Embryonic Development Research Articles

Mechanical forces orchestrate the metabolism of the developing oilseed rape embryo.

The initial free expansion of the embryo within a seed is at some point inhibited by its contact with the testa, resulting in its formation of folds and borders. Although less obvious, mechanical forces appear to trigger and accelerate seed maturation. However, the mechanistic basis for this effect remains unclear. Manipulation of the mechanical constraints affecting either the in vivo or in vitro growth of oilseed rape embryos was combined with analytical approaches, including magnetic resonance imaging and computer graphic reconstruction, immunolabelling, flow cytometry, transcriptomic, proteomic, lipidomic and metabolomic profiling. Our data implied that, in vivo, the imposition of mechanical restraints impeded the expansion of testa and endosperm, resulting in the embryo's deformation. An acceleration in embryonic development was implied by the cessation of cell proliferation and the stimulation of lipid and protein storage, characteristic of embryo maturation. The underlying molecular signature included elements of cell cycle control, reactive oxygen species metabolism and transcriptional reprogramming, along with allosteric control of glycolytic flux. Constricting the space allowed for the expansion of in vitro grown embryos induced a similar response. The conclusion is that the imposition of mechanical constraints over the growth of the developing oilseed rape embryo provides an important trigger for its maturation.

Sperm-borne miR-34c-5p and miR-191-3p as markers for sperm motility and embryo developmental competence.

Sperm-borne microRNAs play a pivotal role in influencing essential cellular processes during fertilization, impacting the quality of embryo development. Dysregulated microRNA profiles have been associated with compromised embryonic development and increased incidences of pregnancy loss. This study aimed to investigate the potential associations between the abundance of miR-34c-5p and miR-191-3p in human spermatozoa with sperm quality, as well as with embryo quality and metabolic performance during in vitro development. Thirteen couples who underwent a total of 13 cycles participated in this study. The sperm quality was assessed using conventional methods following World Health Organization guidelines. Quantitative polymerase chain reaction was employed to measure microRNA abundance in spermatozoa. Embryos were categorized as good, lagging, or bad based on morphokinetic evaluation. Evaluation of embryo metabolic performance involved tracking changes in specific metabolites within the cultured media using nuclear magnetic resonance spectroscopy. Statistical analysis was conducted to explore the correlation between microRNA abundance in human spermatozoa and all other collected data. Our findings revealed a negative correlation between the abundance of miR-34c-5p (but not miR-191-3p) and total sperm motility, potentially mediated by the modulation of key signaling pathways. Additionally, higher levels of miR-34c-5p in spermatozoa were strongly associated with the consumption or release of key metabolites by developing embryos, particularly those linked with lipid and glucose metabolism, suggesting enhanced metabolic performance, while miR-191-3p was mostly associated with glucose consumption. Concurrently, only miR-34c-5p content in spermatozoa correlated with higher embryo quality. This study provides evidence suggesting that the abundance of miR-34c-5p in spermatozoa is correlated not only with total sperm motility but also with markers of embryo developmental competence, highlighting the potential significance of this sperm microRNA content as a biomarker in assisted reproduction.

Bioelectret Materials and Their Bioelectric Effects for Tissue Repair: A Review.

Biophysical and clinical medical studies have confirmed that biological tissue lesions and trauma are related to the damage of an intrinsic electret (i.e., endogenous electric field), such as wound healing, embryonic development, the occurrence of various diseases, immune regulation, tissue regeneration, and cancer metastasis. As exogenous electrical signals, such as conductivity, piezoelectricity, ferroelectricity, and pyroelectricity, bioelectroactives can regulate the endogenous electric field, thus controlling the function of cells and promoting the repair and regeneration of tissues. Materials, once polarized, can harness their inherent polarized static electric fields to generate an electric field through direct stimulation or indirect interactions facilitated by physical signals, such as friction, ultrasound, or mechanical stimulation. The interaction with the biological microenvironment allows for the regulation and compensation of polarized electric signals in damaged tissue microenvironments, leading to tissue regeneration and repair. The technique shows great promise for applications in the field of tissue regeneration. In this paper, the generation and change of the endogenous electric field and the regulation of exogenous electroactive substances are expounded, and the latest research progress of the electret and its biological effects in the field of tissue repair include bone repair, nerve repair, drug penetration promotion, wound healing, etc. Finally, the opportunities and challenges of electret materials in tissue repair were summarized. Exploring the research and development of new polarized materials and the mechanism of regulating endogenous electric field changes may provide new insights and innovative methods for tissue repair and disease treatment in biological applications.

Benzo(a)pyrene exposure impacts cerebrovascular development in zebrafish embryos and the antagonistic effect of berberine

Polycyclic aromatic hydrocarbons (PAHs) widely present in the environment, but their effect on cerebrovascular development has been rarely reported. In this study, dechorionated zebrafish embryos at 24 hpf were exposed to benzo(a)pyrene (BaP) at 0.5, 5 and 50 nM for 48 h, cerebrovascular density showed a significant reduction in the 5 and 50 nM groups. The expression of aryl hydrocarbon receptor (AhR) was significantly increased. Transcriptomic analysis showed that the pathway of positive regulation of vascular development was down-regulated and the pathway of inflammation response was up-regulated. The transcription of main genes related to vascular development, such as vegf, bmper, cdh5, f3b, itgb1 and prkd1, was down-regulated. Addition of AhR-specific inhibitor CH233191 in the 50 nM BaP group rescued cerebrovascular developmental defects and down-regulation of relative genes, suggesting that BaP-induced cerebrovascular defects was AhR-dependent. The cerebrovascular defects were persistent into adult fish raised in clean water, showing that the relative area of vascular network, the length of vessels per unit area and the number of vascular junctions per unit area were significantly decreased in the 50 nM group. Supplementation of berberine (BBR), a naturally derived medicine from a Chinese medicinal herb, alleviated BaP-induced cerebrovascular defects, accompanied by the restoration of altered expression of AhR and relative genes, which might be due to that BBR promoted BaP elimination via enhancing detoxification enzyme activities, suggesting that BBR could be a potential agent in the prevention of cerebrovascular developmental defects caused by PAHs.

Local differences in robustness to ocean acidification.

Ocean acidification (OA) caused by increased atmospheric carbon dioxide is affecting marine systems a globally and is more extreme in coastal waters. A wealth of research to determine how species will be affected by OA, now and in the future, is emerging. Most studies are discrete and generally do not include the full life cycle of animals. Studies that include the potential for adaptation responses of animals from areas with different environmental conditions and the most vulnerable life stages are needed. Therefore, we conducted experiments with the widely-distributed blue mussel, Mytilus edulis, from populations regularly exposed to different OA conditions. Mussels experienced experimental conditions prior to spawning, through embryonic and larval development, a highly vulnerable stage. Survivorship to metamorphosis of larvae from all populations was negatively affected by extreme OA conditions (pH 7.3, Ωar, 0.39, pCO2 2479.74), but, surprisingly, responses to Mid OA (pH 7.6, Ωar 0.77, pCO21167.13) and Low OA (pH 7.9, Ωar 1.53, pCO2 514.50) varied among populations. Two populations were robust and showed no effect of OA on survivorship in this range. One population displayed the expected negative effect on survivorship with increased OA. Unexpectedly survivorship in the fourth population was highest under Mid OA conditions. There were also significant differences in development time among populations that were unaffected by OA. These results suggest that adaptation to OA may already be present in some populations and emphasizes the importance of testing animals from different populations to see the potential for adaptation to OA.

RNA sequencing analysis of sexual dimorphism in Japanese quail

IntroductionJapanese quail are of significant economic value, providing protein nutrition to humans through their reproductive activity; however, sexual dimorphism in this species remains relatively unexplored compared with other model species.MethodA total of 114 RNA sequencing datasets (18 and 96 samples for quail and chicken, respectively) were collected from existing studies to gain a comprehensive understanding of sexual dimorphism in quail. Cross-species integrated analyses were performed with transcriptome data from evolutionarily close chickens to identify sex-biased genes in the embryonic, adult brain, and gonadal tissues.ResultsOur findings indicate that the expression patterns of genes involved in sex-determination mechanisms during embryonic development, as well as those of most sex-biased genes in the adult brain and gonads, are identical between quails and chickens. Similar to most birds with a ZW sex determination system, quails lacked global dosage compensation for the Z chromosome, resulting in directional outcomes that supported the hypothesis that sex is determined by the individual dosage of Z-chromosomal genes, including long non-coding RNAs located in the male hypermethylated region. Furthermore, genes, such as WNT4 and VIP, reversed their sex-biased patterns at different points in embryonic development and/or in different adult tissues, suggesting a potential hurdle in breeding and transgenic experiments involving avian sex-related traits.DiscussionThe findings of this study are expected to enhance our understanding of sexual dimorphism in birds and subsequently facilitate insights into the field of breeding and transgenesis of sex-related traits that economically benefit humans.

Effects of maternal androgens and their metabolite etiocholanolone on prenatal development in birds.

Offspring phenotypes can be affected by maternal testosterone (T) and androstenedione (A4), which are considered a tool of mothers to adjust offspring in a fluctuating environment. Yet T and A4 are found to be very rapidly metabolized by developing avian embryos, suggesting that either the maternal T and A4 have potent organizational effects on the embryos extremely early before being metabolized or it's the metabolites that evoke phenotypic variation in the offspring. One of the metabolites, etiocholanolone, increases substantially during early embryonic development and is a likely candidate for mediating maternal effects as it can promote erythropoiesis. To investigate and compare the effects of T and A4 with the possible effects of etiocholanolone during prenatal embryonic development, we increased their levels in Black-headed gull eggs (Larus ridibundus), and used sham-injected eggs as controls. This species usually has 3-egg clutches in which maternal androgen levels increase with the egg-laying sequence. We analyzed embryonic heart rates, peri-hatching biometric traits, the ratio of white to red blood cells (W/R), and bursa development. We found that T and A4 treatment increased embryonic heart rate irrespective of egg-laying sequence, decreased bill length and W/R, whereas etiocholanolone did not mimic these effects. Instead, etiocholanolone treatment decreased tarsus length and brain mass. Our finding that etiocholanolone does not mimic the effects induced by T and A4 suggests that the embryonic metabolism of maternal T and A4 can potentially diversify the function of these maternal androgens.

3D-bioprinted gelatin methacryloyl hydrogel culture system emulating the oviduct environment for enhanced preimplantation embryo development

3D-bioprinted gelatin methacryloyl hydrogel culture system emulating the oviduct environment for enhanced preimplantation embryo development

Exploring Differentially Expressed Sperm miRNAs in Idiopathic Recurrent Pregnancy Loss and Their Association with Early Embryonic Development

The high incidence of idiopathic recurrent pregnancy loss (iRPL) may stem from the limited research on male contributory factors. Many studies suggest that sperm DNA fragmentation and oxidative stress contribute to iRPL, but their roles are still debated. MicroRNAs (miRNAs) are short non-coding RNAs that regulate various biological processes by modulating gene expression. While differential expression of specific miRNAs has been observed in women suffering from recurrent miscarriages, paternal miRNAs remain unexplored. We hypothesize that analyzing sperm miRNAs can provide crucial insights into the pathophysiology of iRPL. Therefore, this study aims to identify dysregulated miRNAs in the spermatozoa of male partners of iRPL patients. Total mRNA was extracted from sperm samples of iRPL and control groups, followed by miRNA library preparation and high-output miRNA sequencing. Subsequently, raw sequence reads were processed for differential expression analysis, target prediction, and bioinformatics analysis. Twelve differentially expressed miRNAs were identified in the iRPL group, with eight miRNAs upregulated (hsa-miR-4454, hsa-miR-142-3p, hsa-miR-145-5p, hsa-miR-1290, hsa-miR-1246, hsa-miR-7977, hsa-miR-449c-5p, and hsa-miR-92b-3p) and four downregulated (hsa-miR-29c-3p, hsa-miR-30b-5p, hsa-miR-519a-2-5p, and hsa-miR-520b-5p). Functional enrichment analysis revealed that gene targets of the upregulated miRNAs are involved in various biological processes closely associated with sperm quality and embryonic development.

Agenecy of the corposion callosum: report of a clinical case

The agenesis of the corpus callosum (ACC) supposes an interhemispheric disconnection due to lack of formation of said structure in the embryonic development. Prevalence: 0.3-0.5% in the general population and 2.3% in people with disabilities. It is associated with prematurity and advanced maternal age. Agenesis of the corpus callosum is a malformation that can occur in isolation or in association with other systemic or central nervous system disorders and is one of the most common malformations in the brain, with an estimated prevalence of 1 in 4,000 live births. Among the most common clinical findings are mental retardation, visual problems, and seizures. Prenatal diagnosis can be made by ultrasound and magnetic resonance imaging from the 20th week of gestation. Postnatal diagnosis can be made by ultrasound, computed tomography, and magnetic resonance imaging. Currently, there is no specific treatment, although it has been proposed to start an early stimulation program and, if possible, a psychomotor rehabilitation program that offers improvement in motor and learning disorders.

Adult-onset deletion of ATP13A2 in mice induces progressive nigrostriatal pathway dopaminergic degeneration and lysosomal abnormalities

Although most cases of Parkinson’s disease (PD) are sporadic, mutations in over 20 genes are known to cause heritable forms of the disease. Recessive loss-of-function mutations in ATP13A2, a lysosomal transmembrane P5B-type ATPase and polyamine exporter, can cause early-onset familial PD. Familial ATP13A2 mutations are also linked to related neurodegenerative diseases, including Kufor-Rakeb syndrome, hereditary spastic paraplegias, neuronal ceroid lipofuscinosis, and amyotrophic lateral sclerosis. Despite the severe effects of ATP13A2 mutations in humans, ATP13A2 knockout (KO) mice fail to exhibit neurodegeneration even at advanced ages, making it challenging to study the neuropathological effects of ATP13A2 loss in vivo. Germline deletion of ATP13A2 in rodents may trigger the upregulation of compensatory pathways during embryonic development that mask the full neurotoxic effects of ATP13A2 loss in the brain. To explore this idea, we selectively deleted ATP13A2 in the adult mouse brain by the unilateral delivery of an AAV-Cre vector into the substantia nigra of young adult mice carrying conditional loxP-flanked ATP13A2 KO alleles. We observe a progressive loss of striatal dopaminergic nerve terminals at 3 and 10 months after AAV-Cre delivery. Cre-injected mice also exhibit robust dopaminergic neuronal degeneration in the substantia nigra at 10 months. Adult-onset ATP13A2 KO also recreates many of the phenotypes observed in aged germline ATP13A2 KO mice, including lysosomal abnormalities, p62-positive inclusions, and neuroinflammation. Our study demonstrates that the adult-onset homozygous deletion of ATP13A2 in the nigrostriatal pathway produces robust and progressive dopaminergic neurodegeneration that serves as a useful in vivo model of ATP13A2-related neurodegenerative diseases.

Modelling the effect of cell motility on mixing and invasion in epithelial monolayers.

Collective cell invasion underlies several biological processes such as wound healing, embryonic development, and cancerous invasion. Here, we investigate the impact of cell motility on invasion in epithelial monolayers and its coupling to cellular mechanical properties, such as cell-cell adhesion and cortex contractility. We develop a two-dimensional computational model for cells with active motility based on the cellular Potts model, which predicts that the cellular invasion speed is mainly determined by active cell motility and is independent of the biological and mechanical properties of the cells. We also find that, in general, motile cells out-compete and invade non-motile cells, however, this can be reversed by differential cell proliferation. Stable coexistence of motile and static cell types is also possible for certain parameter regimes.

Ontogenic transformation of the ankle from the initial mediolateral arrangement of the calcaneus and talus: Ahistological study of human embryos and early fetuses.

The human calcaneus is robust and provides a prominent heel for effective bipedal locomotion, although the adjacent talus has no muscle attachments. However, there is incomplete information about the morphological changes in these prominent bones during embryo development. We examined serial histological sections of 23 human embryos and early-term fetuses (approximately 5-10 weeks' gestational age [GA]). At a GA of 5 weeks, the precartilage talus was parallel to and on the medial side of the calcaneus, which had a prolate spheroid shape and consisted of three masses. At a GA of 6 weeks, the cartilaginous talus extended along the proximodistal axis, and the tuber calcanei became long and bulky, with a small sustentaculum talus at the "distal" side. At a GA of 6 to 8 weeks, the sustentaculum had a medial extension below the talus so that the talus "rode over" the calcaneus. In contrast, the talus had a more complex shape, depending on the growth of adjacent bones. At a GA of 9 to 10 weeks, the talus was above the calcaneus, but the medial part still faced the plantar subcutaneous tissue because of the relatively small sustentaculum. Therefore, the final morphology appeared after an additional several weeks. Muscle activity seemed to facilitate growth of the tuber calcanei, but growth of the other parts of calcaneus, including the sustentaculum, seemed to depend on active proliferation at the different sites of cartilage. Multiple tendons and ligaments seemed to fix the talus so that it remained close to the calcaneus.

Impact of fluazuron on oocyte maturation: May the antiparasitic affect bovine reproduction?

Fluazuron is a novel veterinary pour-on antitick formulation which can be applied simultaneously with bovine reproduction management strategies. Considering the economic importance of the livestock industry in many countries, it is important to know whether antiparasitics such as fluazuron may cause embryonic loss. The aim of this study was to evaluate the toxicological effect of fluazuron on bovine oocytes during in vitro maturation. The best fluazuron concentrations were determined in a preliminary experiment on Chinese hamster ovary (CHO)-K1 cells and further used to compare fluazuron toxicity in both study models. Results of the annexin V and alkaline single cell gel electrophoresis assays demonstrated that fluazuron caused cytotoxicity and genotoxicity in bovine cumulus cells at all the concentrations tested (50, 75 and 100 μg fluazuron/mL). The evaluation of cortical granules and mitochondria distribution showed that cytoplasmic maturation was not affected by fluazuron treatment. However, a decrease in metaphase II + polar body, degenerate oocytes as well as disorganized chromatin in polar body were observed at all concentrations tested. Whereas the fertilization process was not altered by 50 μg/mL fluazuron, the embryo development rate decreased significantly. No significant differences were observed in any of the oxidative stress parameters assessed. This study contributes to a better understanding of fluazuron in bovines, suggesting that the antiparasitic may affect bovine reproduction and might cause embryo loss.

Deep learning pipeline reveals key moments in human embryonic development predictive of live birth after in vitro fertilisation

Deep learning pipeline reveals key moments in human embryonic development predictive of live birth after in vitro fertilisation

Combining single-cell profiling and functional analysis explores the role of pseudogenes in human early embryonic development

More and more studies have demonstrated that pseudogenes possess coding ability, and the functions of their transcripts in the development of diseases have been partially revealed. However, the role of pseudogenes in maintenance of normal physiological states and life activities has long been neglected. Here we identify pseudogenes that are dynamically expressed during human early embryogenesis, showing different expression pattern from that of adult tissues. We explore the expression correlation between pseudogenes and the parent genes, part due to their shared gene regulatory elements or the potential regulation network between them. The essential role of three pseudogenes, PI4KAP1, TMED10P1, and FBXW4P1, in maintaining self-renewal of human embryonic stem cells is demonstrated. We further find that the three pseudogenes might perform their regulatory functions by binding to proteins or microRNAs. The pseudogene-related single-nucleotide polymorphisms are significantly associated with human congenital disease, further illustrating their importance during early embryonic development. Overall, this study is an excavation and exploration of functional pseudogenes during early human embryonic development, suggesting that pseudogenes are not only capable of being specifically activated in pathological states, but also play crucial functions in the maintenance of normal physiological states.

Periconceptional maternal supplement intake and human embryonic growth, development, and birth outcomes: the Rotterdam Periconception Cohort.

Is periconceptional multiple-micronutrient supplement (MMS) use including folic acid (FA) compared to FA use only associated with increased embryonic growth, development, and birth weight in a high-risk population? Women with MMS intake show no significant differences in first-trimester morphological embryo development, but increased first-trimester embryonic growth trajectories and fewer neonates born small for gestational age (SGA), less than the 3rd percentile (<p3), compared to women using only FA. Periconceptional maternal FA intake in the general population is associated with increased embryonic and fetal growth, and reduced risks of neural tube defects, other congenital malformations, low birth weight, and neonates born SGA. A prospective tertiary hospital-based cohort study (the Rotterdam Periconceptional Cohort) was conducted from January 2010 to December 2020. We included 1076 women from the Rotterdam Periconceptional Cohort, before 10 weeks of pregnancy with follow-up until delivery. Embryonic growth was assessed by measurement of crown-rump length (CRL) and embryonic volume (EV), and embryonic morphology was described by Carnegie stages using longitudinal three-dimensional ultrasound scans and virtual reality techniques. Birth outcomes were extracted from medical records. General characteristics and supplement use were extracted from research questionnaires. This study showed increased embryonic growth trajectories (adjusted models, CRL: β = 0.052, 95% CI 0.012-0.090, EV: β = 0.022, 95% CI 0.002-0.042) in women using MMS compared to those using only FA. Moreover, a 45% reduced risk of a neonate-born SGA (<p3) was shown in women using MMS compared to FA users (adjusted OR = 0.546, 95% CI 0.308, 0.969). Embryonic morphological development (Carnegie stages) and the occurrence of miscarriages did not differ between women using MMS or solely FA. Following the heterogeneity of the composition and dose of MMS preparations, it is unclear which specific micronutrient, combination, or dose explains the increased embryonic growth trajectory and reduction in risk for SGA. This also hampers the possibility of differentiating between the effects of FA alone or as a component of MMS. Our findings emphasize the importance of periconceptional maternal MMS use as a potential preventative intervention against reduced embryonic growth and neonates born SGA. Therefore, we recommend the periconceptional use of MMS in women at risk of inadequate micronutrient intake. However, awareness of potentially harmful side effects of high doses and combinations of micronutrients is essential, therefore the optimal composition and dose need to be investigated, and careful surveillance is recommended. This research was funded by the Department of Obstetrics and Gynaecology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands, and the ZonMw grant Open Competition 2018 (09120011910046). The authors declare that they have no conflict of interest. NTR4356.

Adenosine Deaminase-Like Gene-Carried Lentivirus Toolkit for Identification of DNA N6-Methyladenine Origins.

Post-replicative DNA N6-methyladenine (pr6mdA) can form via bona fide methylase-catalyzed adenine methylation, playing a pivotal role in embryonic development and other biological processes. Surprisingly, pre-methylated adenine can be erroneously incorporated into DNA as misincorporated N6-methyladenine (i6mdA) via DNA polymerase-mediated replication. Despite pr6mdA and i6mdA sharing identical chemical structures, their biological functions diverge significantly, presenting a substantial challenge in distinguishing between the two. Here, for the first-time, it is exploited that the adenosine deaminase-like (Adal) protein and a corresponding activity-null mutant to construct an Adal lentivirus toolkit. With this newly designed toolkit, both pr6mdA and i6mdA can be identified and quantified simultaneously. The presence of 6mdA in the bone marrow cells of mice is shown, with its levels serving as indicators for growth with age, probably reflecting the cellular stress-caused changes in RNA decay, nucleotide pool sanitation, and transcription. Collectively, a powerful toolkit to advance understanding of both pr6mdA and i6mdA is demonstrated.

Mercury compound distribution and stable isotope composition in the different compartments of seabird eggs: the case of three species breeding in East Greenland

Mercury (Hg) is a toxic contaminant of global concern and the impact on Arctic ecosystems, particularly in seabirds, is critical due to large-scale Hg transport towards polar regions and its biomagnification in marine trophic systems. While the adverse effects of Hg on reproductive processes in seabirds are established, the understanding of Hg maternal transfer pathways and their control on Hg reproductive toxicity is limited. The combination of Hg compounds speciation (inorganic mercury and monomethylmercury MMHg) and Hg stable isotope composition in the different egg compartments (yolk, albumen, membrane, and shell) before embryo development was investigated to provide information on (i) Hg maternal transfer mechanisms, (ii) influence of egg biochemical composition on Hg organotropism and (iii) proxies of inputs of Hg contamination. Eggs of three seabird species (the common eider, the black-legged kittiwake and the little auk) collected within the same breeding period (summer 2020) in East Greenland were investigated. For all seabirds, albumen and membrane, the most protein-rich compartments, were the most contaminated (from 1.2 to 2.7 μg.g-1 for albumen and from 0.3 to 0.7 μg.g-1 for membrane). In these two compartments, more than 82% of the total Hg amount was in the form of MMHg. Additionally, mass-dependent fractionation values (δ202Hg) were higher in albumen and membrane in the three species. This result was mainly due the organotropism of MMHg as influenced by the biochemical properties and chemical binding affinity of these proteinous compartments. Among the different egg compartments, individuals and species, mass-independent fractionation values were comparable (mean±sd were 0.99±0.11‰, 0.78±0.11‰, 0.03±0.05‰, 0.04±0.10‰ for Δ199Hg, Δ201Hg, Δ200Hg and Δ204Hg, respectively). We conclude that initial MMHg accumulated in the three species originated from Arctic environmental reservoirs exhibiting similar and low photodemethylation extent. This result suggests a unique major source of MMHg in those ecosystems, potentially influenced by sea ice cover.

SANTO: a coarse-to-fine alignment and stitching method for spatial omics

With the flourishing of spatial omics technologies, alignment and stitching of slices becomes indispensable to decipher a holistic view of 3D molecular profile. However, existing alignment and stitching methods are unpractical to process large-scale and image-based spatial omics dataset due to extreme time consumption and unsatisfactory accuracy. Here we propose SANTO, a coarse-to-fine method targeting alignment and stitching tasks for spatial omics. SANTO firstly rapidly supplies reasonable spatial positions of two slices and identifies the overlap region. Then, SANTO refines the positions of two slices by considering spatial and omics patterns. Comprehensive experiments demonstrate the superior performance of SANTO over existing methods. Specifically, SANTO stitches cross-platform slices for breast cancer samples, enabling integration of complementary features to synergistically explore tumor microenvironment. SANTO is then applied to 3D-to-3D spatiotemporal alignment to study development of mouse embryo. Furthermore, SANTO enables cross-modality alignment of spatial transcriptomic and epigenomic data to understand complementary interactions.