RNA Probes Research Articles

Preparation of RNAs with non-canonical 5' ends using novel di- and trinucleotide reagents for co-transcriptional capping.

Many eukaryotic and some bacterial RNAs are modified at the 5′ end by the addition of cap structures. In addition to the classic 7-methylguanosine 5′ cap in eukaryotic mRNA, several non-canonical caps have recently been identified, including NAD-linked, FAD-linked, and UDP-glucose-linked RNAs. However, studies of the biochemical properties of these caps are impaired by the limited access to in vitro transcribed RNA probes of high quality, as the typical capping efficiencies with NAD or FAD dinucleotides achieved in the presence of T7 polymerase rarely exceed 50%, and pyrimidine derivatives are not incorporated because of promoter sequence limitations. To address this issue, we developed a series of di- and trinucleotide capping reagents and in vitro transcription conditions to provide straightforward access to unconventionally capped RNAs with improved 5′-end homogeneity. We show that because of the transcription start site flexibility of T7 polymerase, R1ppApG-type structures (where R1 is either nicotinamide riboside or riboflavin) are efficiently incorporated into RNA during transcription from dsDNA templates containing both φ 6.5 and φ 2.5 promoters and enable high capping efficiencies (∼90%). Moreover, uridine-initiated RNAs are accessible by transcription from templates containing the φ 6.5 promoter performed in the presence of R2ppUpG-type initiating nucleotides (where R2 is a sugar or phosphate moiety). We successfully employed this strategy to obtain several nucleotide-sugar-capped and uncapped RNAs. The capping reagents developed herein provide easy access to chemical probes to elucidate the biological roles of non-canonical RNA 5′ capping.

Spatiotemporal characteristics of the pharyngeal teeth in interspecific distant hybrids of cyprinid fish: Phylogeny and expression of the initiation marker genes.

As an important feeding organ and taxonomical characteristic, the pharyngeal teeth of cyprinid fish have very high morphological diversity and exhibit species-specific numbers and arrangements. Many genes have been verified to regulate the pharyngeal teeth development and act as the initiation marker for teeth. Six initiation marker genes for pharyngeal teeth were used as RNA probes to investigate the expression pattern, and these genes were further used to construct a phylogenetic tree for cyprinid fish including some distant hybrids. The results from in situ hybridization showed that similarities and differences existed in the expression of dlx2b, dlx4b, dlx5a, pitx2, fth1b, and scpp5 in the pharyngeal region of the hybrids (BT) by the crosses of blunt snout bream (BSB, ♀) × topmouth culter (TC, ♂). Particularly, we found a high specificity marker gene scpp5 for the early development of pharyngeal teeth. The Scpp5 expression pattern established a clear graphic representation on the spatiotemporal characteristics of the early morphogenesis of pharyngeal teeth in BT and BSB. Our results suggested that the scpp5 expression in 4V1, 3V1, and 5V1 in BT occurred earlier than that in BSB, while the replacement rate of pharyngeal teeth (4V2, 3V2, and 5V2) was faster in BSB. Phylogenetic analysis revealed that the six marker genes were highly conserved and could be used as the molecular marker for identifying the parents of the distant hybrids in cyprinid fish. The expression patterns of the scpp5 gene was examined in various tissues, including the brain, gill, heart, liver, muscle, skin, fins, gonad, eye, and kidney, showing that the scpp5 gene was ubiquitously expressed, indicating its important role in cyprinid fish.

Primordial germ cell identification and traceability during the initial development of the Siluriformes fish Pseudopimelodus mangurus.

Primordial germ cells (PGCs) are responsible for generating all germ cells. Therefore, they are essential targets to be used as a tool for the production of germline chimeras. The labeling and route of PGCs were evaluated during the initial embryonic development of Pseudopimelodus mangurus, using whole-mount in situ hybridization (WISH) and mRNA microinjection in zygotes. A specific antisense RNA probe constituted by a partial coding region from P. mangurus nanos3 mRNA was synthesized for the WISH method. RNA microinjection was performed using the GFP gene reporter regulated by translation regulatory P. mangurus buc and nanos3 3'UTR sequences, germline-specific markers used to describe in vivo migration of PGCs. Nanos3 and buc gene expression was evaluated in tissues for male and female adults and initial development phases and larvae from the first to seventh days post-hatching. The results from the WISH technique indicated the origin of PGCs in P. mangurus from the aggregations of nanos3 mRNA in the cleavage grooves and the signals obtained from nanos3 probes corresponded topographically to the migratory patterns of the PGCs reported for other fish species. Diffuse signals were observed in all blastomeres until the 16-cell stage, which could be related to the two sequences of the nanos3 3'UTR observed in the P. mangurus unfertilized egg transcriptome. Microinjection was not successful using GFP-Dr-nanos1 3'UTR mRNA and GFP-Pm-buc 3'UTR mRNA and allowed the identification of potential PGCs with less than 2% efficiency only and after hatching using GFP-Pm-nanos3 3'UTR. Nanos3 and buc gene expression was reported in the female gonads and from fertilized eggs until the blastula phase. These results provide information about the PGC migration of P. mangurus and the possible use of PGCs for the future generation of germline chimeras to be applied in the conservation efforts of Neotropical Siluriformes species. This study can contribute to establishing genetic banks, manipulating organisms, and assisting in biotechnologies such as transplanting germ cells in fish.

Genomic sequence capture of Plasmodium relictum in experimentally infected birds

BackgroundSequencing parasite genomes in the presence of host DNA is challenging. Sequence capture can overcome this problem by using RNA probes that hybridize with the parasite DNA and then are removed from solution, thus isolating the parasite DNA for efficient sequencing.MethodsHere we describe a set of sequence capture probes designed to target 1035 genes (c. 2.5 Mbp) of the globally distributed avian haemosporidian parasite, Plasmodium relictum. Previous sequence capture studies of avian haemosporidians from the genus Haemoproteus have shown that sequencing success depends on parasitemia, with low-intensity, chronic infections (typical of most infected birds in the wild) often being difficult to sequence. We evaluate the relationship between parasitemia and sequencing success using birds experimentally infected with P. relictum and kept under laboratory conditions.ResultsWe confirm the dependence of sequencing success on parasitemia. Sequencing success was low for birds with low levels of parasitemia (< 1% infected red blood cells) and high for birds with higher levels of parasitemia. Plasmodium relictum is composed of multiple lineages defined by their mitochondrial DNA haplotype including three that are widespread (SGS1, GRW11, and GRW4); the probes successfully isolated DNA from all three. Furthermore, we used data from 25 genes to describe both among- and within-lineage genetic variation. For example, two samples of SGS1 isolated from different host species differed by 11 substitutions across those 25 genes.ConclusionsThe sequence capture approach we describe will allow for the generation of genomic data that will contribute to our understanding of the population genetic structure and evolutionary history of P. relictum, an extreme host generalist and widespread parasite.Graphical

Trojan Horse Delivery of Spherical Nucleic Acid Probes into the Cytoplasm for High-Fidelity Imaging of MicroRNAs.

We report a Trojan horse strategy to efficiently deliver the spherical nucleic acid probes (namely, nanoflares) into the cytoplasm for microRNA (miRNA) imaging with high fidelity, breaking through the cytoplasmic transport dilemma of RNA probes in living cells. The nanoflare is encapsulated into a "Trojan horse" consisting of zwitterionic choline phosphates (CPs) and acid-degradable crosslinkers; the former effectively promotes cell uptake and the latter triggers instantaneous liberation of the nanoflare probes from the lysosome to the cytoplasm. The exposed nanoflares in the cytoplasm can be lightened up by the target miRNAs specifically. Compared with the conventional nanoflares as well as the improved ones in previous reports, the "Trojan horse" nanoflares avoid nuclease degradation and thiol displacement during the delivery process, providing unprecedentedly high accuracy for intracellular miRNA imaging.

Detection of Human Papillomavirus in Squamous Lesions of the Conjunctiva Using RNA and DNA In-Situ Hybridization.

In-situ hybridization provides a convenient and reliable method to detect human papillomavirus (HPV) infection in formalin-fixed paraffin-embedded tissue. Cases of conjunctival papillomas, conjunctival intraepithelial neoplasia (CIN), conjunctival carcinoma in situ (cCIS), and invasive squamous cell carcinoma (SCC), in which low-risk (LR) and/or high-risk (HR) HPV types were evaluated by RNA or DNA in-situ hybridization, were retrospectively identified. LR HPV types were frequently detected in conjunctival papillomas (25/30, 83%), including 17/18 (94%) with RNA probes, compared to 8/12 (75%) with DNA probes. None of the CIN/cCIS or SCC cases were positive for LR HPV by either method. HR HPV was detected by RNA in-situ hybridization in 1/16 (6%) of CIN/cCIS cases and 2/4 (50%) of SCC cases, while DNA in-situ hybridization failed to detect HPV infection in any of the CIN/cCIS lesions. Reactive atypia and dysplasia observed in papillomas was generally associated with the detection of LR HPV types. Collectively, our findings indicate RNA in-situ hybridization may provide a high-sensitivity approach for identifying HPV infection in squamous lesions of the conjunctiva and facilitate the distinction between reactive atypia and true dysplasia. There was no clear association between HPV infection and atopy in papillomas or dysplastic lesions.

Exosomal tRF-Leu-AAG-001 derived from mast cell as a potential non-invasive diagnostic biomarker for endometriosis

BackgroundThe diagnosis of endometriosis (EMs) is still based on laparoscopic observation. This study tries to verify whether exosomal tRNA-derived fragments (tRFs) in leucorrhea can be used as non-invasive diagnostic markers.MethodsEndometrial tissues and leucorrhea were sampled from women hospitalized in Ningbo University Affiliated Hospital from January 2021 to July 2021 with (n = 26) and without endometriosis (n = 25). Exosomes were isolated from samples by differential centrifugation. The small RNA sequencing was performed to detect the exosomal tRNA halves (tiRNAs)&tRFs. RNA probe and immunofluorescence antibody were used to localize the origin of tRFs. From mast cell lines infected with tRF-Leu-AAG-001 siRNA, we observed the change in vascular capacity and expression of inflammatory factors. The specificity and sensitivity tRF were determined by receiver operating characteristic analyses.Results63 up-regulated and 45 down-regulated tRFs&tiRNAs were identified in ectopic exosomes. We selected tRF-Leu-AAG-001 as a candidate marker through KEGG pathway enrichment and PCR verification. We found that mast cells highly expressed tRF-Leu-AAG-001 in ectopic foci by immunofluorescence staining. We used siRNA to silenced tRF-Leu-AAG-001 expression in luva, qPCR analysis showed IL-6, IL-10, IL-1β, and TNF-α were significantly decreased. Meanwhile, tRF-Leu-AAG-001 siRNA dramatically reduced the angiogenic ability of luva. Finally, we examined the expression of exosomal tRF-Leu-AAG-001 in the leucorrhea. It was found exosomal tRF-Leu-AAG-001 had high specificity and sensitivity for predicting the occurrence of ectopic disease.ConclusionsExosomal tRF-Leu-AAG-001 derived from mast cells in ectopic foci might promote inflammation and angiogenesis. Meanwhile, leucorrhea exosomal tRF-Leu-AAG-001 could be a potential diagnostic biomarker for endometriosis.

Production of semah mahseer (Tor douronensis) donor-derived offspring through xenogeneic germ cell transplantation

Germ cell transplantation is a powerful technique for the production of gametes of commercially important or endangered fish species. Semah mahseer is a high-value freshwater fish distributed in Southeast Asia; however, they are currently facing extinction. Therefore, in this study, we performed cryopreservation and transplantation of germ cells into Nile tilapia as a host to produce gametes of semah mahseer. As a result, we found that germ cells could be preserved in liquid nitrogen with 10% dimethyl sulfoxide cryoprotectant for at least a year. Through the transplantation of previously frozen germ cells into the peritoneal cavity of tilapia larvae, the colonization of donor germ cells in recipient gonads was observed by the fluorescent signal of PKH26 dye and in situ hybridization using a vasa RNA probe specific to the donor. The recipients were reared to sexual maturity, and the resulting male and female recipients were mated naturally. Remarkably, we found donor-derived offspring from recipients at 14 months post-transplantation. Polymerase chain reaction-restriction fragment length polymorphism, using cytochrome b mitochondrial DNA gene and recombination activating 2 nuclear gene, revealed that they carried identical genotypes to the donor individuals. This is the first report of donor-derived semah mahseer offspring from inter-order germ cell transplantation.

An Unusual U2AF2 Inhibits Splicing and Attenuates the Virulence of the Human Protozoan Parasite Entamoeba histolytica.

E. histolytica is the etiological agent of intestinal amebiasis and liver abscesses, which still poses public health threat globally. Metronidazole is the drug of choice against amebiasis. However, metronidazole-resistant amoebic clinical isolates and strains have been reported recently, challenging the efforts for amebiasis eradication. In search of alternative treatments, E. histolytica transcriptomes have shown the association of genes involved in RNA metabolism with the virulence of the parasite. Among the upregulated genes in amoebic liver abscesses are the splicing factors EhU2AF2 and a paralog of EhSF3B1. For this reason and because EhU2AF2 contains unusual KH-QUA2 (84KQ) motifs in its lengthened C-terminus domain, here we investigated how the role of EhU2AF2 in pre-mRNA processing impacts the virulence of the parasite. We found that 84KQ is involved in splicing inhibition/intron retention of several virulence and non-virulence-related genes. The 84KQ domain interacts with the same domain of the constitutive splicing factor SF1 (SF1KQ), both in solution and when SF1KQ is bound to branchpoint signal RNA probes. The 84KQ–SF1KQ interaction prevents splicing complex E to A transition, thus inhibiting splicing. Surprisingly, the deletion of the 84KQ domain in EhU2AF2 amoeba transformants increased splicing and enhanced the in vitro and in vivo virulence phenotypes. We conclude that the interaction of the 84KQ and SF1KQ domains, probably involving additional factors, tunes down Entamoeba virulence by favoring intron retention.

Probe Capture Enrichment Methods for HIV and HCV Genome Sequencing and Drug Resistance Genotyping.

Human immunodeficiency virus (HIV) infections remain a significant public health concern worldwide. Over the years, sophisticated sequencing technologies such as next-generation sequencing (NGS) have emerged and been utilized to monitor the spread of HIV drug resistance (HIVDR), identify HIV drug resistance mutations, and characterize transmission dynamics. Similar applications also apply to the Hepatitis C virus (HCV), another bloodborne viral pathogen with significant intra-host genetic diversity. Several advantages to using NGS over conventional Sanger sequencing include increased data throughput, scalability, cost-effectiveness when batched sample testing is performed, and sensitivity for quantitative detection of minority resistant variants. However, NGS alone may fail to detect genomes from pathogens present in low copy numbers. As with all sequencing platforms, the primary determinant in achieving quality sequencing data is the quality and quantity of the initial template input. Samples containing degraded RNA/DNA and/or low copy number have been a consistent sequencing challenge. To overcome this limitation probe capture enrichment is a method that has recently been employed to target, enrich, and sequence the genome of a pathogen present in low copies, and for compromised specimens that contain poor quality nucleic acids. It involves the hybridization of sequence-specific DNA or RNA probes to a target sequence, which is followed by an enrichment step via PCR to increase the number of copies of the targeted sequences after which the samples are subjected to NGS procedures. This method has been performed on pathogens such as bacteria, fungus, and viruses and allows for the sequencing of complete genomes, with high coverage. Post NGS, data analysis can be performed through various bioinformatics pipelines which can provide information on genetic diversity, genotype, virulence, and drug resistance. This article reviews how probe capture enrichment helps to increase the likelihood of sequencing HIV and HCV samples that contain low viral loads and/or are compromised.

Abstract 2037: Spatial omic changes of malignant pleural mesothelioma following treatment using tumor-treating fields

Abstract Background: Application of alternating-electric fields as cancer-directed therapy known as Tumor-Treating Fields (TTFields) has been shown to be effective by exerting dipole alignment forces on polar microtubule subunits and dielectrophoretic forces in the cytokinetic furrow. This effect results in disruption of mitosis at the cellular level, and at the clinical level with significantly prolonged overall survival of patients with glioblastoma and malignant pleural mesothelioma (MPM). The molecular alterations that occur at the genomic and transcriptomic levels following TTFields treatment are unknown. We applied a spatial omics approach to elucidate spatial intratumoral effects of TTFields at the molecular level in regions of interest (ROI) in a mouse model of MPM. Methods: Eight Balb/C mice were injected with AB1 MPM cells until sizable tumors were observed (2-3 weeks). TTFields were applied, with heat sham used as a negative control. After 14 days (6 days of treatment, 2 days of rest, then 6 more days of treatment) tumors were resected, fixed and paraffin embedded. Following the Nanostring GeoMx protocol, thin sections of all eight tumors were placed on a slide, and incubated with both Ki-67 antibodies, and a GeoMx Mouse Cancer Transcriptome Atlas RNA probe set. Using Ki-67 staining as a guide, 12 ROIs were selected across each tumor to capture intratumoral heterogeneity, including the core and periphery of each tumor The DSP barcoded RNA probes were cleaved, sequenced and analyzed. We compared differential expression of subset gene classes of TTFields vs heat sham treated tumors; results were further stratified into Ki-67 high and low subsets for each sample. Results were assessed by Gene Set Enrichment. Results: Sham-treated tumors grew to over 300 mm3; TTFields-treated tumors averaged 100 mm3, confirming anti-tumor effect. Gene Set Enrichment Analysis uncovered upregulation of genes associated with interferon-alpha and -gamma responses in TTFields-treated tumors, which also displayed downregulation of pathway components associated with glycolysis, mTOR signaling, oxidative phosphorylation, cell invasion, hypoxia, and TNF-alpha signaling. Spatial analysis detected a heterogeneous response and differential expression between different portions of tumors. Conclusions: TTFields application induces clear patterns of differential expression in the transcriptome of treated tumors, including an increasingly immune-stimulated tumor microenvironment that also affects molecular pathways critical to cellular proliferation and invasion. These findings point the way toward improved understanding of timing and sequences of TTFields in relation to systemic cytotoxic, targeted, and immune modulation forms of therapeutic strategies. Our finding of upregulated immune response implicates TTFields as a potential synergistic tactic when coupled with immunotherapeutic approaches. Citation Format: Emil Lou, Katherine Ladner, Kerem Wainer-Katsir, Karina Deniz, Yaara Porat, Boris Brant, Shiri Davidi, Yuki Padmanabhan, Phillip Wong, Amrinder Nain, Clifford J. Steer, Moshe Giladi. Spatial omic changes of malignant pleural mesothelioma following treatment using tumor-treating fields [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2037.

Abstract 5761: Validation of TMB (tumor mutational burden) quantification using putative driver mutations in customized targeted sequencing platform

Abstract Next generation sequencing has revolutionised genomic studies of cancer, having facilitated the development of precision oncology treatments based on a tumour’s molecular profile. Tumor mutational burden (TMB) measurements aid in identifying patients who are likely to benefit from immunotherapy. In most cases, there is no result of a paired normal tissues. Therefore, it is difficult to effectively exclude germline mutations, so it does not effectively reflect the TMB of cancer driver mutation. We aimed to modify the TMB analysis pipeline to reflect the germline and multi-nucleotide variants (MNVs), specifically for Korean solid tumors. “CancerMaster” is custom RNA probes for target enrichment sequencing. It consists of all unions (7,811 regions, 2.5Mb) of reported exons of 524 tumor and immune related genes. The panel contains special RNA probes, which enables detection of microsatellite instability, Epstein-Barr virus and Human papillomavirus. This Panel sensitivity, precision, and TMB were assessed using immunohistochemistry and TruSight Oncology 500 for well-characterized samples (cellularity ≤ 20% and sequencing QC passed, n = 415). We achieved a mean coverage of 1,183x, with sensitivity and specificity of &amp;gt;99% and precision of &amp;gt;97% in alteration. We performed MNV analysis for more accurate mutation analysis. We used WhatsHap for haplotype phasing and the bcftools to call the MNV. The MNV-rich genes were HLA-A (2019 sites), HLA-B (1284 sites), and HLA-C (825 sites), and BRCA2, BRCA1, ATM and ATR, a DNA repair-related genes, was also identified at more than 30 sites. In addition, up to 14 MNVs were detected in one sample. In this study, we analyzed putative driver mutations that removed germline mutations, referring to the ACMG guidelines for sequence variant interpretation based on the Korean genome database (KOVA and KRGDB) and gnomAD. The TMB was recalculated by reflecting the MNV and the putative driver mutation. As a result, it was confirmed that this upgraded TMB analysis was similar to TMB calculated through actual somatic mutation through comparison with normal tissues. The TMB-high (20≤) sample was 8.4% (36/415) for pan-cancer, but 6.9% (20/289) for gastric cancer and 25% (12/48) for colorectal cancer showed differences by cancer type. In addition, it was confirmed that there is a correlation between TMB-high and MSI-H (sensitivity : 70.0%, specificity 99.5%, accuracy 95.9%) In conclusion, we validated TMB analysis pipeline for the expansion of immunotherapeutic applications in treatment-refractory Korean solid cancers. Citation Format: Woo Sun Kwon, Jingmin Che, Sun Young Rha, Hyun Cheol Chung. Validation of TMB (tumor mutational burden) quantification using putative driver mutations in customized targeted sequencing platform [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5761.

Introducing Ultra-Low Energy Ion Implantation of Radioactive Isotopes at ISOLDE, CERN for (Near-)Surface Characterization: The ASPIC and ASCII Vacuum Chambers

Solid-state physics research has long employed radioactive isotopes to investigate the crystallographic, electric and magnetic properties of nanostructures. Ion implantation (1–100 keV) is the method of choice for incorporating radioactive nuclei into the crystal structure. However, the enormous scientific interest in 2D materials, multiferroics and their interfaces of the last decades has lead to more stringent demands for isotope incorporation. Ultra-low energy (ULE) ion implantation (10–100 eV) provides the ability to precisely tune the depth of the implanted radioactive probes, even in the case of atomically thin 2D materials. To unlock this potential and expand the experimental capabilities of the ISOLDE collaboration in CERN, the apparatus for surface physics and interfaces at CERN (ASPIC), an experienced ultra-high vacuum chamber dedicated to surface characterization and modification, is refurbished and upgraded with a new component: the ASPIC’s ion implantation (ASCII) chamber, designed for ULE ion implantation of radioactive probes. This paper describes the scientific context, design and application of these vacuum chambers.

Rapid and quantitative evaluation of vaccinia virus-induced host shutoff using newly generated cell lines stably expressing secreted Gaussia luciferase.

Host shutoff, characterized by a global decline of cellular protein synthesis, is commonly observed in many viral infections, including vaccinia virus (VACV). Classic methods measuring host shutoff include the use of radioactive or nonradioactive probes to label newly synthesized proteins followed by radioautography or sodium dodecyl-sulfate polyacrylamide gel electrophoresisto resolve the proteins for follow-up detection. Although theseare highly reliable methods, they are time- and labor-consuming. Here, we generated two cell lines stably expressing secreted Gaussia luciferase. These reporter cells allow rapid, quantitative, and consecutive monitoring of host shutoff from a single infection sample. We evaluated host shutoff induced by wild-type and various mutant VACVs using the reporter cell lines. The results validated the utilities of the reporter cells and quantitatively characterized VACV-induced host shutoff at different stages of replication. Notably, the results also indicated additional major unidentified VACV shutoff factors. Our study provides new tools to study host shutoff. The reporter cells are also suitable for high throughput settings and rapid testing of clinically isolated viruses. In combination with classical methods, these tools will greatly facilitate understanding of virus-induced host shutoff, and protein synthesis shutoff caused by other physiologically relevant stresses.

Spatial Expression Patterning of Kelch-Like Protein Homolog 10 (klhl10), Armadillo Repeat-Containing Protein 4 Isoform X2 (armc4), and a Gamete-Specific Mitochondrial Cytochrome C Oxidase (mt-co1) during Spermatogenesis/Spermiogenesis in the Mantle of Male Blue Mussel (Mytilus edulis)

The spatial expression patterns of three genes [kelch-like protein homolog 10 (klhl10); armadillo repeat-containing protein 4 isoform X2 (armc4); mitochondria cytochrome oxidase I (mt-co1)] known to be important mechanistic components of spermatogenesis/spermiogenesis were localized in mantle tissue sections of male Mytilus edulis using nonisotopic in situ hybridization and RNA probes based on sequences derived from available mantle RNA sequencing libraries. The expression patterns showed that all three genes are primarily localized in a layer of cells adjacent to the outer wall of the testicular acini. This layer is known to contain developing stages of spermatogonia, spermatocytes, and spermatids. Kelch-like protein homolog 10 was expressed in immature spermatogonial cells/spermatocytes characterized by large round central nuclei and situated near the periphery of the testicular acini with little to no expression in adjacent populations of spermatids or mature spermatozoa at the center of the acini. Like klhl10, armc4 transcripts were also detected in the cells near the inner periphery of the outer acinar wall. In contrast, however, the armc4 expressing cells appeared to be spatially shifted more toward the inner edge of the cell layer and toward the center of the acini. The localization of cells expressing armc4 transcripts near the inner edge of the developing sperm layer in the testicular acini of M. edulis supports a role for armc4 in spermatid morphogenesis and maturation. Mitochondria-specific cytochrome c oxidase transcripts were localized in cells throughout the inner periphery of the testicular acini wall but not in association with mature spermatozoa in the center of the acini reflecting the significant level of cellular activity that occurs during early sperm development. This supports an important mitochondrial role in early and mid-spermatogenesis in M. edulis potentially related to sperm quality control. This work provides a first view into the molecular mechanisms behind spermatogenesis/spermiogenesis in M. edulis.

A standardized assay for the quantitative detection of serum HBV RNA in chronic hepatitis B patients

ABSTRACT Serum hepatitis B virus (HBV) pregenomic RNA (pgRNA) is a surrogate marker for reflecting the transcriptional activity of covalently closed circular DNA. However, there is still no standardized assay for the quantitative detection of serum HBV RNA in chronic hepatitis B patients. In this study, quantitative polymerase chain reactions for detecting the preC/C-RNA (preC/C region HBV pgRNA), SF-RNA (splicing variants-free pgRNA) and XR-RNA (X region remained pgRNA) regions were set up. The dynamic changes of serum pgRNA splicing variants and 3′ terminal truncations were analysed in three retrospective cohorts: 35 treatment-naive chronic HBV-infected patients (cohort A), 52 chronic hepatitis B (CHB) patients who received nucleos(t)ide analogs (NAs) therapy for 48 weeks (cohort B) and eight CHB patients who are under long-term NAs treatment (cohort C). The accuracy and sensitivity of HBV RNA detection were assessed by the National Standard of HBV RNA. We confirmed that high proportions of pgRNA splicing variants and 3′ terminal truncations were present and significantly affect the quantitative detection of serum HBV RNA in both treatment-naive and NAs-treated CHB patients. To achieve the higher accuracy and sensitivity on the detection of HBV RNA level, the primers and probes should be designed at the 5′ terminal region of HBV genome and outside the mainly spliced sequence of pgRNA, especially for CHB patients under long-term NAs treatment. This study would help to better understand the significance of the pgRNA splicing variants and 3′ terminal truncations, and further guide the clinical detection of serum HBV RNA.

64Cu radiolabeled nanomaterials for positron emission tomography (PET) imaging

The prevalence of positron emission tomography (PET) imaging has advanced biomedical applications for its ultrahigh sensitivity, deep tissue penetration and quantitative visualization of diseases in vivo. 64Cu with ideal half-life and decay characteristics has been designed as radioactive probes for disease diagnosis. The currently reported 64Cu-labeled nanomaterials have the advantages of long circulation time in serum, good biocompatibility and mature preparation methods, and have been used in vivo PET imaging, biodistribution and pharmacokinetic monitoring, and imaging guided therapy. At the same time, suitable carrier characteristics and radiolabeling strategies are particularly important in the 64Cu PET imaging process. In this review, we summarize different imaging probe designs and 64Cu radiolabeling strategies, as well as their eventual applications in biomedicine. The potential challenges and prospects of 64Cu labeled nanomaterials are also described, which provides broad prospects for radiolabeling strategies and further applications.

Direct detection of RNA modifications and structure using single-molecule nanopore sequencing

SUMMARYModifications are present on many classes of RNA, including tRNA, rRNA, and mRNA. These modifications modulate diverse biological processes such as genetic recoding and mRNA export and folding. In addition, modifications can be introduced to RNA molecules using chemical probing strategies that reveal RNA structure and dynamics. Many methods exist to detect RNA modifications by short-read sequencing; however, limitations on read length inherent to short-read-based methods dissociate modifications from their native context, preventing single-molecule modification analysis. Here, we demonstrate direct RNA nanopore sequencing to detect endogenous and exogenous RNA modifications on long RNAs at the single-molecule level. We detect endogenous 2'-O-methyl and base modifications across E. coli and S. cerevisiae ribosomal RNAs as shifts in current signal and dwell times distally through interactions with the helicase motor protein. We further use the 2'-hydroxyl reactive SHAPE reagent acetylimidazole to probe RNA structure at the single-molecule level with readout by direct nanopore sequencing.

Serotonergic Neurons in the Chick Brainstem Express Various Serotonin Receptor Subfamily Genes.

Serotonin (5-hydroxytryptamine, 5-HT) is a phylogenetically conserved modulatory neurotransmitter. In mammals, 5-HT plays an important role in the regulation of many mental states and the processing of emotions in the central nervous system. Serotonergic neurons in the central nervous system, including the dorsal raphe (DR) and median raphe (MR) nuclei, are spatially clustered in the brainstem and provide ascending innervation to the entire forebrain and midbrain. Both between and within the DR and MR, these serotonergic neurons have different cellular characteristics, developmental origin, connectivity, physiology, and related behavioral functions. Recently, an understanding of the heterogeneity of the DR and MR serotonergic neurons has been developed at the molecular level. In birds, emotion-related behavior is suggested to be modulated by the 5-HT system. However, correspondence between the raphe nuclei of birds and mammals, as well as the cellular heterogeneity in the serotonergic neurons of birds are poorly understood. To further understand the heterogeneity of serotonergic neurons in birds, we performed a molecular dissection of the chick brainstem using in situ hybridization. In this study, we prepared RNA probes for chick orthologs of the following serotonin receptor genes: 5-HTR1A, 5-HTR1B, 5-HTR1D, 5-HTR1E, 5-HTR1F, 5-HTR2A, 5-HTR2B, 5-HTR2C, 5-HTR3A, 5-HTR4, 5-HTR5A, and 5-HTR7. We showed that the expression pattern of 5-HT receptors in the serotonin neurons of chick DR and MR may vary, suggesting heterogeneity among and within the serotonin neurons of the DR and MR in the chick brainstem. Our findings regarding the molecular properties of serotonergic neurons in the bird raphe system will facilitate a good understanding of the correspondence between bird and mammalian raphes.

Hot-Band Absorption of a Cationic RNA Probe Enables Visualization of ΔΨm via the Controllable Anti-Stokes Shift Emission

Mitochondrial membrane potential (ΔΨm) is an important biophysical parameter playing central roles in cell apoptosis, mitochondrial dysfunction, and other biological and pathological processes. Herein, we have rationally designed and fabricated a unique fluorescent probe for convenient ΔΨm visualization based on hot-band absorption and controllable anti-Stokes shift emission. The robust probe was excitable via hot-band absorption and emitted anti-Stokes upconversion emission and Stokes downconversion fluorescence simultaneously. The anti-Stokes emission could be efficiently inhibited upon the binding to RNA. The cationic probe targeted mitochondria in living cells with high ΔΨm and displayed both anti-Stokes green emission and ordinary red fluorescence. After the decrease of ΔΨm, the probe immigrated out of mitochondria to RNA and nucleolus, which showed only red emission owing to the inhibition of anti-Stokes fluorescence. In this manner, the ΔΨm could be visualized in dual-color mode. The probe enabled clearly monitoring the reversible changes in ΔΨm and was successfully employed to visualize oxidative damage of living cells. The decrease of ΔΨm in living tissues was also successfully observed with the newly designed probe.