One-Shot Single-Cell Proteome and Metabolome Analysis Strategy for the Same Single Cell.

Characterizing the profiles of proteome and metabolome at the single-cell level is of great significance in single-cell multiomic studies. Herein, we proposed a novel strategy called one-shot single-cell proteome and metabolome analysis (scPMA) to acquire the proteome and metabolome information in a single-cell individual in one injection of LC-MS/MS analysis. Based on the scPMA strategy, a total workflow was developed to achieve the single-cell capture, nanoliter-scale sample pretreatment, one-shot LC injection and separation of the enzyme-digested peptides and metabolites, and dual-zone MS/MS detection for proteome and metabolome profiling. Benefiting from the scPMA strategy, we realized dual-omic analysis of single tumor cells, including A549, HeLa, and HepG2 cells with 816, 578, and 293 protein groups and 72, 91, and 148 metabolites quantified on average. A single-cell perspective experiment for investigating the doxorubicin-induced antitumor effects in both the proteome and metabolome aspects was also performed.

Pick-up single-cell proteomic analysis for quantifying up to 3000 proteins in a Mammalian cell.

The shotgun proteomic analysis is currently the most promising single-cell protein sequencing technology, however its identification level of ~1000 proteins per cell is still insufficient for practical applications. Here, we develop a pick-up single-cell proteomic analysis (PiSPA) workflow to achieve a deep identification capable of quantifying up to 3000 protein groups in a mammalian cell using the label-free quantitative method. The PiSPA workflow is specially established for single-cell samples mainly based on a nanoliter-scale microfluidic liquid handling robot, capable of achieving single-cell capture, pretreatment and injection under the pick-up operation strategy. Using this customized workflow with remarkable improvement in protein identification, 2449-3500, 2278-3257 and 1621-2904 protein groups are quantified in single A549 cells (n = 37), HeLa cells (n = 44) and U2OS cells (n = 27) under the DIA (MBR) mode, respectively. Benefiting from the flexible cell picking-up ability, we study HeLa cell migration at the single cell proteome level, demonstrating the potential in practical biological research from single-cell insight.

Simultaneous deep transcriptome and proteome profiling in a single mouse oocyte.

Although single-cell multi-omics technologies are undergoing rapid development, simultaneous transcriptome and proteome analysis of a single-cell individual still faces great challenges. Here, we developed a single-cell simultaneous transcriptome and proteome (scSTAP) analysis platform based on microfluidics, high-throughput sequencing, and mass spectrometry technology to achieve deep and joint quantitative analysis of transcriptome and proteome at the single-cell level, providing an important resource for understanding the relationship between transcription and translation in cells. This platform was applied to analyze single mouse oocytes at different meiotic maturation stages, reaching an average quantification depth of 19,948 genes and 2,663 protein groups in single mouse oocytes. In particular, we analyzed the correlation of individual RNA and protein pairs, as well as the meiosis regulatory network with unprecedented depth, and identified 30 transcript-protein pairs as specific oocyte maturational signatures, which could be productive for exploring transcriptional and translational regulatory features during oocyte meiosis.

Aflatoxin B1 triggers apoptosis in rabbit hepatocytes via mediating oxidative stress and switching on the mitochondrial apoptosis pathway.

Aflatoxin B1 (AFB1) is considered the most toxic carcinogenic compound, and exposure to AFB1 is highly associated with hepatocellular carcinoma. The aim of this study was to investigate the effects of different doses of AFB1 on growth performance and the liver of rabbits, as well as explore its underlying mechanisms. A total of eighty 30-day-old meat rabbits were randomly divided into four treatments. The control group was fed a pollution-free diet, while the AFL, AFM, and AFH groups were fed contaminated diets containing 13 µg/kg, 19 µg/kg, and 25 µg/kg of AFB1, respectively. The results showed that AFB1 had detrimental effects on the production performance of rabbits, resulting in decreased weight gain. Additionally, AFB1 exposure was associated with increased activity of Aspartate aminotransferase (AST) and Alanine aminotransferase (ALT), as well as decreased levels of total protein (TP) and albumin (ALB) in the serum. AFB1 induced the production of reactive oxygen species (ROS) and malondialdehyde (MDA) while inhibiting the activity of glutathione (GSH), superoxide dismutase (SOD), and catalase (CAT) activity in liver tissues. AFB1 decreased the mRNA transcription and protein expression of nuclear factor-erythroid 2-related factor 2 (Nrf2), heme oxygenase-1 (HO-1), and NAD(P)H dehydrogenase quinone-1 (NQO-1). AFB1 not only decreased the contents of cytochrome P4501A2 (CYP1A2), cytochrome P4502A6 (CYP2A6) and cytochrome P4503A4 (CYP3A4) but also increased the content of AFB1-DNA adducts in the liver. Furthermore, AFB1 enhanced the expression of cytochrome c (cyt-c), caspase-9, caspase-3, and Bcl-2-associated X protein (Bax), while inhibiting the expression of B-cell lymphoma 2 (Bcl-2). Therefore, we demonstrated that AFB1 triggered apoptosis in rabbit hepatocytes via mediating oxidative stress and switching on the mitochondrial apoptosis pathway, and decreased rabbit performance.

Chromosomal microarray analysis vs. karyotyping for fetal ventriculomegaly: a meta-analysis.

BACKGROUND: Chromosomal abnormalities are important causes of ventriculomegaly (VM). In mild and isolated cases of fetal VM, obstetricians rarely give clear indications for pregnancy termination. We aimed to calculate the incidence of chromosomal abnormalities and incremental yield of chromosomal microarray analysis (CMA) in VM, providing more information on genetic counseling and prognostic evaluation for fetuses with VM. METHODS: The Chinese language databases Wanfang Data, China National Knowledge Infrastructure, and China Biomedical Literature Database (from January 1, 1991 to April 29, 2020) and English language databases PubMed, Embase, and Cochrane Library (from January 1, 1945 to April 29, 2020) were systematically searched for articles on fetal VM. Diagnostic criteria were based on ultrasonographic or magnetic resonance imaging (MRI) assessment of lateral ventricular atrium width: ≥10 to <15 mm for mild VM, and ≥15 mm for severe VM. Isolated VM was defined by the absence of structural abnormalities other than VM detected by ultrasonography or MRI. R software was used for the meta-analysis to determine the incidence of chromosomal abnormalities and incremental yield of CMA in VM, and the combined rate and 95% confidence interval (CI) were calculated. RESULTS: Twenty-three articles involving 1635 patients were included. The incidence of chromosomal abnormalities in VM was 9% (95% CI: 5%-12%) and incremental yield of CMA in VM was 11% (95% CI: 7%-16%). The incidences of chromosomal abnormalities in mild, severe, isolated, and non-isolated VM were 9% (95% CI: 4%-16%), 5% (95% CI: 1%-11%), 3% (95% CI: 1%-6%), and 13% (95% CI: 4%-25%), respectively. CONCLUSIONS: Applying CMA in VM improved the detection rate of abnormalities. When VM is confirmed by ultrasound or MRI, obstetricians should recommend fetal karyotype analysis to exclude chromosomal abnormalities. Moreover, CMA should be recommended preferentially in pregnant women with fetal VM who are undergoing invasive prenatal diagnosis. CMA cannot completely replace chromosome karyotype analysis.

Petrel Probe: An Integrated In Situ Sampling and Injection Interface for Fast, High-Efficiency Liquid Chromatography-Mass Spectrometry Analysis.

Herein, we describe an in situ analysis probe, Petrel probe, highly integrating multiple functions of in situ sampling, in situ sample injection, high-performance liquid chromatography (HPLC) separation, and mass spectrometry (MS) electrospray. The Petrel probe was fabricated based on a single capillary, which consists of a micrometer-sized hole for sampling, a packed column for LC separation, and a tapered tip for MS electrospray. The design of the Petrel probe was optimized to obtain higher structural strength, and a polytetrafluoroethylene (PTFE) chip was used for sealing the probe-sampling hole to meet the high-pressure (∼30 MPa) requirement of LC manifold. On the basis of the Petrel probe, we developed a novel valveless LC injection method, that is, the probe pressing microamount in situ (PPMI) injection method, which performs sample injection by pressing the probe-sampling hole on the PTFE chip, using the mobile phase to dissolve the sample dry spot in the sampling area on the chip, and injecting it into the LC column under high-pressure conditions for separation and subsequent MS analysis. The LC-MS system with the PPMI injection method exhibits rapid injection and separation speed, as well as minimum injection dead volume. It can yield a high separation efficiency comparable to those of conventional HPLC systems. The present system was optimized using standard peptide samples, and four peptides were separated within 11 min in a probe with an effective column length of 5 cm, achieving the highest theoretical plate number up to ∼5,500,000/m. The system was also applied in the separation of cytochrome C digest to demonstrate its separation ability for complex samples, and 21 peptides were detected in 8 min with an amino-acid coverage of 83%.

Arthrobacter crusticola sp. nov., Isolated from Biological Soil Crusts in the Mu Us Sandy Land, China.

Mu Us Sandy Land in China is a very fragile ecological environment due to serious desertification. While attempting to gain insights into the biodiversity of biological soil crusts of Mu Us Sandy Land, a novel bacterial strain, SLN-3T, was isolated. It was phylogenetically placed into the genus Arthrobacter within the family Micrococcaceae based on its 16S rRNA gene sequence. The most closely related species were Arthrobacter ruber MDB1-42T (98.6%) and Arthrobacter agilis DSM 20550T (98.3%). Cells of the novel species were Gram-stain-positive, aerobic, and non-endospore-forming. The values of average nucleotide identity and the digital DNA-DNA hybridization between SLN-3T and MDB1-42T were 84.9% and 21.3%, respectively. The draft genome size of strain SLN-3T was 3.67 Mb, and its genomic G+C content was 68.1%. The predominant cellular fatty acids were anteiso-C15:0 and C17:0 anteiso. Glucose, galactose, and ribose were the whole-cell sugars. The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, glycolipid, and phospholipid. The peptidoglycan contained lysine, glutamic acid, and alanine. The predominant menaquinone was MK-9(H2). Based on the data from the chemotaxonomic, phylogenetic, and phenotypic evidence, a novel species named Arthrobacter crusticola sp. nov is proposed, whose type strain is SLN-3T (= ACCC 61595T = JCM 33723T).

LC-Swan Probe: An Integrated In Situ Sampling Interface for Liquid Chromatography Separation and Mass Spectrometry Analysis.

In situ sampling mass spectrometry (MS) systems can achieve rapid analysis of samples, while most of them do not have the pretreatment capability of chromatographic separation. This Article describes the design, fabrication, and application of a swan-shaped in situ sampling MS probe with liquid chromatography (LC) separation capacity. The LC-Swan probe was fabricated based on a single capillary with a micrometer-sized hole at its U-shaped bottom for sampling, a monolithic column for separation, and a tapered tip for electrospray. Four functions including in situ sampling, sample injection, chromatographic separation, and MS electrospray were integrated in the LC-Swan probe. Direct sampling and contacting-dissolution-injection sampling modes were developed to perform in situ sampling and injection of liquid samples and dry spot samples, respectively, in the high flow-resistance LC system. A pressing-sealing method was also developed using a polydimethylsiloxane (PDMS) sealer to achieve the sealing of the probe sampling hole during the high-pressure chromatographic separation process. The LC-Swan probe-based system exhibited effective desalting capacity in the analysis of angiotensin II with similar relative standard deviations (RSDs) of retention time and peak area below 3% and 19% (n = 3) for both salt-containing and salt-free samples. The present system was applied for analyzing cytochrome C digest to test its separation capability for samples with complex compositions, and 19 peptides were detected in 13 min with an amino acid coverage of 85%. We also applied the system in metabolite analysis of mouse organ sections of brain, liver, and kidney to preliminarily demonstrate its application potential in MS imaging analysis.

Neorhizobium lilium sp. nov., an endophytic bacterium isolated from Lilium pumilum bulbs in Hebei province.

A novel gram-negative, aerobic, non-spore-forming, rod-shaped and non-nitrogen fixing bacterium named strain 24NRT was isolated from wild Lilium pumilum bulbs in Fuping, Baoding City, Hebei province, PR China. The 16S rRNA gene sequences of strains 24NRT showed the highest similarity to Neorhizobium alkalisoli DSM 21826T (98.5%) and N. galegae HAMBI 540T (98.1%). Phylogenetic analysis based on 16S rRNA genes and multilocus sequence analysis (MLSA) based on the partial sequences of atpD-glnII-glnA-recA-ropD-thrC housekeeping genes both indicated that strain 24NRT is a member of the genus Neorhizobium. The average nucleotide identity between the genome sequence of strain 24NRT and that of the isolate N. alkalisoli DSM 21826T was 83.1%, and the digital DNA-DNA hybridization was 20.1%. The G+C content of strain 24NRT was 60.3 mol %. The major cellular fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c) and C19:0 cyclo ω8c. Based on phenotypic, phylogenetic, and genotypic data, strain 24NRT is considered to represent a novel species of the genus Neorhizobium, for which the name Neorhizobium lilium sp. nov. is proposed. The type strain is 24NRT (= ACCC 61588T = JCM 33731T).