Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis.

Nematodes encompass more than 24,000 described species, which were discovered in almost every ecological habitat, and make up >80% of metazoan taxonomic diversity in soils. The last common ancestor of nematodes is believed to date back to ∼650-750 million years, generating a large and phylogenetically diverse group to be explored. However, for most species high-quality gene annotations are incomprehensive or missing. Combining short-read RNA sequencing with mass spectrometry-based proteomics and machine-learning quality control in an approach called proteotranscriptomics, we improve gene annotations for nine genome-sequenced nematode species and provide new gene annotations for three additional species without genome assemblies. Emphasizing the sensitivity of our methodology, we provide evidence for two hitherto undescribed genes in the model organism Caenorhabditis elegans Extensive phylogenetic systems analysis using this comprehensive proteome annotation provides new insights into evolutionary processes of this metazoan group.

The Caenorhabditis elegans TDRD5/7-like protein, LOTR-1, interacts with the helicase ZNFX-1 to balance epigenetic signals in the germline.

LOTUS and Tudor domain containing proteins have critical roles in the germline. Proteins that contain these domains, such as Tejas/Tapas in Drosophila, help localize the Vasa helicase to the germ granules and facilitate piRNA-mediated transposon silencing. The homologous proteins in mammals, TDRD5 and TDRD7, are required during spermiogenesis. Until now, proteins containing both LOTUS and Tudor domains in Caenorhabditis elegans have remained elusive. Here we describe LOTR-1 (D1081.7), which derives its name from its LOTUS and Tudor domains. Interestingly, LOTR-1 docks next to P granules to colocalize with the broadly conserved Z-granule helicase, ZNFX-1. The Tudor domain of LOTR-1 is required for its Z-granule retention. Like znfx-1 mutants, lotr-1 mutants lose small RNAs from the 3' ends of WAGO and mutator targets, reminiscent of the loss of piRNAs from the 3' ends of piRNA precursor transcripts in mouse Tdrd5 mutants. Our work shows that LOTR-1 acts with ZNFX-1 to bring small RNA amplifying mechanisms towards the 3' ends of its RNA templates.

Presentation and management of cerebral proliferative angiopathy: a systematic review and meta-analysis on treatment outcomes.

Cerebral Proliferative Angiopathy (CPA) is a rare brain vascular malformation, similar to Arteriovenous Malformations (AVM) but lacking of early venous drainage. Presentation and treatment outcomes were investigated, examining for morbidity, mortality and complications. A meta-analysis was conducted according to PRISMA guidelines. PubMed, Embase and Web Of Science were searched with keywords such as "cerebral proliferative angiopathy" and "management". We pooled and meta-analyzed outcomes on documented CPA cases. 11,079 studies were pooled as a result of manual citation searching, 50 studies were included, adding up to 115 CPA cases. The majority of patients were females (1.38:1), with a mean age of presentation of 26.9 (19.4) years. Headache (46%) and seizures (34%) were the most common presenting symptoms. 37% of patients presented with focal neurologic deficit. Patients managed conservatively from the surgical standpoint (i.e. nonoperative management) did not undergo homogenous treatment strategies, and major complications were at 47% (95% CI: 17%, 76%), with a 1% mortality (95% CI: 0%, 6%). Surgical and embolization interventions presented the highest proportion of major complications, 66% (95% CI: 33%, 99%) and 73% (95% CI: 42%, 100%), respectively. The embolization subgroup led in mortality, with 3% (95% CI: 0%, 10%). No death was documented in patients undergoing surgery. CPA has a similar presentation to brain arteriovenous malformations, but its treatment outcomes are potentially worse. This difference is not attributable to heterogeneity in assigning patient treatment strategies. This highlights the need for more accurate diagnostic methods.

Age- and caste-independent piRNAs in the germline and miRNA profiles linked to caste and fecundity in the ant Temnothorax rugatulus.

Social insects are models for studies of phenotypic plasticity. Ant queens and workers vary in fecundity and lifespan, which are enhanced and extended in queens. Yet, the regulatory mechanisms underlying this variation are not well understood. Ant queens live and reproduce for years, so that they need to protect their germline from transposable element (TE) activity, which may be redundant in short-lived, often sterile workers. We analysed the expression of two protective classes of small RNAs, microRNAs (miRNAs) and Piwi-interacting RNAs (piRNAs), in various tissues, castes and age classes of the ant Temnothorax rugatulus. In queens, piRNAs were highly abundant in ovaries with TEs being their clear targets, with reduced but still detectable piRNA-specific ping-pong signatures in thorax and brains. piRNA pathway activity varied little with age in queens. Moreover, the reduced ovaries of workers also exhibited similar piRNA activity and this not only in young, fertile workers, but also in older foragers with regressed ovaries. Therefore, these ants protect their germline through piRNA activity, regardless of ovarian development, age or caste, even in sterile workers often considered the soma of the superorganism. Our tissue-specific miRNA analysis detected the expression of 304 miRNAs, of which 105 were expressed in all tissues, 10 enriched in the brain, three in the thorax, whereas 83 were ovarian-specific. We identified ovarian miRNAs whose expression was related to caste, fecundity and age, and which likely regulate group-specific gene expression. sRNA shifts in young- to middle-aged queens were minor, suggesting delayed senescence in this reproductive caste.

Ultrasound-Guided Resection of High-Grade Gliomas: A Single-Arm Meta-Analysis.

BACKGROUND: High-grade gliomas (HGGs) present a challenge in neuro-oncology, often necessitating surgical resection for optimal management. Ultrasound holds promise in achieving better gross total resection (GTR) and improving outcomes. This meta-analysis systematically evaluates literature providing robust evidence on the use of intraoperative ultrasonography (iUSG) in HGG resection. METHODS: Following Preferred Reporting Items for Systematic Reviews and Meta-Analysis guidelines a comprehensive search was made across PubMed, Embase, Cochrane, and Web of Science utilized terms related to iUSG for HGG resection. The meta-analysis examined randomized trials and observational cohort studies on iUSG-guided HGG resection. GTR, subtotal resection, and postresection complications were assessed. Statistical analysis, employing R software for a single proportion analysis with confidence intervals of 95%, I2 statistics for heterogeneity, and the instrumental variables method with restricted maximum likelihood for a random effects model. RESULTS: A total of 178 patients were included in our study. The GTR overall rate in patients with iUSG-guided resection was found to be 64% (95% confidence interval: 46%-81%). Two-dimensional ultrasound remains dominant at 80% against other options of ultrasound. Complications were reported at a 15% rate (95% confidence interval: 7%-23%). CONCLUSIONS: Our study provided robust data on the utilization of iUSG-guided resection regarding the attainment of GTR and the complications related to resection. However, challenges such as outcome heterogeneity and limited complication reporting highlight the need for further research to optimize iUSG in HGG treatment. Long-term follow-up studies on patient survival and postsurgery quality of life will complement existing literature, guiding clinical practices in managing HGG.