Characterization of the Nucleus Pulposus Progenitor Cells via Spatial Transcriptomics

Loss of refreshment in nucleus pulposus (NP) cellularity leads to intervertebral disc (IVD) degeneration. Nevertheless, the cellular sequence of NP cell differentiation remains unclear, although an increasing body of literature has identified markers of NP progenitor cells (NPPCs). Notably, due to their fragility, the physical enrichment of NP-derived cells has limited conventional transcriptomic approaches in multiple studies. To overcome this limitation, a spatially resolved transcriptional atlas of the mouse IVD is generated via the 10x Genomics Visium platform dividing NP spots into two clusters. Based on this, most reported NPPC-markers, including Cathepsin K (Ctsk), are rare and predominantly located within the NP-outer subset. Cell lineage tracing further evidence that a small number of Ctsk-expressing cells generate the entire adult NP tissue. In contrast, Tie2, which has long suggested labeling NPPCs, is actually neither expressed in NP subsets nor labels NPPCs and their descendants in mouse models; consistent with this, an in situ sequencing (ISS) analysis validated the absence of Tie2 in NP tissue. Similarly, no Tie2-cre-mediated labeling of NPPCs is observed in an IVD degenerative mouse model. Altogether, in this study, the first spatial transcriptomic map of the IVD is established, thereby providing a public resource for bone biology.

Adaptive expansion of ERVK solo-LTRs is associated with Passeriformes speciation events

Endogenous retroviruses (ERVs) are ancient retroviral remnants integrated in host genomes, and commonly deleted through unequal homologous recombination, leaving solitary long terminal repeats (solo-LTRs). This study, analysing the genomes of 362 bird species and their reptilian and mammalian outgroups, reveals an unusually higher level of solo-LTRs formation in birds, indicating evolutionary forces might have purged ERVs during evolution. Strikingly in the order Passeriformes, and especially the parvorder Passerida, endogenous retrovirus K (ERVK) solo-LTRs showed bursts of formation and recurrent accumulations coinciding with speciation events over past 22 million years. Moreover, our results indicate that the ongoing expansion of ERVK solo-LTRs in these bird species, marked by high transcriptional activity of ERVK retroviral genes in reproductive organs, caused variation of solo-LTRs between individual zebra finches. We experimentally demonstrated that cis-regulatory activity of recently evolved ERVK solo-LTRs may significantly increase the expression level of ITGA2 in the brain of zebra finches compared to chickens. These findings suggest that ERVK solo-LTRs expansion may introduce novel genomic sequences acting as cis-regulatory elements and contribute to adaptive evolution. Overall, our results underscore that the residual sequences of ancient retroviruses could influence the adaptive diversification of species by regulating host gene expression.

Spatial analysis toolkits for RNA in situ sequencing

Spatial transcriptomics (ST) is featured by high-throughput gene expression profiling within their native cell and tissue context, offering a means to investigate gene regulatory networks in tissue microenvironment. In situ sequencing (ISS) is an imaging-based ST technology that simultaneously detects hundreds to thousands of genes at subcellular resolution. As a highly reproducible and robust technique, ISS has been widely adapted and undergone a series of technical iterations. As the interest in ISS-based spatial transcriptomic analysis grows, scalable and integrated data analysis workflows are needed to facilitate the applications of ISS in different research fields. This review presents the state-of-the-art bioinformatic toolkits for ISS data analysis, which covers the upstream and downstream analysis workflows, including image analysis, cell segmentation, clustering, functional enrichment, detection of spatially variable genes and cell clusters, spatial cell-cell interactions, and trajectory inference. To assist the community in choosing the right tools for their research, the application of each tool and its compatibility with ISS data are reviewed in detailed. Finally, future perspectives and challenges concerning how to integrate heterogeneous tools into a user-friendly analysis pipeline are discussed. This article is categorized under: RNA Methods > RNA Analyses In Vitro and In Silico.

Combined amplification-based single-molecule fluorescence in situ hybridization with immunofluorescence for simultaneous in situ detection of RNAs and proteins

We present a combined amplification-based single-molecule fluorescence in situ hybridization and immunofluorescence (asmFISH-IF) method for the detection of multiple RNAs and proteins simultaneously in cells and formaldehyde-fixed and paraffin-embedded tissue sections. We showed that performing asmFISH before immunofluorescence gives a better IF signal than the opposite. Our asmFISH-IF method could help study the interplay of RNA and protein, helping to understand their functions.

Lymphatic endothelial transcription factor Tbx1 promotes an immunosuppressive microenvironment to facilitate post-myocardial infarction repair

The heart is an autoimmune-prone organ. It is crucial for the heart to keep injury-induced autoimmunity in check to avoid autoimmune-mediated inflammatory disease. However, little is known about how injury-induced autoimmunity is constrained in hearts. Here, we reveal an unknown intramyocardial immunosuppressive program driven by Tbx1, a DiGeorge syndrome disease gene that encodes a T-box transcription factor (TF). We found induced profound lymphangiogenic and immunomodulatory gene expression changes in lymphatic endothelial cells (LECs) after myocardial infarction (MI). The activated LECs penetrated the infarcted area and functioned as intramyocardial immune hubs to increase the numbers of tolerogenic dendritic cells (tDCs) and regulatory T (Treg) cells through the chemokine Ccl21 and integrin Icam1, thereby inhibiting the expansion of autoreactive CD8+ T cells and promoting reparative macrophage expansion to facilitate post-MI repair. Mimicking its timing and implementation may be an additional approach to treating autoimmunity-mediated cardiac diseases.

Improved in situ sequencing for high-resolution targeted spatial transcriptomic analysis in tissue sections

Spatial transcriptomics enables the study of localization-indexed gene expression activity in tissues, providing the transcriptional landscape that in turn indicates the potential regulatory networks of gene expression. In situ sequencing (ISS) is a targeted spatial transcriptomic technique, based on padlock probe and rolling circle amplification combined with next-generation sequencing chemistry, for highly multiplexed in situ gene expression profiling. Here, we present improved in situ sequencing (IISS) that exploits a new probing and barcoding approach, combined with advanced image analysis pipelines for high-resolution targeted spatial gene expression profiling. We develop an improved combinatorial probe anchor ligation chemistry using a 2-base encoding strategy for barcode interrogation. The new encoding strategy results in higher signal intensity as well as improved specificity for in situ sequencing, while maintaining a streamlined analysis pipeline for targeted spatial transcriptomics. We show that IISS can be applied to both fresh frozen tissue and formalin-fixed paraffin-embedded tissue sections for single-cell level spatial gene expression analysis, based on which the developmental trajectory and cell-cell communication networks can also be constructed.

Chromogenic Visualization of Single RNA Molecules In Situ with Duplex Capability by Rolling Circle Amplification with Alkaline Phosphatase

Visualizing spatial patterns of gene expression by optical microscopy at single-molecule resolution represents a long-standing challenge for imaging and molecular engineering technologies. In this study, we developed a method for visualizing mRNA with duplex capability by optical microscopy using rolling circle amplification with streptavidin-modified alkaline phosphatase (SA-ALP) to provide highly selective and sensitive RNA detection. ALP-based RNA detection provides comparable sensitivity and specificity to fluorescence-based in situ assays and similar performance to the current RNAscope technique for single-molecule RNA detection, but with improved ease of operation. This versatile and relatively user-friendly method of single-molecule RNA visualization can also overcome common problems of background interference. Our findings show that the red spots generated by the Fast Red staining in situ are readily quantified by image analysis, even in samples with heavy melanin deposition, supporting the clinical translation of this assay to improve diagnostic assays for recalcitrant tissues. This system was adaptable for duplex assays with multiple probes and multiple stains, which is ALP with horseradish peroxidase to produce red and brown signals to simultaneously visualize two different RNA targets. The duplex assay can be successfully applied to quantify mRNA expression from two genes in situ within single cells and multiple cell types. With the advantages of high sensitivity and low hardware requirements, this versatile and user-friendly method of RNA visualization may enable low-resource institutions to conduct previously inaccessible diagnostic or research questions about the in situ expression and distribution of RNAs at single-molecule resolution.

Single-molecule RNA in situ detection in clinical FFPE tissue sections by vsmCISH

Although RNA plays a vital role in gene expression, it is less used as an in situ biomarker for clinical diagnostics than DNA and protein. This is mainly due to technical challenges caused by the low expression level and easy degradation of RNA molecules. To tackle this issue, methods that are sensitive and specific are needed. Here, we present an RNA single-molecule chromogenic in situ hybridization assay based on DNA probe proximity ligation and rolling circle amplification. When the DNA probes hybridize into close proximity to the RNA molecules, they form a V-shape structure and mediate the circularization of circle probes. Thus, our method was termed vsmCISH. We successfully applied our method to assess HER2 mRNA expression status in invasive breast cancer tissue and investigated the utility of albumin mRNA ISH for differentiating primary from metastatic liver cancer. The promising results on clinical samples indicate that our method has great potential for application in diagnosing diseases using RNA biomarkers.

Novel In Situ Hybridization Assay for Chromogenic Single-Molecule Detection of Human Papillomavirus E6/E7 mRNA

RNA plays a vital role in the physiological and pathological processes of cells and tissues. However, RNA in situ hybridization applications in clinical diagnostics are still limited to a few examples. In this study, we developed a novel in situ hybridization assay for human papillomavirus (HPV) E6/E7 mRNA by taking advantage of specific padlock probing and rolling circle amplification, combined with chromogenic readout. We designed padlock probes for 14 types of high-risk HPV and demonstrated that E6/E7 mRNA could be visualized in situ as discrete dot-like signals using bright-field microscopy. Overall, the results are consistent with the clinical diagnostics lab's hematoxylin and eosin (H&E) staining and p16 immunohistochemistry test results. Our work thus shows the potential applications of RNA in situ hybridization for clinical diagnostics using chromogenic single-molecule detection, offering an alternative technical option to the current commercially available kit based on branched DNA technology. IMPORTANCE In situ detection of viral mRNA expression in tissue samples is of great value for pathological diagnosis to access viral infection status. Unfortunately, conventional RNA in situ hybridization assays lack sensitivity and specificity for clinical diagnostic purposes. Currently, the commercially available branched DNA technology-based single-molecule RNA in situ detection method offers satisfactory results. Here, we present our padlock probe- and rolling circle amplification-based RNA in situ hybridization assay for detecting HPV E6/E7 mRNA expression in formalin-fixed paraffin-embedded tissue sections, providing an alternative yet robust method for viral RNA in situ visualization that is also applicable to different types of diseases.

Catalytic DNA-Assisted Mass Production of Arbitrary Single-Stranded DNA

Synthetic single-stranded (ss) DNA is a cornerstone for life and materials science, yet the purity, quantity, length, and customizability of synthetic DNA are still limiting in various applications. Here, we present PECAN, paired-end cutting assisted by DNAzymes (DNA enzymes or deoxyribozymes), which enables mass production of ssDNA of arbitrary sequence (up to 7000 nucleotides, or nt) with single-base precision. At the core of PECAN technique are two newly identified classes of DNAzymes, each robustly self-hydrolyzing with minimal sequence requirement up- or down-stream of its cleavage site. Flanking the target ssDNA with a pair of such DNAzymes generates a precursor ssDNA amplifiable by pseudogene-recombinant bacteriophage, which subsequently releases the target ssDNA in large quantities after efficient auto-processing. PECAN produces ssDNA of virtually any terminal bases and compositions with >98.5 % purity at the milligram-to-gram scale. We demonstrate the feasibility of using PECAN ssDNA for RNA in situ detection, homology-directed genome editing, and DNA-based data storage.

Integrated 2D beam emission spectroscopy diagnostic at the Huan-Liuqi-2A (HL-2A) tokamak

Two newly developed, eight-channel, integrated Beam Emission Spectroscopy (BES) detectors have been installed at Huan-Liuqi-2A tokamak, which extends the existing 16 single-channel modular BES system with additional 16 spatial channels. The BES collects the Doppler-shifted Balmer D_α emission with a spatial resolution of 1 cm (radial) × 1.5 cm (poloidal) and a temporal resolution of 0.5 µs to measure long-wavelength (k_⊥ρ_i < 1) density fluctuations. Compared to the modular BES, the dark noise of the integrated BES is reduced by 50%-60% on average. The signal-to-noise ratio of the integrated BES system is optimized by the high light throughput front-end optics, high quantum efficiency photodiodes, high-gain, low-noise preamplifiers, and sufficient cooling capacity provided by the thermoelectric cooling (TEC) units that maintain the detectors at -20 °C. Crosstalk between channels that share the same optical system is found to be negligible. High-quality density fluctuation data enables 2D (radial-poloidal) imaging of turbulence, which allows for multi-channel spectral analysis, multi-channel cross-correlation analysis and velocimetry analysis. Preliminary results show that BES successfully captures the spatiotemporal features of the local turbulence and obtains statistically consistent turbulence characterization results.

Spatial Transcriptomics for Tumor Heterogeneity Analysis

The molecular heterogeneity of cancer is one of the major causes of drug resistance that leads to treatment failure. Thus, better understanding the heterogeneity of cancer will contribute to more precise diagnosis and improved patient outcomes. Although single-cell sequencing has become an important tool for investigating tumor heterogeneity recently, it lacks the spatial information of analyzed cells. In this regard, spatial transcriptomics holds great promise in deciphering the complex heterogeneity of cancer by providing localization-indexed gene expression information. This study reviews the applications of spatial transcriptomics in the study of tumor heterogeneity, discovery of novel spatial-dependent mechanisms, tumor immune microenvironment, and matrix microenvironment, as well as the pathological classification and prognosis of cancer. Finally, future challenges and opportunities for spatial transcriptomics technology’s applications in cancer are also discussed.

Two modified density gradient centrifugation methods facilitate the isolation of mouse Leydig cells

Preparation of sufficient mouse Leydig cells (LCs) with high purity is a prerequisite for investigations of the biological/pathological functions of LCs in mouse models. Density gradient centrifugation based on discontinuous Percoll gradients is an effective method (defined as regular method) for LC isolation. In this study, we developed two modified methods for LC isolation and compared their performance with that of the regular method. Modified method 1 integrated the crude LCs into the 50% Percoll solution before centrifugation. Modified method 2 sequentially used 50 and 60% Percoll solutions to isolate LCs. The purity of LCs was approximately 88.4, 91.3, and 79.7% derived from the regular, modified 1, and modified 2 methods, respectively. The yields of LCs in the same respective order were approximately 1.7 × 10⁵, 3.9 × 10⁵, and 11.9 × 10⁵ cells per 10⁸ interstitial cells input. Modified method 1 attained higher purity and yields than those of the regular method. Although the purity of LCs was relatively low for modified method 2, it could be used before further purification by, for example, fluorescence-activated or magnetic-activated cell sorting, owing to its simplicity and high yields. Therefore, our study provided alternative methods to facilitate LC isolation in mice.

Interneuron origin and molecular diversity in the human fetal brain

Precise generation of excitatory neurons and inhibitory interneurons is crucial for proper formation and function of neural circuits in the mammalian brain. Because of the size and complexity of the human brain, it is a challenge to reveal the rich diversity of interneurons. To decipher origin and diversity of interneurons in the human fetal subpallium, here we show molecular features of diverse subtypes of interneuron progenitors and precursors by conducting single-cell RNA sequencing and in situ sequencing. Interneuron precursors in the medial and lateral ganglionic eminence simultaneously procure temporal and spatial identity through expressing a combination of specific sets of RNA transcripts. Acquisition of various interneuron subtypes in adult human brains occurs even at fetal stages. Our study uncovers complex molecular signatures of interneuron progenitors and precursors in the human fetal subpallium and highlights the logic and programs in the origin and lineage specification of various interneurons.

Glycogen accumulation and phase separation drives liver tumor initiation

Glucose consumption is generally increased in tumor cells to support tumor growth. Interestingly, we report that glycogen accumulation is a key initiating oncogenic event during liver malignant transformation. We found that glucose-6-phosphatase (G6PC) catalyzing the last step of glycogenolysis is frequently downregulated to augment glucose storage in pre-malignant cells. Accumulated glycogen undergoes liquid-liquid phase separation, which results in the assembly of the Laforin-Mst1/2 complex and consequently sequesters Hippo kinases Mst1/2 in glycogen liquid droplets to relieve their inhibition on Yap. Moreover, G6PC or another glycogenolysis enzyme-liver glycogen phosphorylase (PYGL) deficiency in both human and mice results in glycogen storage disease along with liver enlargement and tumorigenesis in a Yap-dependent manner. Consistently, elimination of glycogen accumulation abrogates liver growth and cancer incidence, whereas increasing glycogen storage accelerates tumorigenesis. Thus, we concluded that cancer-initiating cells adapt a glycogen storing mode, which blocks Hippo signaling through glycogen phase separation to augment tumor incidence.

Liquid Biopsy, ctDNA Diagnosis through NGS

Liquid biopsy with circulating tumor DNA (ctDNA) profiling by next-generation sequencing holds great promise to revolutionize clinical oncology. It relies on the basis that ctDNA represents the real-time status of the tumor genome which contains information of genetic alterations. Compared to tissue biopsy, liquid biopsy possesses great advantages such as a less demanding procedure, minimal invasion, ease of frequent sampling, and less sampling bias. Next-generation sequencing (NGS) methods have come to a point that both the cost and performance are suitable for clinical diagnosis. Thus, profiling ctDNA by NGS technologies is becoming more and more popular since it can be applied in the whole process of cancer diagnosis and management. Further developments of liquid biopsy ctDNA testing will be beneficial for cancer patients, paving the way for precision medicine. In conclusion, profiling ctDNA with NGS for cancer diagnosis is both biologically sound and technically convenient.

CENPL, ISG20L2, LSM4, MRPL3 are four novel hub genes and may serve as diagnostic and prognostic markers in breast cancer

As a highly prevalent disease among women worldwide, breast cancer remains in urgent need of further elucidation its molecular mechanisms to improve the patient outcomes. Identifying hub genes involved in the pathogenesis and progression of breast cancer can potentially help to unveil mechanism and also provide novel diagnostic and prognostic markers. In this study, we integrated multiple bioinformatic methods and RNA in situ detection technology to identify and validate hub genes. EZH2 was recognized as a key gene by PPI network analysis. CENPL, ISG20L2, LSM4, MRPL3 were identified as four novel hub genes through the WGCNA analysis and literate search. Among these, many studies on EZH2 in breast cancer have been reported, but no studies are related to the roles of CENPL, ISG20L2, MRPL3 and LSM4 in breast cancer. These four novel hub genes were up-regulated in tumor tissues and associated with cancer progression. The receiver operating characteristic analysis and Kaplan–Meier survival analysis indicated that these four hub genes are promising candidate genes that can serve as diagnostic and prognostic biomarkers for breast cancer. Moreover, these four newly identified hub genes as aberrant molecules in the maintenance of breast cancer development, their exact functional mechanisms deserve further in-depth study.

Imaging of individual transcripts by amplification-based single-molecule fluorescence in situ hybridization

An amplification-based single-molecule fluorescence in situ hybridization (asmFISH) assay is introduced that exploits improved probe design for highly specific imaging of individual transcripts in fixed cells and tissues. In this method, a pair of DNA ligation probes are ligated on RNA templates upon specific hybridization, followed by probe circularization based on enzymatic DNA ligation and rolling circle amplification for signal boosting. The method is more efficient and specific than the padlock probe assay for detection of the same RNA molecules and discrimination of single nucleotide polymorphisms. Moreover, asmFISH is a versatile method which can be applied not only to cultured cells, but also to fresh frozen and formalin-fixed, paraffin-embedded tissue sections.

Single Cell RNA Expression Analysis Using Flow Cytometry Based on Specific Probe Ligation and Rolling Circle Amplification

Conventional flow cytometry has been widely used for high-throughput single-cell gene expression analysis using specific antibody staining. However, this is limited by the availability of high-quality antibodies. We developed a novel flow cytometry RNA detection technique termed RCA-Flow for single-cell RNA expression analysis. We showed that it is able to analyze not only mRNAs but also microRNAs and circular RNAs that are otherwise difficult to analyze by other flow cytometry techniques. The versatility for high-throughput analysis of different types of RNA molecules makes our method possess great potential for both biomedical and clinical applications.

Doppler coherence imaging of scrape-off-layer impurity flows in the HL-2A tokamak

A new Doppler coherence imaging spectroscopy interferometer has been developed on the HL-2A tokamak for the scrape-off-layer impurity flow measurement. Its spatial resolution is estimated to be up to ∼0.8 mm in the horizontal direction and ∼9 mm in the vertical direction, with a field of view of ∼34°. Its typical temporal resolution is about 1 ms. This salient feature allows for time-resolved 2D measurements in short-time phenomena on HL-2A, such as edge localized modes. Group delay and interference fringe pattern were calibrated with a dedicated calibration system. The robustness of group delay calibration and the feasibility of the extrapolation model for fringe pattern calibration are demonstrated. In this paper, we report the details of the optical instruments, calibration, and the initial experimental results of this Doppler coherence imaging spectroscopy interferometer.

Development of a multi-color gas puff imaging diagnostic on HL-2A tokamak

A Multi-Color (MC) gas puff imaging diagnostic has been developed on HL-2A tokamak. This diagnostic can simultaneously measure two-dimensional (2D, radial, and poloidal) electron density and temperature distributions with a good spatial resolution of 2.5 × 2.5 mm² and a temporal resolution of about 100 µs at best in edge plasmas. The 2D electron density and temperature distributions are inferred from the ratios of intensities of three different neutral helium emission lines; therefore, it is also referred to as helium beam probe or beam emission spectroscopy on thermal helium. A compact light splitter is used to split the inlet visible emission beam into four channels, and the specific neutral helium lines of the wavelengths λ₁ = 587.6 nm, λ₂ = 667.8 nm, λ₃ = 706.5 nm, and λ₄ = 728.1 nm are measured, respectively. This MC diagnostic has been experimentally tested and calibrated on a linear magnetic confinement device Peking University Plasma Test device, and the measured 2D electron density and temperature distributions are compared with the Langmuir probe measurements.

Visualization of individual microRNA molecules in fixed cells and tissues using target-primed padlock probe assay

MicroRNAs (miRNAs) are key regulators of gene expression at the posttranscriptional level. Precisely profiling of miRNA expression will help us to better understand their roles in normal and diseased cells and tissues. Here we describe in situ miRNA detection by padlock probing and miRNA target-primed rolling circle amplification. We optimized our protocol and showed it can be applied to both fixed cells and tissue sections. The method can be used in basic research and potentially in clinical diagnostics in the future.

Detection of Individual RNA in Fixed Cells and Tissues by Chromogenic ISH

Visualization of RNA molecules in situ helps to better understand the functions of expressed genes. Currently, most conventional in situ hybridization methods for visualization of individual RNAs are based on fluorescence detection. Herein we present a chromogenic in situ hybridization protocol for visualization of single RNA molecules in fixed cells and tissues. The protocol is based on padlock probing and rolling circle amplification to generate detectable chromogenic signal from single RNA molecules. Chromogenic signal can avoid background autofluorescence and can be preserved for a longer period than fluorescence signal.

A case of intracranial molluscum contagiosum virus infection diagnosed by metagenomic sequencing of cerebrospinal fluid

Molluscum contagiosum is a common, self-limiting infectious disease of the skin caused by molluscum contagiosum virus (MCV). The disease primarily affects children, sexually active adults, and immunocompromised individuals. Transmission of the virus occurs by direct skin contact. Therefore, the virus is usually detected in the skin and genitals of patients. However, the diagnosis of intracranial infection by the virus is difficult if the skin/mucosa lessons are atypical or absent, and the presence of the virus in the cerebrospinal fluid has not been reported. We report a very rare case of intracranial infection by molluscum contagiosum virus. A 25-year-old girl was admitted to our hospital due to severe headache but no fever or other symptoms. Upon examination, some small flesh-colored flattened papules on both arms were noticed. Blood tests showed slightly reduced levels of CD3 and CD4 T lymphocytes. Three-dimensional time-of-flight magnetic resonance angiography (3D-TOF-MRA) and head magnetic resonance (MR) were both normal. Lumbar puncture was performed, and metagenomic sequencing was applied to the spinal fluid. The unique sequences of the molluscum contagiosum virus were identified in the fluid. The patient was then diagnosed with intracranial molluscum contagiosum virus infection. No special treatment was given. The headache gradually disappeared, and the patient was discharged. During our quarterly follow-up, the girl appeared normal, and her skin lesions disappeared. However, her CD3 and CD4 T lymphocyte counts were still slightly lower than the normal level. Our case shows that the application of metagenomic sequencing to cerebrospinal fluid is a sensitive and powerful means to detect pathogens causing intracranial infection. Keywords: Molluscum contagiosum; intracranial infection; metagenomics sequencing.

Single molecule chromogenic in situ hybridization assay for RNA visualization in fixed cells and tissues

Visualization of gene expression at single RNA molecular level represents a great challenge to both imaging technologies and molecular engineering. Here we show a single molecule chromogenic in situ hybridization (smCISH) assay that enables counting and localizing individual RNA molecules in fixed cells and tissue under bright-field microscopy. Our method is based on in situ padlock probe assays directly using RNA as a ligation template and rolling circle amplification combined with enzyme catalyzed chromogenic reaction for amplification product visualization. We show potential applications of our method by detecting gene expression variations in single cells, subcellular localization information of expressed genes, and gene expression heterogeneity in formalin-fixed, paraffin-embedded tissue sections. This facile and straightforward method can in principle be applied to any type of RNA molecules in different samples.

Initial beam emission spectroscopy diagnostic system on HL-2A tokamak

A beam emission spectroscopy system is being developed and deployed on the HL-2A tokamak to measure local low wavenumber (k _⊥ ρ _i < 1) density fluctuations by measuring the Doppler-shifted emission from a 50 kV deuterium heating neutral beam. High spatial resolution (Δr ≤ 1 cm, Δz ≤ 1.5 cm) measurements are achieved with customized in-vacuum optics. High frequency, high-gain preamplifiers sample the light intensity at a Nyquist frequency of 1 MHz and achieve a high S/N ratio via high optical throughput, low-noise preamplifiers, and high quantum efficiency photodiodes. A first set of 16 detector channels [configured in an 8 (radial) × 2 (poloidal) array] has been installed and tested at HL-2A, covering the radial range r/a = 0.8-1.1. The frequency and wavenumber spectra have been measured under different plasma conditions. Initial measurements have demonstrated the capability of measuring edge plasma density fluctuation spectra and the poloidal flow velocity fields with a high S/N ratio.

Fourth Generation of Next-Generation Sequencing Technologies: Promise and Consequences

In this review, we discuss the emergence of the fourth‐generation sequencing technologies that preserve the spatial coordinates of RNA and DNA sequences with up to subcellular resolution, thus enabling back mapping of sequencing reads to the original histological context. This information is used, for example, in two current large‐scale projects that aim to unravel the function of the brain. Also in cancer research, fourth‐generation sequencing has the potential to revolutionize the field. Cancer Research UK has named “Mapping the molecular and cellular tumor microenvironment in order to define new targets for therapy and prognosis” one of the grand challenges in tumor biology. We discuss the advantages of sequencing nucleic acids directly in fixed cells over traditional next‐generation sequencing (NGS) methods, the limitations and challenges that these new methods have to face to become broadly applicable, and the impact that the information generated by the combination of in situ sequencing and NGS methods will have in research and diagnostics.

Viral dynamic modelling of Hepatitis C and resistance-associated variants in haemophiliacs

AIM

Chronic hepatitis C virus (HCV) infection is an important source of morbidity and mortality among haemophiliacs. Limited data are available regarding treatment intervention using direct-acting antivirals (DAAs) and theoretical concerns regarding accumulation of drug-associated resistance variants (RAVs) remain. We conducted a pilot study of treatment with telaprevir/pegylated interferon-alfa/ribavirin to evaluate treatment response and the role of lead-in DAA therapy on mutational selection of resistance variants.

METHODS

Ultra-deep sequence analysis was performed at baseline, 48 hours and 168 hours after treatment initiation.

RESULTS

No dominant RAVs were identified at baseline, but low-level RAVs were noted at baseline in all subjects. Viral dynamic models were used to assess treatment responses. The efficacy parameter (Ɛ) for lead-in ranged from 0 to 0.9745 (mean = 0.514). Subsequent addition of telaprevir resulted in a mean efficacy of more than 0.999. This was comparable to subjects who started all three medications simultaneously. A total of 80% achieved SVR. While rapid shifts in the RAV population following DAA initiation were observed, treatment failure associated with A156V was observed in only one patient. Adverse event profiles were similar to that observed in non-haemophilia cohorts. There was no evidence of factor inhibitor formation. There was no evidence that lead-in provided benefit in terms of response efficacy.

CONCLUSION

These data support DAA-based therapy in those with inherited bleeding disorders.

New technologies for DNA analysis--a review of the READNA Project

The REvolutionary Approaches and Devices for Nucleic Acid analysis (READNA) project received funding from the European Commission for 41/2 years. The objectives of the project revolved around technological developments in nucleic acid analysis. The project partners have discovered, created and developed a huge body of insights into nucleic acid analysis, ranging from improvements and implementation of current technologies to the most promising sequencing technologies that constitute a 3(rd) and 4(th) generation of sequencing methods with nanopores and in situ sequencing, respectively.

Interleukin-6 gene -174G>C polymorphism and chronic obstructive pulmonary disease risk: a meta-analysis

Association studies of interleukin-6 (IL-6) -174G>C polymorphism and chronic obstructive pulmonary disease (COPD) have yielded inconsistent results, possibly because single studies often lack sufficient statistical power. A comprehensive search was performed in the PubMed, Embase, Elsevier, Web of Science databases, Wanfang, and the Chinese National Knowledge Infrastructure (CNKI) databases for published studies investigating the associations between IL-6 -174G>C polymorphism and COPD. Odds ratios (OR) and 95% confidence intervals (95%CI) were used to assess the possible associations. Seven studies with a total of 2701 subjects were included in this meta-analysis. A significantly increased risk was detected in the C allele of the IL-6 -174G>C in Caucasians (C vs G: OR = 1.16, 95%CI = 1.03-1.30; CC+GC vs GG: OR = 1.21, 95%CI = 1.02-1.42; CC vs GG: OR = 1.32, 95%CI = 1.03-1.70). This meta-analysis suggests that the C allele of the IL-6 -174G>C might act as a COPD risk factor in Caucasians. Further well-designed case-control studies with larger sample sizes are needed to confirm these conclusions.

Multiplex detection of antibiotic resistance genes using padlock probes

The elucidation of resistance mechanisms is of central importance to providing and maintaining efficient medical treatment. However, molecular detection methods covering the complete set of resistance genes with a single test are still missing. Here, we present a novel 100-plex assay based on padlock probes in combination with a microarray that allows the simultaneous large-scale identification of highly diverse β-lactamases. The specificity of the assay was performed using 70 clinical bacterial isolates, recovering 98% of the β-lactamase nucleotide sequences present. Additionally, the sensitivity was evaluated with PCR products and genomic bacterial DNA, revealing a detection limit of 10(4) DNA copies per reaction when using PCR products as the template. Pre-amplification of genomic DNA in a 25-multiplex PCR further facilitated the detection of β-lactamase genes in dilutions of 10(7) cells/mL. In summary, we present an efficient, highly specific, and highly sensitive multiplex detection method for any gene.

Improving precision of proximity ligation assay by amplified single molecule detection

Proximity ligation assay (PLA) has been proven to be a robust protein detection method. The technique is characterized by high sensitivity and specificity, but the assay precision is probably limited by the PCR readout. To investigate this potential limitation and to improve precision, we developed a digital proximity ligation assay for protein measurement in fluids based on amplified single molecule detection. The assay showed significant improvements in precision, and thereby also detection sensitivity, over the conventional real-time PCR readout.

Genome-wide detection of spontaneous chromosomal rearrangements in bacteria

Genome rearrangements have important effects on bacterial phenotypes and influence the evolution of bacterial genomes. Conventional strategies for characterizing rearrangements in bacterial genomes rely on comparisons of sequenced genomes from related species. However, the spectra of spontaneous rearrangements in supposedly homogenous and clonal bacterial populations are still poorly characterized. Here we used 454 pyrosequencing technology and a ‘split mapping’ computational method to identify unique junction sequences caused by spontaneous genome rearrangements in chemostat cultures of Salmonella enterica Var. Typhimurium LT2. We confirmed 22 unique junction sequences with a junction microhomology more than 10 bp and this led to an estimation of 51 true junction sequences, of which 28, 12 and 11 were likely to be formed by deletion, duplication and inversion events, respectively. All experimentally confirmed rearrangements had short inverted (inversions) or direct (deletions and duplications) homologous repeat sequences at the endpoints. This study demonstrates the feasibility of genome wide characterization of spontaneous genome rearrangements in bacteria and the very high steady-state frequency (20–40%) of rearrangements in bacterial populations.

Rapid identification of bio-molecules applied for detection of biosecurity agents using rolling circle amplification

Detection and identification of pathogens in environmental samples for biosecurity applications are challenging due to the strict requirements on specificity, sensitivity and time. We have developed a concept for quick, specific and sensitive pathogen identification in environmental samples. Target identification is realized by padlock- and proximity probing, and reacted probes are amplified by RCA (rolling-circle amplification). The individual RCA products are labeled by fluorescence and enumerated by an instrument, developed for sensitive and rapid digital analysis. The concept is demonstrated by identification of simili biowarfare agents for bacteria (Escherichia coli and Pantoea agglomerans) and spores (Bacillus atrophaeus) released in field.

[Traumatic intraventricular hemorrhage in severe head injury]

Among 329 cases with comatose state caused by severe head injury, 32 had primary intraventricular hemorrhage as revealed on initial CT scan (13.4%). We divided traumatic intraventricular hemorrhage into 4 types. Type 1: massive hemorrhage (9 cases). Type 2: subependymal hemorrhage (8 cases). Type 3: damage of fornix or septum pellucidum (8 cases). Type 4: Nieveau (7 cases). Most of these cases were caused by traffic accident. Shearing injury may be the most accurate mechanism to produce the intraventricular hemorrhage. Shear strain in severe head injury should cause tears of the subependymal vein, fornix, septum pellucidum and choroid plexus. 8 cases out of 32 ventricular hemorrhage showed tear of the subependymal vein. 8 of our cases showed damage of the fornix of septum pellucidum. These results suggested that the anatomical structure of the fornix and septum pellucidum were weak points for shearing force. 20 cases in 32 with ventricular hemorrhage died. These cases were frequently associated with other traumatic lesions, namely contusion of white matter and grey matter, brain stem lesions and cerebellar contusion, caused by shearing injury. Therefore, the prognosis of severe head injury with intraventricular hemorrhage is poor.

Prolonged inhibition of human myometrial contractility by intermittent isoproterenol

Regular, spontaneous contractions of human myometrial strips obtained at the time of elective cesarean section were recorded in a tissue bath in five experiments. Administration of the beta-adrenergic agonist isoproterenol (1 mumol/L) resulted in the rapid onset of myometrial relaxation. In the continuous presence of the beta-agonist, myometrial contractions of amplitude equal to or greater than that of baseline resumed after 10 to 40 minutes (mean +/- SEM = 29.7 +/- 7.3), indicating the development of desensitization of the tissue to the tocolytic effects of isoproterenol. In contrast, intermittent exposure of the myometrial strips to isoproterenol prevented the onset of desensitization and resulted in prolonged inhibition of myometrial contractions. These findings suggest that modification of the present regimen of administration of beta-adrenergic agonists from continuous to intermittent infusion may improve the success of these agents in the prevention of preterm births.