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.

Taming transposable elements in vertebrates: from epigenetic silencing to domestication.

Transposable element (TE)-derived sequences are ubiquitous in most eukaryotic genomes known to date. Because their expression and mobility can lead to genomic instability, several pathways have evolved to control TEs. Nevertheless, TEs represent an important source of genomic novelty and are often co-opted for novel functions that are relevant for phenotypic divergence and adaptation. Here, we review how animals, in particular vertebrates, mitigate TE mobility and expression, alongside known examples of TE domestication. We argue that the next frontier is to understand the determinants and dynamics of TE domestication: how they shift from 'non-self' targets of epigenetic silencing to 'self' genetic elements. New technologies enable avenues of research that may close the gap between epigenetic silencing and domestication of TEs.

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.

Beyond surgical resection: evaluating stereotactic brachytherapy iodine-125 for low-grade gliomas: a systematic review and meta-analysis.

Stereotactic Brachytherapy Iodine-125 (SBT I-125) has been investigated by some studies for the treatment of lowgrade gliomas. We performed a meta-analysis to assess the efficacy and safety of SBT I-125 Brachytherapy for treatment of patients with Low-Grade Gliomas. PubMed, Cochrane, Web of Science, and EMBASE databases were searched for randomized and observational studies. This systematic review and meta-analysis was conducted according to the Cochrane Collaboration and the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) statement guidelines. We used relative risk (RR) with 95% confidence intervals and random effects model to compare the effects of I-125 SBT treatment on the interest outcomes. We evaluated heterogeneity using I2 statistics; we considered heterogeneity to be significant if the p-value was less than 0.05 and I2 was higher than 35%. We performed statistical analysis using the software R (version 4.2.3). A total of 20 studies with a cohort of 988 patients with low grade gliomas who received SBT I-125 as a treatment option. The pooled analysis evidenced: (1) Complication rate of 10% (95% CI: 7-12%; I² = 60%); (2) 5-year PFS of 66% (99% CI: 45-86%; I²= 98%); (3) 10-year PFS was 66% (99% CI: 45-86%; I²= 98%); (4) Malignant transformation rate of 26% (95% CI: 8-45%; I²=0); (5) Mortality of 33% (95% CI: 15-51%; I² = 0%). Our systematic review and meta-analysis of SBT I-125 for low-grade gliomas have revealed significant concerns regarding its safety and efficacy. Despite a proportion of patients remaining progression-free, elevated rates of complications and mortality cast doubt on the intervention's reliability. Future research should prioritize long-term follow-up studies, standardized protocols, and comparative effectiveness research.

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.

Primary EGIST of the greater omentum - a rare presentation.

Extragastrointestinal stromal tumors (EGISTs) are rare mesenchymal neoplasms, which develop in the retroperitoneum, mesentery, and omentum, lacking continuity to the stomach or intestines. Authors hereby present a female patient with a large heterogeneous abdominal mass as a case of an omental EGIST. A 46-year-old woman was referred to our hospital due to an insidious enlargement and colicky pain in the right iliac fossa. Abdominal palpation revealed a voluminous, freely mobile, and non-pulsatile mesoabdominal bulge expanding to the hypogastrium. On exploratory midline laparotomy, the tumor was densely fused to the greater omentum, not connected to the stomach, without gross involvement of adjacent structures. The large mass was completely excised after adequate mobilization. Immunohistochemical techniques showed strong and diffuse expression of WT1, actin and DOG-1, as well as multifocal c-KIT marking. Mutational study concluded a double mutation of KIT exon 9 and a mutation of PDGFRA exon 18. The patient was submitted to adjuvant treatment with imatinib mesylate 800 mg/day. Despite an extremely diverse presentation, omental EGISTs often remain clinically silent for a long time having enough space to grow before becoming symptomatic. These tumors have a consistent pattern of metastasis that typically spares lymph nodes unlike epithelial gut neoplasms. Surgery remains the preferred treatment for non-metastatic EGISTs of the greater omentum. It is possible that DOG-1 will supplant KIT as the leading marker in the future. The scarcity of knowledge on omental EGISTs implies a close monitoring of these patients to detect local relapse or distant metastasis.

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.

GTSF-1 is required for formation of a functional RNA-dependent RNA Polymerase complex in Caenorhabditis elegans.

Argonaute proteins and their associated small RNAs (sRNAs) are evolutionarily conserved regulators of gene expression. Gametocyte-specific factor 1 (Gtsf1) proteins, characterized by two tandem CHHC zinc fingers and an unstructured C-terminal tail, are conserved in animals and have been shown to interact with Piwi clade Argonautes, thereby assisting their activity. We identified the Caenorhabditis elegans Gtsf1 homolog, named it gtsf-1 and characterized it in the context of the sRNA pathways of C. elegans We report that GTSF-1 is not required for Piwi-mediated gene silencing. Instead, gtsf-1 mutants show a striking depletion of 26G-RNAs, a class of endogenous sRNAs, fully phenocopying rrf-3 mutants. We show, both in vivo and in vitro, that GTSF-1 interacts with RRF-3 via its CHHC zinc fingers. Furthermore, we demonstrate that GTSF-1 is required for the assembly of a larger RRF-3 and DCR-1-containing complex (ERIC), thereby allowing for 26G-RNA generation. We propose that GTSF-1 homologs may act to drive the assembly of larger complexes that act in sRNA production and/or in imposing sRNA-mediated silencing activities.

Maternal and zygotic gene regulatory effects of endogenous RNAi pathways.

Endogenous small RNAs (sRNAs) and Argonaute proteins are ubiquitous regulators of gene expression in germline and somatic tissues. sRNA-Argonaute complexes are often expressed in gametes and are consequently inherited by the next generation upon fertilization. In Caenorhabditis elegans, 26G-RNAs are primary endogenous sRNAs that trigger the expression of downstream secondary sRNAs. Two subpopulations of 26G-RNAs exist, each of which displaying strongly compartmentalized expression: one is expressed in the spermatogenic gonad and associates with the Argonautes ALG-3/4; plus another expressed in oocytes and in embryos, which associates with the Argonaute ERGO-1. The determinants and dynamics of gene silencing elicited by 26G-RNAs are largely unknown. Here, we provide diverse new insights into these endogenous sRNA pathways of C. elegans. Using genetics and deep sequencing, we dissect a maternal effect of the ERGO-1 branch of the 26G-RNA pathway. We find that maternal primary sRNAs can trigger the production of zygotic secondary sRNAs that are able to silence targets, even in the absence of zygotic primary triggers. Thus, the interaction of maternal and zygotic sRNA populations, assures target gene silencing throughout animal development. Furthermore, we explore other facets of 26G-RNA biology related to the ALG-3/4 branch. We find that sRNA abundance, sRNA pattern of origin and the 3' UTR length of target transcripts are predictors of the regulatory outcome by the Argonautes ALG-3/4. Lastly, we provide evidence suggesting that ALG-3 and ALG-4 regulate their own mRNAs in a negative feedback loop. Altogether, we provide several new regulatory insights on the dynamics, target regulation and self-regulation of the endogenous RNAi pathways of C. elegans.

Thermal Infrared Sensing for Near Real-Time Data-Driven Fire Detection and Monitoring Systems.

With the increasing interest in leveraging mobile robotics for fire detection and monitoring arises the need to design recognition technology systems for these extreme environments. This work focuses on evaluating the sensing capabilities and image processing pipeline of thermal imaging sensors for fire detection applications, paving the way for the development of autonomous systems for early warning and monitoring of fire events. The contributions of this work are threefold. First, we overview image processing algorithms used in thermal imaging regarding data compression and image enhancement. Second, we present a method for data-driven thermal imaging analysis designed for fire situation awareness in robotic perception. A study is undertaken to test the behavior of the thermal cameras in controlled fire scenarios, followed by an in-depth analysis of the experimental data, which reveals the inner workings of these sensors. Third, we discuss key takeaways for the integration of thermal cameras in robotic perception pipelines for autonomous unmanned aerial vehicle (UAV)-based fire surveillance.