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Gonadal development is a complex process that involves sex determination followed by divergent maturation into either testes or ovaries 1 . Historically, limited tissue accessibility, a lack of reliable in vitro models and critical differences between humans and mice have hampered our knowledge of human gonadogenesis, despite its importance in gonadal conditions and infertility. Here, we generated a comprehensive map of first- and second-trimester human gonads using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays and fluorescent microscopy. We extracted human-specific regulatory programmes that control the development of germline and somatic cell lineages by profiling equivalent developmental stages in mice. In both species, we define the somatic cell states present at the time of sex specification, including the bipotent early supporting population that, in males, upregulates the testis-determining factor SRY and sPAX8s, a gonadal lineage located at the gonadal–mesonephric interface. In females, we resolve the cellular and molecular events that give rise to the first and second waves of granulosa cells that compartmentalize the developing ovary to modulate germ cell differentiation. In males, we identify human SIGLEC15 + and TREM2 + fetal testicular macrophages, which signal to somatic cells outside and inside the developing testis cords, respectively. This study provides a comprehensive spatiotemporal map of human and mouse gonadal differentiation, which can guide in vitro gonadogenesis. This study provides a comprehensive spatiotemporal map of human and mouse gonadal differentiation, using a combination of single-cell and spatial transcriptomics, chromatin accessibility assays and fluorescent microscopy, which can guide in vitro gonadogenesis.

The endometrium, the mucosal lining of the uterus, undergoes dynamic changes throughout the menstrual cycle in response to ovarian hormones. We have generated dense single-cell and spatial reference maps of the human uterus and three-dimensional endometrial organoid cultures. We dissect the signaling pathways that determine cell fate of the epithelial lineages in the lumenal and glandular microenvironments. Our benchmark of the endometrial organoids reveals the pathways and cell states regulating differentiation of the secretory and ciliated lineages both in vivo and in vitro. In vitro downregulation of WNT or NOTCH pathways increases the differentiation efficiency along the secretory and ciliated lineages, respectively. We utilize our cellular maps to deconvolute bulk data from endometrial cancers and endometriotic lesions, illuminating the cell types dominating in each of these disorders. These mechanistic insights provide a platform for future development of treatments for common conditions including endometriosis and endometrial carcinoma. Single-cell and spatial transcriptomic profiling of the human endometrium highlights pathways governing the proliferative and secretory phases of the menstrual cycle. Analyses of endometrial organoids show that WNT and NOTCH signaling modulate differentiation into the secretory and ciliated epithelial lineages, respectively.

Multiomic droplet-based technologies allow different molecular modalities, such as chromatin accessibility and gene expression (scATAC-seq and scRNA-seq), to be probed in the same nucleus. We develop EmptyDropsMultiome, an approach that distinguishes true nuclei-containing droplets from background. Using simulations, we show that EmptyDropsMultiome has higher statistical power and accuracy than existing approaches, including CellRanger-arc and EmptyDrops. On real datasets, we observe that CellRanger-arc misses more than half of the nuclei identified by EmptyDropsMultiome and, moreover, is biased against certain cell types, some of which have a retrieval rate lower than 20%.

Myeloid cells are central to homeostasis and immunity. Characterising in vitro myelopoiesis protocols is imperative for their use in research, immunotherapies, and understanding human myelopoiesis. Here, we generate a >470K cells molecular map of human induced pluripotent stem cells (iPSC) differentiation into macrophages. Integration with in vivo single-cell atlases shows in vitro differentiation recapitulates features of yolk sac hematopoiesis, before definitive hematopoietic stem cells (HSC) emerge. The diversity of myeloid cells generated, including mast cells and monocytes, suggests that HSC-independent hematopoiesis can produce multiple myeloid lineages. We uncover poorly described myeloid progenitors and conservation between in vivo and in vitro regulatory programs. Additionally, we develop a protocol to produce iPSC-derived dendritic cells (DC) resembling cDC2. Using CRISPR/Cas9 knock-outs, we validate the effects of key transcription factors in macrophage and DC ontogeny. This roadmap of myeloid differentiation is an important resource for investigating human fetal hematopoiesis and new therapeutic opportunities. The myeloid lineage is central to homeostasis and immunity. The authors provide an atlas of human iPSC-to-myeloid cell differentiation and demonstrate that the in vitro system recapitulates yolk sac differentiation, opening new avenues to human myelopoiesis.

Antimicrobial use (AMU) in livestock species and the associated antimicrobial resistance are a global concern, thus strategies for their reduction and a more judicious use are needed. Previous research has revealed a link between improved animal welfare, biosecurity and AMU reduction in pig and dairy sectors, however, little is known about the beef sector. This study aimed to investigate the impact of welfare standards and biosecurity on AMU in beef cattle. Data on performance traits and AMU were collected over a 3.5 year time from 27 specialised beef farms and a treatment incidence was calculated using the defined daily dose for animals. An on-farm assessment was carried out by assigning a score from 0 (very poor) to 100% (very good) to 3 sections: welfare, biosecurity and emergency management. The highest average score was obtained for the welfare section (76%) followed by emergency management (39%) and biosecurity (24%). This suggests that major focus on strategies for the implementation of biosecurity measures and emergency management is needed, due to the low scores reported. A statistically significant lower AMU was observed with improved level of welfare. These results may be helpful for farm benchmarking and highlight the importance of improved animal welfare for an efficient antimicrobial stewardship.

Honey bees are vital to ecosystem conservation, agricultural production, and biodiversity, yet their welfare has often been overlooked. This study introduces the integration of Honey Bee Welfare Practices (HBWPs) into the One Welfare framework, addressing the interconnectedness of honey bee welfare, environmental welfare, and human wellbeing. We analysed and re-evaluated the 243 HBWPs already identified and categorised within the context of the Five Domains model in 2024 by Giovanni Formato et al., and we explored their broader impacts. By incorporating the One Welfare approach, we assessed each practice’s effect on bee welfare both as individuals and as a superorganism, human wellbeing, and environmental welfare, as well as their economic and time-related implications for beekeepers. The aim of this study was to obtain a list of One Welfare Practices in Beekeeping, considering all stakeholders as equally important. The analysis highlights the multidimensional nature of beekeeping, with 280 practices positively affecting honey bee welfare, while also considering their potential impact on human wellbeing, environmental health, and production. Challenges such as balancing beekeeper time constraints and welfare goals are discussed, with recommendations for practical compromises. This approach can offer a holistic and sustainable model for apiculture, ensuring that welfare is maintained across all stakeholders, and provides a flexible framework applicable to various beekeeping systems worldwide.

We investigated the effect of the welfare level measured with the Italian ClassyFarm protocol on bulk milk quality traits, differentiating between loose (LHS) and tied housing system (THS). The overall welfare ClassyFarm score combines the scores of management, biosecurity, structures, and animal-based measures. The scores of 89 THS farms and 105 LHS farms located in Northern Italy were merged with the milk analyses carried out in 2022 for milk payment systems (n = 6971). The fixed effects of welfare level (3 classes: <65%, insufficient; 65–84%, intermediate; and ≥85%, excellent), type of housing system, month, and interaction between type of housing system and welfare score were tested. Herd season was the random effect. On average, the THS farms' welfare score was 72.56%, while LHS farms had a score equal to 78.82%. For THS, 80 farms were intermediate, 4 excellent, and 5 insufficient, while for LHS, 79 were intermediate, 21 excellent, and 5 insufficient. A significant effect of welfare level was found for lactose, total bacterial count (TBC), and fat-to-protein ratio. The first-order interaction affected more traits, namely fat, protein, and casein content, somatic cell score and TBC. Farms classified as insufficient exhibited the worst/highest somatic cell score and TBC and the lowest lactose content. Results indicated that rearing conditions, here evaluated with the ClassyFarm protocol, affect bulk milk quality. At the same time, this system presents a multifaceted nature, owing to the intricate interactions among various factors. Additional research is warranted to provide clearer insights and a better understanding of cause-and-effect relationships.

The urokinase receptor (uPAR) is a glycosylphosphatidylinositol (GPI)-anchored protein that promotes tissue remodeling, tumor cell adhesion, migration and invasion. uPAR mediates degradation of the extracellular matrix through protease recruitment and enhances cell adhesion, migration and signaling through vitronectin binding and interactions with integrins. Full-length uPAR is released from the cell surface, but the mechanism and significance of uPAR shedding remain obscure. Here we identify transmembrane glycerophosphodiesterase GDE3 as a GPI-specific phospholipase C that cleaves and releases uPAR with consequent loss of function, whereas its homologue GDE2 fails to attack uPAR. GDE3 overexpression depletes uPAR from distinct basolateral membrane domains in breast cancer cells, resulting in a less transformed phenotype, it slows tumor growth in a xenograft model and correlates with prolonged survival in patients. Our results establish GDE3 as a negative regulator of the uPAR signaling network and, furthermore, highlight GPI-anchor hydrolysis as a cell-intrinsic mechanism to alter cell behavior. Every process in the body, from how cells divide to how they move around, is tightly regulated. For example, cells only migrate when they receive the correct signals from their environment. These signals are recognised by receptor proteins that sit on the cell surface and connect the outside signal with the cell’s response. However, in cancer cells, these processes are out of control, which is why cancer cells can grow very quickly or spread to many different parts of the body. One important receptor protein is the urokinase receptor, which helps to reorganize the tissue, for example, when wounds heal, but also enables cancer cells to grow and spread. A special feature of urokinase receptor is the way it is connected to the cell surface, namely through a molecule that acts as an anchor, called the GPI anchor. The urokinase receptor and some other GPI-anchored proteins can be released from their anchor. However, until now it was not clear why and how the urokinase receptor is released from cells, or how losing the receptor affects the cell. Now, van Veen, Matas-Rico et al. studied breast cancer cells, and discovered that an enzyme called GDE3 cuts the urokinase receptor off its GPI anchor to release the receptor from the cells. However, when breast cancer cells shed the urokinase receptor, they also lost the receptor from the cell surface in specific areas. As a result, the receptor could not work anymore. When breast cancer cells were experimentally modified to produce high levels of GDE3, the cancer cells became less mobile and aggressive. Van Veen, Matas-Rico et al. then implanted ‘normal’ breast cancer cells, and breast cancer cells with extra GDE3 into mice, and observed that the tumors of mice with additional GDE3 grew less quickly. Moreover, breast cancer patients with high levels of GDE3 tend to live longer than patients with low levels of GDE3. These results suggest that the enzyme GDE3 can suppress tumor growth. These findings uncover a new way how cells can alter their behavior, namely by cleaving GPI anchors at the cell surface. Future experiments will need to address how GDE3 itself is controlled, and if it releases other GPI-anchored proteins from cells. Once we know how to increase GDE3 activity in tumor cells, the new knowledge could one day lead to therapies to help patients with cancer.

On-farm emergency slaughter (OFES) is employed when cattle are unfit for transport but still suitable for human consumption, thereby ensuring animal welfare and reducing food waste. This study analysed OFES patterns in Northern Italy, where a large cattle population is housed but information on the practice is rarely analysed. A total of 12,052 OFES cases from 2021 to 2023 were analysed. Most involved female cattle (94%) from dairy farms (79%). Locomotor disorders were the leading reason (70%), particularly trauma and fractures, followed by recumbency (13%) and calving-related issues (10%). Post-mortem findings showed limbs and joints as the most frequent condemnation sites (36%), often linked to trauma. A significant reduction in OFES cases occurred over time, mainly due to fewer recumbency and calving issues, likely reflecting stricter eligibility criteria introduced in 2022. Weekly variations, with peaks on Mondays and lows on Saturdays, suggest that logistical constraints may sometimes influence OFES promptness. These findings suggest that on-farm management and animal handling could be improved further to reduce welfare risks and carcass waste. Due to the lack of standardised data collection and regulatory harmonisation, a multi-country investigation could improve our understanding of this topic and inform best practice.

Poor welfare can exist also in animals that appear healthy and productive, and its negative outcomes become evident only when coping mechanisms fail, leading to issues like illness, lack of productivity, infertility, and behavioral anomalies (Bottaccioli and Rulli, 2014;Fraser, 2008;Moberg, 1985;Sandfoss et al., 2020;Yeates, 2024). Since the beginning of the 21st century, ensuring good levels of animal welfare has shown to improve production outcomes, maintain healthy animals, and reduce intervention costs (Fernandes et al., 2021), while enhancing the living conditions of animals, humans, and the environment in various aspects, including social, health, economic, behavioral, and mental domains (Bayvel, 2004;Beausoleil and Mellor, 2015;Browning, 2022). 1.1 Apis mellifera welfare definition: current state and development The concept of welfare has been explored through various lenses, primarily focusing on either the subjective experiences and consciousness (Experience Welfare) or on the physical health, biological functioning, and the ability of animals to perform natural behaviors (Functional Welfare) (Birch, 2022;Mellor, 2016). [...]the welfare of insects in captivity encompasses a complex array of issues, like stress, loss of individual choice, suffering, pain and sentience (Boppré and Vane-Wright, 2019). Even in the absence of conclusive evidence of sentience, the precautionary principle and the Terrestrial Animal Code (WOAH, 2013), along with the Animal Welfare Act, grant welfare considerations to all animals (Birch, 2017;Knutsson and Munthe, 2017;Lundmark et al., 2013). [...]animal welfare assessments should be carried out also in the beekeeping sector and the methods used can be supported by established Good Beekeeping Practices and Biosecurity Measures and can benefit from comprehensive data and insights from surveys, studies, beekeeper experiences, and in-hive monitoring (Precision Beekeeping).