Complex Analysis of Single-Cell RNA Sequencing Data.

Single-cell RNA sequencing (scRNA-seq) is a revolutionary tool for studying the physiology of normal and pathologically altered tissues. This approach provides information about molecular features (gene expression, mutations, chromatin accessibility, etc.) of cells, opens up the possibility to analyze the trajectories/phylogeny of cell differentiation and cell-cell interactions, and helps in discovery of new cell types and previously unexplored processes. From a clinical point of view, scRNA-seq facilitates deeper and more detailed analysis of molecular mechanisms of diseases and serves as a basis for the development of new preventive, diagnostic, and therapeutic strategies. The review describes different approaches to the analysis of scRNA-seq data, discusses the advantages and disadvantages of bioinformatics tools, provides recommendations and examples of their successful use, and suggests potential directions for improvement. We also emphasize the need for creating new protocols, including multiomics ones, for the preparation of DNA/RNA libraries of single cells with the purpose of more complete understanding of individual cells.

Femtosecond laser-assisted anterior capsulotomy in children undergoing cataract surgery: a large case series.

OBJECTIVE: To evaluate safety and postoperative visual outcomes of low-energy femtosecond laser-assisted (FLA) anterior capsulotomy in paediatric cataract surgery. METHODS AND ANALYSIS: We report a retrospective single-centre consecutive case series of 51 eyes of 33 paediatric cataract patients with a mean age of 3.22 years (range: 2 months to 13 years) who underwent cataract surgery with FLA anterior capsulotomy, using FEMTO LDV Z8 femtosecond laser (Ziemer Ophthalmic Systems). Anterior laser capsulotomy, phacoaspiration and intraocular lens implantation were performed in all eyes. Both intraoperative and long-term postoperative complications, along with long-term monocular corrected distance visual acuity (CDVA), were assessed during average follow-up period of 32.96 months (range: 13-69 months). RESULTS: In 48 out of 51 eyes, a well-sized and well-located anterior capsulotomy was achieved without intraoperative complications. Anterior capsule tears occurred in three eyes; however, they did not extend posteriorly and the intraocular lens were placed in the bags without any further complications. Posterior capsular opacification developed in 45.10% of eyes (23 out of 51) and was subsequently treated with neodymium:yttrium-aluminum-garnet (Nd:YAG) laser capsulotomy. Mean CDVA at final follow-up was 20/40 (range: 20/63 to 20/32) in unilateral cases younger than 12 months, 20/40 (range: 20/1000 to 20/25) in unilateral cases older than 12 months, 20/66 (range: 20/400 to 20/32) in bilateral cases younger than 12 months and 20/40 (range: 20/200 to 20/20) in bilateral cases older than 12 months. CONCLUSIONS: Paediatric cataract surgery with low-energy FLA anterior capsulotomy is a procedure with long-term safety, resulting in significant improvement in CDVA.

Dicyemida and Orthonectida: Two Stories of Body Plan Simplification.

Two enigmatic groups of morphologically simple parasites of invertebrates, the Dicyemida (syn. Rhombozoa) and the Orthonectida, since the 19th century have been usually considered as two classes of the phylum Mesozoa. Early molecular evidence suggested their relationship within the Spiralia (=Lophotrochozoa), however, high rates of dicyemid and orthonectid sequence evolution led to contradicting phylogeny reconstructions. Genomic data for orthonectids revealed that they are highly simplified spiralians and possess a reduced set of genes involved in metazoan development and body patterning. Acquiring genomic data for dicyemids, however, remains a challenge due to complex genome rearrangements including chromatin diminution and generation of extrachromosomal circular DNAs, which are reported to occur during the development of somatic cells. We performed genomic sequencing of one species of Dicyema, and obtained transcriptomic data for two Dicyema spp. Homeodomain (homeobox) transcription factors, G-protein-coupled receptors, and many other protein families have undergone a massive reduction in dicyemids compared to other animals. There is also apparent reduction of the bilaterian gene complements encoding components of the neuromuscular systems. We constructed and analyzed a large dataset of predicted orthologous proteins from three species of Dicyema and a set of spiralian animals including the newly sequenced genome of the orthonectid Intoshia linei. Bayesian analyses recovered the orthonectid lineage within the Annelida. In contrast, dicyemids form a separate clade with weak affinity to the Rouphozoa (Platyhelminthes plus Gastrotricha) or (Entoprocta plus Cycliophora) suggesting that the historically proposed Mesozoa is a polyphyletic taxon. Thus, dramatic simplification of body plans in dicyemids and orthonectids, as well as their intricate life cycles that combine metagenesis and heterogony, evolved independently in these two lineages.