells and enriching guard cells. For this study, abaxial leaf peels of Arabidopsis thaliana were sonicated for 1, 3, 5, and 7-minute intervals at a set amplitude to analyze the removal of mesophyll cells. To juxtapose the leaves and to determine guard cell enrichment, microscopic images were taken prior to and after sonication. Furthermore, to establish that the stomata are alive, neutral red staining was used in conjunct with 40x magnification. It was hypothesized that sonication is an effective method for the removal of mesophyll cells and the enrichment of guard cells. The results of this study suggest that sonication is in fact an effective protocol for guard cell enrichment; however, it is not as effective for guard cell purification. This is due to the presence of mesophyll cells and epidermal layers present after sonication. Previous research dealing with sonication is very prevalent; however, research on sonication dealing with the removal of mesophyll cells in Arabidopsis thaliana is not widely studied. Thus, previous information to support this study could not be attained. Results from the first part of the experiment were then extended to determine how sonication affects stomatal movement. It was determined that in the experimental group, the average stomatal aperture decreased over a two-hour period.