Clinical implications of different specimen types for nucleic acid testing in two cases of COVID-19

The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid test is currently the gold standard for diagnosing coronavirus disease 2019 (COVID-19). This disease requires high-quality viral nucleic acid tests, and selecting the type of specimen from patients, who are at different disease stages, to use in the nucleic acid test is challenging. This article reports in detail the diagnosis and treatment process for two patients with confirmed COVID-19 and analyzes the results of the SARS-CoV-2 nucleic acid tests that were used for different types of specimens (sputum from deep cough, nasopharyngeal swab, and feces). The nucleic acid testing results of sputum from deep cough showed the best performance for positive detection. Our findings provide a reference for selecting the most suitable specimen for the clinical diagnosis of COVID-19 and improving the positive detection rate.

Olivine-norite rock detected by the lunar rover Yutu-2 likely crystallized from the SPA-impact melt pool

Chang'E-4 landed in the South Pole-Aitken (SPA) basin, providing a unique chance to probe the composition of the lunar interior. Its landing site is located on ejecta strips in Von Kármán crater that possibly originate from the neighboring Finsen crater. A surface rock and the lunar regolith at 10 sites along the rover Yutu-2 track were measured by the onboard Visible and Near-Infrared Imaging Spectrometer in the first three lunar days of mission operations. In situ spectra of the regolith have peak band positions at 1 and 2 μm, similar to the spectral data of Finsen ejecta from the Moon Mineralogy Mapper, which confirms that the regolith's composition of the landing area is mostly similar to that of Finsen ejecta. The rock spectrum shows similar band peak positions, but stronger absorptions, suggesting relatively fresh exposure. The rock may consist of 38.1 ± 5.4% low-Ca pyroxene, 13.9 ± 5.1% olivine and 48.0 ± 3.1% plagioclase, referred to as olivine-norite. The plagioclase-abundant and olivine-poor modal composition of the rock is inconsistent with the origin of the mantle, but representative of the lunar lower crust. Alternatively, the rock crystallized from the impact-derived melt pool formed by the SPA-impact event via mixing the lunar crust and mantle materials. This scenario is consistent with fast-cooling thermal conditions of a shallow melt pool, indicated by the fine to medium-sized texture (<3 mm) of the rock and the SPA-impact melting model [Icarus 2012; 220: 730-43].

Downregulation of nuclear protein-1 induces cell cycle arrest in G0/G1 phase in glioma cells in vivo and in vitro via P27

Nuclear protein-1 (NUPR1), also named as p8 or Com1, has been since found overexpressed in several human malignant tumor cells, such as glioma. NUPR1 also regulates cell cycle progression, however, the role of NUPR1 in regulating glioma cell cycle remains poorly understood. Knockdown efficiency of U87 and U251 cells infected with the lentiviral vector was detected by quantitative real-time PCR and western blot in vitro and in vivo. Flow cytometry and western blot were used to explore a mechanism by which NUPR1 modulates cell cycle in U87 and U251 cells. Immunohistochemistry was applied to detect expression levels of P27, CDK2, and cyclin E in human glioma tissues with NUPR1 positive expression and tumorigenesis in nude mice. We confirmed that the downregulation of NUPR1 arrested the cell cycle in the G0/G1 phase in U87 and U251 cells in vitro. Furthermore, the expression level of P27 was increased, and CDK2 and cyclin E were decreased upon silencing NUPR1 expression in vitro and in vivo. In conclusion, the knockdown of NUPR1 induces cell cycle arrest in the G0/G1 phase in glioma cells via P27.

Protecting quantum entanglement from leakage and qubit errors via repetitive parity measurements

Protecting quantum information from errors is essential for large-scale quantum computation. Quantum error correction (QEC) encodes information in entangled states of many qubits and performs parity measurements to identify errors without destroying the encoded information. However, traditional QEC cannot handle leakage from the qubit computational space. Leakage affects leading experimental platforms, based on trapped ions and superconducting circuits, which use effective qubits within many-level physical systems. We investigate how two-transmon entangled states evolve under repeated parity measurements and demonstrate the use of hidden Markov models to detect leakage using only the record of parity measurement outcomes required for QEC. We show the stabilization of Bell states over up to 26 parity measurements by mitigating leakage using postselection and correcting qubit errors using Pauli-frame transformations. Our leakage identification method is computationally efficient and thus compatible with real-time leakage tracking and correction in larger quantum processors.

Anomalous Nematic States in High Half-Filled Landau Levels

It is well established that the ground states of a two-dimensional electron gas with half-filled high (N≥2) Landau levels are compressible charge-ordered states, known as quantum Hall stripe (QHS) phases. The generic features of QHSs are a maximum (minimum) in a longitudinal resistance R_{xx} (R_{yy}) and a nonquantized Hall resistance R_{H}. Here, we report on emergent minima (maxima) in R_{xx} (R_{yy}) and plateaulike features in R_{H} in half-filled N≥3 Landau levels. Remarkably, these unexpected features develop at temperatures considerably lower than the onset temperature of QHSs, suggestive of a new ground state.

Potential Mechanisms for Marbling Content Differences in M. Longissimus Dorsi From Wagyu And Brahman Cattle

ObjectivesIntramuscular fat (marbling) affects consumer perceptions of meat quality. Recent studies indicated that intramuscular adipocytes are derived from fibroadipogenic progenitors (FAPs), a type of bipotent mesenchymal progenitor cells in extracellular matrix of muscle fiber. Platelet-derived growth factor receptor α (PDGFRa) is a marker in identifying FAPs. The amount of PDGFRa positive cells refers to the abundance of FAPs, a key factor determining the intramuscular adipogenic efficiency of the animal. In addition, it has been shown that both satellite cells and skeletal muscle fibers regulate the activity of FAPs. In this study, we aimed to identify some underlying mechanisms for the differences in intramuscular fat accumulation between Wagyu, a high marbling breed, and Brahman, a low marbling breed, through a comparison study.Materials and MethodsFive cattle of each breed approaching mature body composition (Wagyu born January to May 2017; Brahman two 2-yr-old and three 3-yr-old, born April 2017 and 2015) were selected for this study. Biopsy samples of M. Longissimus muscle (LM) were taken after local anesthesia between the 12th and 13th ribs. Fresh samples were frozen in isopentane chilled by liquid nitrogen immediately after trimming fat and connective tissue. Other samples were fixed for 4 h in ice-cold 4% paraformaldehyde, soaked overnight in 30% sucrose solution, and then processed in Optimal Cutting Temperature embedding medium. Frozen samples were stored at –80°C before cryosectioning (5 mm) at –25°C for immunochemical staining. Unfixed muscle tissue sections were only used for muscle fiber determinations by rinsing with 1X Tris Buffer Saline (TBS) 3 times, 5 min each, before blocking in 10% goat serum and 1% bovine serum albumin, followed by overnight incubation with primary antibodies at 4°C. Subsequent secondary antibody staining at room temperature for 1 h. TBS/T (0.3% Triton) was used for membrane permeabilization to identify satellite cells, FAPs, and basement membrane. Mounting media containing 4,6-diamidino-2-phenylindole (DAPI) was used for nucleus staining. Primary antibodies against PDGFRα, paired box 7 (PAX7), laminin, and different isoforms of skeletal muscle myosins were used to identify FAPs, satellite cells, basement membrane, and different types of muscle fiber, respectively. All the sections were visualized under a Nikon inflorescence microscope, and images were analyzed by Image J software to identify different muscle fiber types and positive signals of PDGFRα and PAX7. Minimum diameter of each muscle fiber type was the average of 30 randomly selected fibers per section. Data were analyzed with R-studio using ‘t.test ()’ function with the critical value being equal to 0.05.ResultsWagyu muscle demonstrated a greater (P = 0.01) number of FAPs compared with Brahman muscle. A trend toward a higher (P = 0.06) abundance of satellite cells in Wagyu muscle than in Brahman muscles was also identified. No differences were found in muscle fiber diameter or muscle fiber type composition between these two breeds of cattle.ConclusionThe greater number of FAP cells observed in the LM of Wagyu cattle than in Brahman cattle suggests that the higher marbling content of Wagyu meat is at least partially attributed to the more abundant adipogenic progenitor cells, which increases the capacity and efficiency of intramuscular adipogenesis in Wagyu cattle.

The Efficacy of Laser Zona Thinning on the Outcomes of Vitrified Human Embryo Transfers is Related to Fertilization Method and Not Vitrification Per Se

BACKGROUND

Embryo vitrification induces zona hardening, which can further influence the pregnancy outcome after vitrified human embryo transfer. However, the factors in fertilization or cryopreservation that contribute to zona hardening and influence the efficacy of laser zona thinning (LZT) is not well studied.

OBJECTIVE

To investigate whether fertilization methods and vitrification affect the efficacy of LZT treatment.

MATERIALS AND METHODS

The present study is a retrospective analysis of embryo transfers. The process involves two fertilization methods before embryo vitrification. LZT is used to deal with zona hardening. The pregnancy outcomes of 1274 embryo transfer cycles were reviewed statistically.

RESULTS

LZT treatment on vitrified embryos fertilized with intracytoplasmic sperm injection (ICSI) resulted in a significantly lower pregnancy rate and live birth rate compared to that by in vitro fertilization (IVF) (43.0% vs 54.3%, P=0.023; 34.4% vs 45.7%, P=0.021). LZT treatment on vitrified embryos fertilized with ICSI had a negative impact on pregnancy rate and live birth rate.

CONCLUSION

The efficacy of LZT treatment is related to the fertilization method rather than vitrification. LZT treatment for zona hardening of the vitrified embryos fertilized with ICSI leads to a lower pregnancy rate and live birth rate.

Adaptive regulation of detoxification enzymes in Helicoverpa armigera to different host plants

Cotton plants produce gossypol as a major secondary metabolite to resist insect herbivores and pathogens. Helicoverpa armigera may employ multigene families of detoxification enzymes to deal with this metabolite. So far, the strength of the transcriptional response to gossypol detoxification in the cotton bollworms remains poorly understood. Here, we investigated the genomewide transcriptional changes that occur in cotton bollworm larvae after one generation feeding on various host plants (cotton, corn, soybean and chili) or an artificial diet. Six genes potentially involved in detoxification of xenobiotics were highly upregulated in bollworms fed on cotton, and the expression of five of these differed significantly in insects that fed on gossypol diet compared with the artificial diet. When these six genes were downregulated using RNA interference, downregulation only of CYP4L11, CYP6AB9 and CCE001b led to reduced growth of bollworm larvae feeding on gossypol diets. These data suggest that the three genes are involved in response of H. armigera to gossypol of cotton. Our results proved that H. armigera may have a broad mechanism for gossypol detoxification.

RP11-284F21.9 promotes oral squamous cell carcinoma development via the miR-383-5p/MAL2 axis

BACKGROUND

Increasing evidence suggests that dysregulated long non-coding RNAs (lncRNAs) are involved in tumorigenesis and progression. RP11-284F21.9, one of the temporally expressed S-phase lncRNAs in cancer cells, was recently identified by nascent RNA capture sequencing.

METHODS

Cal-27, Tca8113, SCC-9, HB56, and oral squamous cell carcinoma (OSCC) tissues were used in the experiment. RNA extraction, qRT-PCR, plasmid construction, cell proliferation, EdU labeling, Transwell migration, luciferase reporter, and western blotting were used to investigate the exact role and function of RP11-284F21.9 in cancer.

RESULTS

RP11-284F21.9 was upregulated in human OSCC samples and cell lines. RP11-284F21.9 depletion suppressed the proliferation, migration, and invasion of OSCC cell lines. There was interaction between RP11-284F21.9, miR-383-5p, and MAL2. Increased MAL2 and decreased miR-383-5p expression were also detected in OSCC tissues and cell lines. In addition, RP11-284F21.9 knockdown could reduce MAL2 expression, while miR-383-5p inhibitors abolished this repressive effect. RP11-284F21.9 acted as a competing endogenous RNA (ceRNA) of miR-383-5p, leading to MAL2 upregulation, and subsequently promoted OSCC progression.

CONCLUSION

RP11-284F21.9/miR-383-5p represents a novel and potential therapeutic target for the treatment of OSCC.

High prevalence of norovirus GII.P16/GII.2 and chicken anemia virus in two acute gastroenteritis outbreaks in Huzhou, China

Acute gastroenteritis (AGE) is one of the most frequently occuring illnesses in children and adults worldwide. In February 2017, two AGE outbreaks occurred in two adjacent schools in Huzhou city, Zhenjiang province of China. We detected high percentages of recombinant norovirus GII.P16/GII.2 in one school and chicken anemia virus (CAV) in another school using next generation sequencing (NGS) and specific PCR. The results highlight the importance of continuous surveillance of GII.P16/GII.2, and suggest the need of further studies on whether CAV causes AGE. Keywords: acute gastroenteritis; norovirus; chicken anemia virus; Huzhou; School.

Abstract 2292: Bile cell-free DNA as a powerful liquid biopsy of the somatic variants in biliary tract cancer

Purpose: Biliary tract cancers (BTCs) are less common, but rapidly lethal tumors. Despite recent improvements in multimodal therapy, the 5-year survival rate is less than 10% in patients with advanced or metastatic BTC. BTC patients lack personalized treatment options, partly because tissue samplings are often inadequate for molecular characterization. Thus, this study examined the use of bile cell-free DNA (cfDNA), which is released by tumor and normal cells, as a potential liquid biopsy able to provide genomic information for the whole tumor.

Materials and Methods: Ten BTC patients, four with gallbladder carcinomas and six with cholangiocarcinomas, were enrolled in this study August 2017 to March 2018. To investigate the use of bile cfDNA as a liquid biopsy in BTC patients, targeted deep sequencing, with a panel of 150 tumor-related genes, was used to analyze paired bile cfDNA and tumor DNA for mutational variants individually and then compared. The sensitivites and specificities of detecting mutations including SNV/Indel and copy number variation (CNV) in bile cfDNA were analyzed.

Results: This study is the first to show that bile cfDNA is predominantly comprised of long DNA fragments, which is not the case in plasma cfDNA. Herein, paired bile cfDNA and tumors from ten BTC patients were examined using targeted deep sequencing. The mutational profiles of bile cfDNA showed that of the SNV/Indel mutations, the highest variation was seen in TP53, followed by KRAS, NOTCH1, NOTCH2 and KMT2A. Among the CNV mutations, low recurrent amplified genes, such as CCNE1, ERBB2, CDKN1B, ZNF217, and CDK6, were identified; with CDKN2A shown to have a deep deletion. Among these genes, NOTCH1, NOTCH2, ERBB2 and CDK6 are of interest as potential drug targets. When comparing bile cfDNA and tumor SNV/Indel detection results using targeted deep sequencing, a high sensitivity (94.7%) and specificity (99.9%) were obtained. Additionally, the sensitivity of detecting a copy number variation (CNV) was 75.0%, with a specificity of 98.9%. When comparing two bile extraction methods, including percutaneous transhepatic cholangial drainage and operation, no significant difference in SNV/Indel or CNV detection sensitivity was noted. Moreover, when examining the tumor stage and incidence site, AJCC stage II and the distal bile duct both had significantly decreased CNV detection sensitivities.

Conclusions: This study shows that long DNA fragments are prevalent in bile cfDNA samples and targeted deep sequencing can reliably detect mutational variants within bile cfDNA obtained from BTC patients. This is the first time that a mutational landscape, including SNVs, Indels and CNVs, has been obtained for bile cfDNA from BTC patients. These preliminary results maybe shed light on bile cfDNA as a promising liquid biopsy for BTC patients.

Citation Format: Ningjia Shen, Dadong Zhang, Lei Yin, Yinghe Qiu, Jian Liu, Wenlong Yu, Xiaohui Fu, Bin Zhu, Xiaoya Xu, Anqi Duan, Zishuo Chen, Xiang Wang, Xinkai Cao, Teng Zhao, Zisong Zhou, Lianghe Yu, Hao Qin, Zheng Fang, Jing-Yu Li, Yuanjin Liu, Lei Xiong, Bo Yuan, Fugen Li, Yongjie Zhang. Bile cell-free DNA as a powerful liquid biopsy of the somatic variants in biliary tract cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2292.