Specialized replication mechanisms maintain genome stability at human centromeres.

The high incidence of whole-arm chromosome aneuploidy and translocations in tumors suggests instability of centromeres, unique loci built on repetitive sequences and essential for chromosome separation. The causes behind this fragility and the mechanisms preserving centromere integrity remain elusive. We show that replication stress, hallmark of pre-cancerous lesions, promotes centromeric breakage in mitosis, due to spindle forces and endonuclease activities. Mechanistically, we unveil unique dynamics of the centromeric replisome distinct from the rest of the genome. Locus-specific proteomics identifies specialized DNA replication and repair proteins at centromeres, highlighting them as difficult-to-replicate regions. The translesion synthesis pathway, along with other factors, acts to sustain centromere replication and integrity. Prolonged stress causes centromeric alterations like ruptures and translocations, as observed in ovarian cancer models experiencing replication stress. This study provides unprecedented insights into centromere replication and integrity, proposing mechanistic insights into the origins of centromere alterations leading to abnormal cancerous karyotypes.

BirthSeq, a new method to isolate and analyze dated cells in different vertebrates.

Embryonic development is a complex and dynamic process that unfolds over time and involves the production and diversification of increasing numbers of cells. The impact of developmental time on the formation of the central nervous system is well documented, with evidence showing that time plays a crucial role in establishing the identity of neuronal subtypes. However, the study of how time translates into genetic instructions driving cell fate is limited by the scarcity of suitable experimental tools. We introduce BirthSeq, a new method for isolating and analyzing cells based on their birth date. This innovative technique allows for in vivo labeling of cells, isolation via fluorescence-activated cell sorting, and analysis using high-throughput techniques. We calibrated the BirthSeq method for developmental organs across three vertebrate species (mouse, chick and gecko), and utilized it for single-cell RNA sequencing and novel spatially resolved transcriptomic approaches in mouse and chick, respectively. Overall, BirthSeq provides a versatile tool for studying virtually any tissue in different vertebrate organisms, aiding developmental biology research by targeting cells and their temporal cues.

CeLaVi: an interactive cell lineage visualization tool.

Recent innovations in genetics and imaging are providing the means to reconstruct cell lineages, either by tracking cell divisions using live microscopy, or by deducing the history of cells using molecular recorders. A cell lineage on its own, however, is simply a description of cell divisions as branching events. A major goal of current research is to integrate this description of cell relationships with information about the spatial distribution and identities of the cells those divisions produce. Visualizing, interpreting and exploring these complex data in an intuitive manner requires the development of new tools. Here we present CeLaVi, a web-based visualization tool that allows users to navigate and interact with a representation of cell lineages, whilst simultaneously visualizing the spatial distribution, identities and properties of cells. CeLaVi's principal functions include the ability to explore and manipulate the cell lineage tree; to visualise the spatial distribution of cell clones at different depths of the tree; to colour cells in the 3D viewer based on lineage relationships; to visualise various cell qualities on the 3D viewer (e.g. gene expression, cell type) and to annotate selected cells/clones. All these capabilities are demonstrated with four different example data sets. CeLaVi is available at http://www.celavi.pro.

Risk Factors for Testicular Cancer: Environment, Genes and Infections-Is It All?

The incidence of testicular cancer is steadily increasing over the past several decades in different developed countries. If on one side better diagnosis and treatment have shone a light on this disease, on the other side, differently from other malignant diseases, few risk factors have been identified. The reasons for the increase in testicular cancer are however unknown while risk factors are still poorly understood. Several studies have suggested that exposure to various factors in adolescence as well as in adulthood could be linked to the development of testicular cancer. Nevertheless, the role of environment, infections, and occupational exposure are undoubtedly associated with an increase or a decrease in this risk. The aim of this narrative review is to summarize the most recent evidence regarding the risk factors associated with testicular cancer, starting from the most commonly evaluated (cryptorchidism, family history, infections) to the newer identified and hypothesized risk factors.

The role of SUMOylation during development.

During the development of multicellular organisms, transcriptional regulation plays an important role in the control of cell growth, differentiation and morphogenesis. SUMOylation is a reversible post-translational process involved in transcriptional regulation through the modification of transcription factors and through chromatin remodelling (either modifying chromatin remodelers or acting as a 'molecular glue' by promoting recruitment of chromatin regulators). SUMO modification results in changes in the activity, stability, interactions or localization of its substrates, which affects cellular processes such as cell cycle progression, DNA maintenance and repair or nucleocytoplasmic transport. This review focuses on the role of SUMO machinery and the modification of target proteins during embryonic development and organogenesis of animals, from invertebrates to mammals.

Planktonic, benthic and sympagic copepods collected from the desalination unit of Mario Zucchelli Research Station in Terra Nova Bay (Ross Sea, Antarctica).

Background: Distributional data on planktonic, benthic and sympagic copepods collected in the framework of the XXXIVth Expeditions of the Italian National Antarctic Programme (PNRA) to the Ross Sea sector from 2018-2019 are here provided. These occurrences correspond to specimens collected from the 25 µm filters used in the desalination plant of the Italian research station "Mario Zucchelli" (MZS), located in the Terra Nova Bay area (TNB; Ross Sea, Antarctica). This dataset is a contribution to the Antarctic Biodiversity Portal, the thematic Antarctic node for both the Ocean Biogeographic Information System (AntOBIS) and the Global Biodiversity Information Facility Antarctic Biodiversity Information Facility (ANTABIF). The dataset was uploaded and integrated with the SCAR-AntOBIS database (the geospatial component of SCAR-MarBIN). Please follow the guidelines from the SCAR Data Policy (ISSN 1998-0337) when using the data. If you have any questions regarding this dataset, please contact us via the contact information provided in the metadata or via data-biodiversity-aq@naturalsciences.be. Issues with the dataset can be reported at the biodiversity-aq GitHub project. New information: We describe the diversity of marine copepods Terra Nova Bay sampled by the filters installed in the desalination unit (DU) of the Italian research station "Mario Zucchelli" described in recent work. The opening of the intake pipe of the DU is positioned at a depth of 4 m and allowed a total of 2,116 specimens to be sampled and recognised. In addition, new occurrence records of copepod genera and species are reported in the same zone. We provide an overview of the marine copepod diversity reported for TNB. The total of 2,116 individuals corresponds to 14 genera and 15 species and is represented by 136 occurrence records in this dataset. Around 52% of the total number of species are new records for the TNB area. The publication of this data paper was funded by the Belgian Science Policy Office (BELSPO, contract n°FR/36/AN1/AntaBIS) in the Framework of EU-Lifewatch as a contribution to the SCAR Antarctic biodiversity portal (biodiversity.aq).

COVID-19-related retinal microvasculopathy and systemic implications in patients with severe disease: results from the Methuselah study.

Objectives: To assess the reversibility of retinal microvascular changes in the long term and to investigate the potential links with other vascular diseases of COVID-19. Methods: We designed a prospective multicenter observational study. Patients were enrolled from the Methuselah study cohort. Retinal vascular function was studied in these patients using optical coherence tomography angiography (OCTA); aortic stiffness was measured using aortic pulse wave velocity. These examinations were performed 1 (Visit 1) and 12 (Visit 2) months after the hospital discharge for severe COVID-19. A control subject group matched for age and sex was included to define normal values. Results: A total of 28 control subjects (56 eyes) and 25 patients (50 eyes) completed the scheduled OCTA assessment; 18 patients (36 eyes) also completed the macrovascular examination. Compared to controls, the vessel density of the superficial capillary plexus (SCP) was reduced, whereas the foveal avascular zone area was enlarged at Visit 1 (p = 0.016 and < 0.001, respectively) and was not modified after the 12-month follow-up in COVID-19 patients (p = 0.011 and 0.001, respectively). Higher inflammation and lower renal function during hospitalization were linked to higher aortic stiffness and reduced vessel density of the SCP 1 month after the acute phase of COVID-19. A slower recovery of aortic dysfunction was linked to worse retinal vascular outcomes at Visit 2. Conclusion: Retinal vascular alterations were not reversible 12 months after COVID-19 and were linked to inflammation and renal dysfunction during hospitalization as well as to aortic stiffness measured during follow-up.

Cymbuliaparvidentata Pelseneer, 1888 (Mollusca, Cymbuliidae) in the Ligurian Sea: further evidence of Atlantic species incursions in the Mediterranean area.

We report the first record of a stranded specimen of Cymbuliaparvidentata, a pteropod species of Atlantic origin, in the Ligurian Sea. On 27 February 2022, six C.peronii and one C.parvidentata were collected on Borgio-Verezzi Beach (Savona, Italy - 44.16° N, 8.304633° W). Specimens were examined morphologically and biometrically. Measurements (length, width, height and wet weight) separated the two taxa, C.peronii being larger than C.parvidentata. The finding of C.parvidentata, which has only occasionally been reported in southern Italy, is remarkable and may be due to ascending Atlantic water (AW) pulses that reach the Ligurian Sea. This finding adds to the previous knowledge of other pelagic species of Atlantic origin that were found in the Ligurian Sea, suggesting the possibility of major on-going changes and a general "Atlantification". In order to determine the frequency of such events, it will be highly desirable to design specific citizen-science campaigns.

Reliability of Multiparametric Magnetic Resonance Imaging in Patients with a Previous Negative Biopsy: Comparison with Biopsy-Naïve Patients in the Detection of Clinically Significant Prostate Cancer.

Background: Multiparametric magnetic resonance is an established imaging utilized in the diagnostic pathway of prostate cancer. The aim of this study is to evaluate the accuracy and reliability of multiparametric magnetic resonance imaging (mpMRI) in the detection of clinically significant prostate cancer, defined as Gleason Score ≥ 4 + 3 or a maximum cancer core length 6 mm or longer, in patients with a previous negative biopsy. Methods: The study was conducted as a retrospective observational study at the University of Naples "Federico II", Italy. Overall, 389 patients who underwent systematic and target prostate biopsy between January 2019 and July 2020 were involved and were divided into two groups: Group A, which included biopsy-naïve patients; Group B, which included re-biopsy patients. All mpMRI images were obtained using three Tesla instruments and were interpreted according to PIRADS (Prostate Imaging Reporting and Data System) version 2.0. Results: 327 patients were biopsy-naïve, while 62 belonged to the re-biopsy group. Both groups were comparable in terms of age, total PSA (prostate-specific antigen), and number of cores obtained at the biopsy. 2.2%, 8.8%, 36.1%, and 83.4% of, respectively, PIRADS 2, 3, 4, and 5 biopsy-naïve patients reported a clinically significant prostate cancer compared to 0%, 14.3%, 39%, and 66.6% of re-biopsy patients (p < 0.0001-p = 0.040). No difference was reported in terms of post-biopsy complications. Conclusions: mpMRI confirms its role as a reliable diagnostic tool prior to performing prostate biopsy in patients who underwent a previous negative biopsy, reporting a comparable detection rate of clinically significant prostate cancer.

Microvascular Changes after Scleral Buckling for Rhegmatogenous Retinal Detachment: An Optical Coherence Tomography Angiography Study.

This retrospective study aimed to investigate macular microvascular alterations after successful scleral buckling (SB) for rhegmatogenous retinal detachment (RRD). Nineteen eyes with macula-on RRD and 18 eyes with macula-off RRD were included. In all cases, an encircling band was placed. Optical coherence tomography angiography (OCTA) was performed at baseline and postoperatively. Changes in the foveal avascular zone (FAZ) area and vessel density (VD) of the superficial capillary plexus (SCP) and deep capillary plexus (DCP) were the primary outcomes. Correlations between OCTA findings and clinical variables were considered secondary outcomes. In both the macula-on and macula-off groups, the FAZ area was comparable with controls. In the macula-on group, VD in the whole SCP was lower compared with controls at both baseline (p < 0.001) and 6 months (p = 0.03), but showed a significant increase after surgery (p = 0.004). In the macula-off group, postoperative VD in both whole SCP and whole DCP was lower compared with controls (p < 0.001). In the macula-on group, there was an inverse correlation between axial length increase and SCP VD change (r = −0.508; p = 0.03). These findings demonstrated microvascular alterations after SB for RRD. However, VD impairment seems to be mitigated after surgery. A greater increase in postoperative axial length was associated with a poorer VD outcome.

Retinal thickness and microvascular pathway in Idiopathic Rapid eye movement sleep behaviour disorder and Parkinson's disease.

INTRODUCTION: Retinal impairment has previously been described in Parkinson's Disease (PD), also in early stage of disease. Idiopathic Rapid-eye-movement sleep Behavior Disorder (iRBD) is considered the strongest marker in the diagnosis of "Prodromal PD". Thus, we evaluated the thickness of retinal layers and the microvascular retinal pattern in a group of iRBD patients compared to PD and healthy subjects (HCs). METHODS: retinal layer's thickness and microvascular pattern among PD, iRBD and HCs were assessed using Spectral-Density Optical Coherence Tomography (SD-OCT) and OCT-Angiography (OCT-A), respectively. RESULTS: Forty-one eyes from 21 PD, 37 eyes from 19 iRBD and 33 eyes from 17 HCs were analysed. Peripapillary Retinal Nerve Fiber Layer (RNFL) was thinner in PD and RBD compared to HCs. All macular retinal layers, except for retinal pigment epithelium, resulted to be significantly thinner in iRBD and in PD compared to HCs, also adjusting by age, sex and hypertension. Macular RNFL and ganglionic cell layer were thinner in PD compared to iRBD. Moreover, in iRBD, a peculiar microvascular pattern was found, characterized by a higher vascularization of the deep capillary plexus with respect both PD patients and HCs. CONCLUSION: in PD and iRBD patients retina was thinner than HCs, and values of iRBD were between PD and HCs. Moreover, in iRBD, a peculiar microvascular pattern has been found, characterized by a higher vascularization of the deep capillary plexus. Our findings suggest that retina might be considered a biomarker of neurodegeneration in iRBD, easily estimable using non-invasive tool such as OCT and OCT-A.

SUMOylation in the control of cholesterol homeostasis.

SUMOylation-protein modification by the small ubiquitin-related modifier (SUMO)-affects several cellular processes by modulating the activity, stability, interactions or subcellular localization of a variety of substrates. SUMO modification is involved in most cellular processes required for the maintenance of metabolic homeostasis. Cholesterol is one of the main lipids required to preserve the correct cellular function, contributing to the composition of the plasma membrane and participating in transmembrane receptor signalling. Besides these functions, cholesterol is required for the synthesis of steroid hormones, bile acids, oxysterols and vitamin D. Cholesterol levels need to be tightly regulated: in excess, it is toxic to the cell, and the disruption of its homeostasis is associated with various disorders like atherosclerosis and cardiovascular diseases. This review focuses on the role of SUMO in the regulation of proteins involved in the metabolism of cholesterol.

Distributional records of Ross Sea (Antarctica) planktic Copepoda from bibliographic data and samples curated at the Italian National Antarctic Museum (MNA): checklist of species collected in the Ross Sea sector from 1987 to 1995.

Distributional data on planktic copepods (Crustacea, Copepoda) collected in the framework of the IIIrd, Vth, and Xth Expeditions of the Italian National Antarctic Program (PNRA) to the Ross Sea sector from 1987 to 1995 are here provided. Sampling was performed with BIONESS and WP2 nets at 94 sampling stations at depths of 0-1,000 m, with a special focus on the Terra Nova Bay area. Altogether, this dataset comprises 6,027 distributional records, out of which 5,306 were obtained by digitizing original data reports and 721 are based on physical museum vouchers curated by the Italian National Antarctic Museum (MNA, Section of Genoa). The MNA samples include 8,224 individual specimens that were identified to the lowest possible taxonomic level. They belong to four orders, 25 families, 52 genera, and 82 morphological units (out of which 17 could be determined at the genus level only). A variety of environmental data were also recorded at each of the sampling stations, and we report original abundances (ind/m3) to enable future species distribution modelling. From a biogeographic point of view, the distributional data here reported represented new records for the Global Biogeographic Information Facility (GBIF) registry. In particular, 62% of the total number of species are new records for the Ross Sea sector and another 28% new records for the Antarctic region.

Retinal Thickness and Microvascular Pattern in Early Parkinson's Disease.

A thinning of intraretinal layers has been previously described in Parkinson's disease (PD) patients compared to healthy controls (HCs). Few studies evaluated the possible correlation between retinal thickness and retinal microvascularization. Thus, here we assessed the thickness of retinal layers and microvascular pattern in early PD patients and HCs, using, respectively, spectral-domain optical coherence tomography (SD-OCT) and SD-OCT-angiography (SD-OCT-A), and more interestingly, we evaluated a possible correlation between retinal thickness and microvascular pattern. Patients fulfilling criteria for clinically established/clinically probable PD and HCs were enrolled. Exclusion criteria were any ocular, retinal, and systemic disease impairing the visual system. Retinal vascularization was analyzed using SD-OCT-A, and retinal layer thickness was assessed using SD-OCT. Forty-one eyes from 21 PD patients and 33 eyes from 17 HCs were evaluated. Peripapillary retinal nerve fiber layer (RNFL) and macular RNFL, ganglionic cell layer (GCL), inner plexiform layer (IPL), and inner nuclear layer (INL), resulted to be thinner in PD compared to HCs. Among PD patients, a positive correlation between RNFL, GCL, and IPL thickness and microvascular density was found in the foveal region, also adjusting by age, sex, and, especially, hypertension. Such findings were already present in the early stage of disease and were irrespective of dopaminergic treatment. Thus, the retina might be considered a biomarker of PD and could be a useful instrument for onset and disease progression.

Is it possible to reconstruct an accurate cell lineage using CRISPR recorders?

Cell lineages provide the framework for understanding how cell fates are decided during development. Describing cell lineages in most organisms is challenging; even a fruit fly larva has ~50,000 cells and a small mammal has >1 billion cells. Recently, the idea of applying CRISPR to induce mutations during development, to be used as heritable markers for lineage reconstruction, has been proposed by several groups. While an attractive idea, its practical value depends on the accuracy of the cell lineages that can be generated. Here, we use computer simulations to estimate the performance of these approaches under different conditions. We incorporate empirical data on CRISPR-induced mutation frequencies in Drosophila. We show significant impacts from multiple biological and technical parameters - variable cell division rates, skewed mutational outcomes, target dropouts and different sequencing strategies. Our approach reveals the limitations of published CRISPR recorders, and indicates how future implementations can be optimised. Editorial note: This article has been through an editorial process in which the authors decide how to respond to the issues raised during peer review. The Reviewing Editor's assessment is that all the issues have been addressed (see decision letter).

Old questions, new models: unraveling complex organ regeneration with new experimental approaches.

How do some animals like crabs, flatworms and salamanders regenerate entire body parts after a severe injury? Which are the mechanisms and how did that regenerative ability evolve over time? The ability to regenerate complex organs is widespread in the animal kingdom, but fundamental, centuries-old questions remain unanswered. Forward genetics approaches that were so successful in probing embryonic development are lacking in most regenerative models, and candidate gene approaches can be biased and misleading. We summarize recent progress in establishing new genetic tools and approaches to study regeneration and provide a personal perspective on the feasibility and value of establishing such tools, based on our experience with a new experimental model, the crustacean Parhyale hawaiensis.

The genome of the crustacean Parhyale hawaiensis, a model for animal development, regeneration, immunity and lignocellulose digestion.

The amphipod crustacean Parhyale hawaiensis is a blossoming model system for studies of developmental mechanisms and more recently regeneration. We have sequenced the genome allowing annotation of all key signaling pathways, transcription factors, and non-coding RNAs that will enhance ongoing functional studies. Parhyale is a member of the Malacostraca clade, which includes crustacean food crop species. We analysed the immunity related genes of Parhyale as an important comparative system for these species, where immunity related aquaculture problems have increased as farming has intensified. We also find that Parhyale and other species within Multicrustacea contain the enzyme sets necessary to perform lignocellulose digestion ('wood eating'), suggesting this ability may predate the diversification of this lineage. Our data provide an essential resource for further development of Parhyale as an experimental model. The first malacostracan genome will underpin ongoing comparative work in food crop species and research investigating lignocellulose as an energy source.

Development: a deep breath for endocrine organ evolution.

Developmental biologists have made surprising discoveries on the evolutionary origins of cell types, organs and body plans. Now, an elegant study in Drosophila raises interesting questions about the origin of two major endocrine organs of insects.

Conserved and divergent elements in Torso RTK activation in Drosophila development.

The repeated use of signalling pathways is a common phenomenon but little is known about how they become co-opted in different contexts. Here we examined this issue by analysing the activation of Drosophila Torso receptor in embryogenesis and in pupariation. While its putative ligand differs in each case, we show that Torso-like, but not other proteins required for Torso activation in embryogenesis, is also required for Torso activation in pupariation. In addition, we demonstrate that distinct enhancers control torso-like expression in both scenarios. We conclude that repeated Torso activation is linked to a duplication and differential expression of a ligand-encoding gene, the acquisition of distinct enhancers in the torso-like promoter and the recruitment of proteins independently required for embryogenesis. A combination of these mechanisms is likely to allow the repeated activation of a single receptor in different contexts.

Control of germline torso expression by the BTB/POZ domain protein pipsqueak is required for embryonic terminal patterning in Drosophila.

Early embryogenesis in Drosophila melanogaster is controlled by maternal gene products, which are deposited in the egg during oogenesis. It is not well understood how maternal gene expression is controlled during germline development. pipsqueak (psq) is a complex locus that encodes several nuclear protein variants containing a PSQ DNA-binding domain and a BTB/POZ domain. Psq proteins are thought to regulate germline gene expression through epigenetic silencing. While psq was originally identified as a posterior-group gene, we show here a novel role of psq in embryonic terminal patterning. We characterized a new psq loss-of-function allele, psq(rum), which specifically affects signaling by the Torso (Tor) receptor tyrosine kinase (RTK). Using genetic epistasis, gene expression analyses, and rescue experiments, we demonstrate that the sole function impaired by the psq(rum) mutation in the terminal system is an essential requirement for controlling transcription of the tor gene in the germline. In contrast, the expression of several other maternal genes, including those encoding Tor pathway components, is not affected by the mutation. Rescue of the psq(rum) terminal phenotype does not require the BTB/POZ domain, suggesting that the PSQ DNA-binding domain can function independently of the BTB/POZ domain. Our finding that tor expression is subject to dedicated transcriptional regulation suggests that different maternal genes may be regulated by multiple distinct mechanisms, rather than by a general program controlling nurse-cell transcription.