Open-ST: High-resolution spatial transcriptomics in 3D.

Spatial transcriptomics (ST) methods unlock molecular mechanisms underlying tissue development, homeostasis, or disease. However, there is a need for easy-to-use, high-resolution, cost-efficient, and 3D-scalable methods. Here, we report Open-ST, a sequencing-based, open-source experimental and computational resource to address these challenges and to study the molecular organization of tissues in 2D and 3D.

SLAM-Drop-seq reveals mRNA kinetic rates throughout the cell cycle.

RNA abundance is tightly regulated in eukaryotic cells by modulating the kinetic rates of RNA production, processing, and degradation. To date, little is known about time‐dependent kinetic rates during dynamic processes. Here, we present SLAM‐Drop‐seq, a method that combines RNA metabolic labeling and alkylation of modified nucleotides in methanol‐fixed cells with droplet‐based sequencing to detect newly synthesized and preexisting mRNAs in single cells.

Rapid nuclear deadenylation of mammalian messenger RNA.

Poly(A) tails protect RNAs from degradation and their deadenylation rates determine RNA stability. Although poly(A) tails are generated in the nucleus, deadenylation of tails has mostly been investigated within the cytoplasm. Here, we combined long-read sequencing with metabolic labeling, splicing inhibition and cell fractionation experiments to quantify, separately, the genesis and trimming of nuclear and cytoplasmic tails and .

Structural and functional investigation of the human snRNP assembly factor AAR2 in complex with the RNase H-like domain of PRPF8.

Small nuclear ribonucleoprotein complexes (snRNPs) represent the main subunits of the spliceosome. While the assembly of the snRNP core particles has been well characterized, comparably little is known of the incorporation of snRNP-specific proteins and the mechanisms of snRNP recycling. U5 snRNP assembly in yeast requires binding of the the Aar2 protein to Prp8p as a placeholder to preclude premature assembly of the SNRNP200 helicase, but the role of the human AAR2 homolog has not yet been investigated in detail.

FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control.

Although messenger RNAs are key molecules for understanding life, until now, no method has existed to determine the full-length sequence of endogenous mRNAs including their poly(A) tails. Moreover, although non-A nucleotides can be incorporated in poly(A) tails, there also exists no method to accurately sequence them. Here, we present full-length poly(A) and mRNA sequencing (FLAM-seq), a rapid and simple method for high-quality sequencing of entire mRNAs.

Differential expression of miR-23a/b-3p and its target genes in male patients with subfertility.

Objective: To elucidate the potential regulatory function of miR-23a/b-3p on spermatogenesis-specific genes.

Design: Reverse transcription quantitative polymerase chain reaction (RT-qPCR) validation, Northern blot, dual luciferase assay, and Western blot confirmation.

Setting: University research and clinical institutes.

An estimate of the total number of true human miRNAs.

While the number of human miRNA candidates continuously increases, only a few of them are completely characterized and experimentally validated. Toward determining the total number of true miRNAs, we employed a combined in silico high- and experimental low-throughput validation strategy. We collected 28 866 human small RNA sequencing data sets containing 363.

Large-scale validation of miRNAs by disease association, evolutionary conservation and pathway activity.

The validation of microRNAs (miRNAs) identified by next generation sequencing involves amplification-free and hybridization-based detection of transcripts as criteria for confirming valid miRNAs. Since respective validation is frequently not performed, miRNA repositories likely still contain a substantial fraction of false positive candidates while true miRNAs are not stored in the repositories yet. Especially if downstream analyses are performed with these candidates (e.

A high-resolution map of the human small non-coding transcriptome.

Motivation: Although the amount of small non-coding RNA-sequencing data is continuously increasing, it is still unclear to which extent small RNAs are represented in the human genome.

Results: In this study we analyzed 303 billion sequencing reads from nearly 25 000 datasets to answer this question. We determined that 0.

MiR-148a impairs Ras/ERK signaling in B lymphocytes by targeting SOS proteins.

Although microRNAs have been recognized as central cellular regulators, there is an evident lack of knowledge about their targets. Here, we analyzed potential target genes for miR-148a functioning in Ras signaling in B cells, including SOS1 and SOS2. A dual-luciferase reporter assay showed significantly decreased luciferase activity upon ectopic overexpression of miR-148a in HEK-293T cells that were co-transfected with the 3'UTR of either SOS1 or SOS2.

The embryo at single-cell transcriptome resolution.

By the onset of morphogenesis, embryos consist of about 6000 cells that express distinct gene combinations. Here, we used single-cell sequencing of precisely staged embryos and devised DistMap, a computational mapping strategy to reconstruct the embryo and to predict spatial gene expression approaching single-cell resolution. We produced a virtual embryo with about 8000 expressed genes per cell.

Cell fixation and preservation for droplet-based single-cell transcriptomics.

Background: Recent developments in droplet-based microfluidics allow the transcriptional profiling of thousands of individual cells in a quantitative, highly parallel and cost-effective way. A critical, often limiting step is the preparation of cells in an unperturbed state, not altered by stress or ageing. Other challenges are rare cells that need to be collected over several days or samples prepared at different times or locations.

miRNA expression profiling of Epstein-Barr virus-associated NKTL cell lines by Illumina deep sequencing.

The aim of this work was to establish the microRNA profile of SNK6 and SNT16, two Epstein-Barr virus (EBV)-infected cell lines derived from nasal NK/T-cell lymphoma (NKTL). The oncogenic EBV is strongly associated with the pathogenesis of nasal and extranodal NK/T-cell lymphoma and expresses 44 mature microRNAs and two noncoding EBV-encoded RNAs (EBERs). miRNAs are 19-25nt noncoding RNAs that affect host and viral gene expression post-transcriptionally.

Epstein-Barr Virus EBER Transcripts Affect miRNA-Mediated Regulation of Specific Targets and Are Processed to Small RNA Species.

The oncogenic Epstein-Barr virus (EBV) expresses 44 mature microRNAs and two non-coding EBER RNAs of 167 (EBER1) and 172 (EBER2) nt length. MiRNA profiling of NK/T cell lines and primary cells and Northern blotting of EBV-infected cell lines and primary tumors revealed processing of EBER1 to short 5'-derived RNAs of approximately 23, 52 and 70 nt (EBER123, EBER152, and EBER170) and of EBER2 to 3' fragments. The biogenesis of these species is independent of Dicer, and EBER123 does not act like a miRNA OPEN ACCESS Non-Coding RNA 2015, 1 171 to target its complementary sequence.

MicroRNA-142 is mutated in about 20% of diffuse large B-cell lymphoma.

MicroRNAs (miRNAs) are short 18-23 nucleotide long noncoding RNAs that posttranscriptionally regulate gene expression by binding to mRNA. Our previous miRNA profiling of diffuse large B-cell lymphoma (DLBCL) revealed a mutation in the seed sequence of miR-142-3p. Further analysis now showed that miR-142 was mutated in 11 (19.

MicroRNA profiling of Epstein-Barr virus-associated NK/T-cell lymphomas by deep sequencing.

The Epstein-Barr virus (EBV) is an oncogenic human Herpes virus involved in the pathogenesis of nasal NK/T-cell lymphoma. EBV encodes microRNAs (miRNAs) and induces changes in the host cellular miRNA profile. MiRNAs are short non-coding RNAs of about 19-25 nt length that regulate gene expression by post-transcriptional mechanisms and are frequently deregulated in human malignancies including cancer.

Multiple involvement of the central nervous system in Rosai-Dorfman disease.

Rosai-Dorfman disease is a rare, benign, idiopathic histio-proliferative disorder. Only 5% of cases involve the central nervous system. We describe a 10-year-old girl with pain in her lower limbs and back.

Androgen receptor expression in primary breast cancer and its predictive and prognostic value in patients treated with neoadjuvant chemotherapy.

The androgen receptor (AR) has been shown to be of potential prognostic importance in retrospective cohorts. We evaluated immunohistochemical AR expression on a tissue microarray of 673 core biopsies from primary breast cancer patients treated with neoadjuvant docetaxel/doxorubicin/cyclophosphamide (TAC) chemotherapy in the prospective GeparTrio phase-III trial. AR was detected in 53.

[75-year old female with progressive idiopathic lung fibrosis].

A 75-year old female was admitted to the intensive care unit because of a respiratory insufficiency during a bronchoscopy. Extubation was done rapidly. Two months before, the patient suffering from breast cancer without metastases underwent a radical mastectomy.

Molecular genetic analysis of surveillance biopsy samples from Barrett's mucosa--significance of sampling.

Our aim was to determine the spectrum and accumulation of mutations in surveillance biopsies from Barrett's mucosa of individual patients during follow-up. We performed loss of heterozygosity (LOH) analysis of six recently described tumor suppressor genes relevant for the carcinogenesis of Barrett's adenocarcinoma from laser-microdissected, paraffin-embedded biopsy samples of Barrett's mucosa without or with low-grade dysplastic change. 118 biopsy samples from 26 patients were taken during surveillance programs in time intervals ranging between 6 and 51 months.

Beam hardening: analytical considerations of the effective attenuation coefficient of X-ray tomography.

Polychromatic x-ray beams traveling though material are prone to beam hardening, i.e., the high energy part of the incident spectrum gets over represented when traveling farther into the material.

[Obligation to report occupational diseases. Importance of external post-mortem examinations before cremation].

The practical use of the legally required documentation of occupational diseases is demonstrated by a case of asbestos-related pleural mesothelioma. During the mandatory inquest before cremation, information of manifest pleural mesothelioma had been relayed to the widow of the patient, and an investigation for a possible occupational disease was performed. Reconstruction of the case showed that in the course of 3 months at least 13 physicians had been involved in in-hospital as well as ambulatory therapeutic measures.

[Tuberculosis of the large intestine--a differential diagnosis of inflammatory and neoplastic colon tumors].

We report on a case of ileocoecal tuberculosis. The clinical, radiological, endoscopic and pathologic findings are considered. The differential diagnosis between tuberculosis, chronic inflammatory bowel diseases and carcinoma of the colon are described.

Immunocytochemistry of eruptive haemangiomas (pyogenic granulomas).

Eight eruptive haemangiomas (pyogenic granulomas) were stained immunocytochemically. Many of the cells reacted with markers for endothelial cells. The reactions with anti-vWF antibody were weaker than those with UEA-I-lectin and with the monoclonal antibody BMA 120.

[Satellite recurrence of eruptive angioma. A clinical, histologic and immunocytochemical study].

Some weeks after operative removal of an eruptive angioma, satellite angiomas may develop within and around the scar. During the further course they remit spontaneously. So far these recurrences have been observed almost exclusively on the trunk in children and young adults, especially in male patients.