One-Tip enables comprehensive proteome coverage in minimal cells and single zygotes.

Mass spectrometry (MS)-based proteomics workflows typically involve complex, multi-step processes, presenting challenges with sample losses, reproducibility, requiring substantial time and financial investments, and specialized skills. Here we introduce One-Tip, a proteomics methodology that seamlessly integrates efficient, one-pot sample preparation with precise, narrow-window data-independent acquisition (nDIA) analysis. One-Tip substantially simplifies sample processing, enabling the reproducible identification of >9000 proteins from ~1000 HeLa cells. The versatility of One-Tip is highlighted by nDIA identification of ~6000 proteins in single cells from early mouse embryos. Additionally, the study incorporates the Uno Single Cell Dispenser™, demonstrating the capability of One-Tip in single-cell proteomics with >3000 proteins identified per HeLa cell. We also extend One-Tip workflow to analysis of extracellular vesicles (EVs) extracted from blood plasma, demonstrating its high sensitivity by identifying >3000 proteins from 16 ng EV preparation. One-Tip expands capabilities of proteomics, offering greater depth and throughput across a range of sample types.

Comparative N-glycoproteomic analysis of Tibetan and lowland chicken fertilized eggs: Implications on proteins biofunction and species evolution.

The characterization and functionality of protein glycosylation among different related species are of common interest. Herein, non-standard quantification and N-glycosylation enrichment technology combined with ultra-high liquid chromatography-tandem mass spectrometry were used to establish detailed N-glycoproteomics of fertilized eggs, and quantitatively compared between Tibetan and lowland chicken. A total of 396N-glycosites from 143 glycoproteins were found. Specifically, compared with lowland chicken egg white, 32N-glycosites of 22 glycoproteins were up-regulated and 57N-glycosites of 25 glycoproteins were down-regulated in Tibetan chicken egg white. Also, 137N-glycosites in 72 glycoproteins showed much higher-degree glycosylation and 36N-glycosites in 15 glycoproteins displayed lower-degree glycosylation in Tibetan chicken egg yolk than those in lowland chicken egg yolk. Through bioinformatic analysis, these varied glycoproteins were highly associated with antifreeze activity, hypoxia adaptation, coagulation cascade, and binding/immunity activities, which may be related to plateau hypoxia and cold stress. PRACTICAL APPLICATIONS: These findings provide a new insight on the role of biological egg N-glycoproteins related to environmental adaptation and evolution, which may be further applied in improving egg processing and human health, by developing biomolecules for food and medical industry.

Fast and precise single-cell data analysis using a hierarchical autoencoder.

A primary challenge in single-cell RNA sequencing (scRNA-seq) studies comes from the massive amount of data and the excess noise level. To address this challenge, we introduce an analysis framework, named single-cell Decomposition using Hierarchical Autoencoder (scDHA), that reliably extracts representative information of each cell. The scDHA pipeline consists of two core modules. The first module is a non-negative kernel autoencoder able to remove genes or components that have insignificant contributions to the part-based representation of the data. The second module is a stacked Bayesian autoencoder that projects the data onto a low-dimensional space (compressed). To diminish the tendency to overfit of neural networks, we repeatedly perturb the compressed space to learn a more generalized representation of the data. In an extensive analysis, we demonstrate that scDHA outperforms state-of-the-art techniques in many research sub-fields of scRNA-seq analysis, including cell segregation through unsupervised learning, visualization of transcriptome landscape, cell classification, and pseudo-time inference.

Interactions between egg storage duration and broiler breeder age on egg fat content, chicken organ weights, and growth performance.

Egg storage and breeder age are between the most important factors affecting egg lipids, chicken quality, and posthatch performance. To evaluate these factors, including their interaction, the impact of egg storage duration (5, 12, and 19 D), and breeder age (47 and 67 wk) was investigated in Arbor Acres broiler eggs and chickens. Total yolk fat content, chicken organ development at hatch and at 6 D of age, and posthatch performance (at 7 D and 35 D of age) were determined. Total fat content in fresh yolk was lower in 12 and 19 D stored eggs than in 5 D stored eggs (Δ = -2.42% on average). In hatchlings, the heart percentage was not affected by storage duration in the younger flock but was higher after 19 D than after 5 and 12 D of storage in the old flock (Δ = +0.09% on average). Residual yolk weight was higher after 12 D egg storage than after 5 D egg storage (Δ = +1.7 g), with 19 D egg storage in between. Liver and intestine percentage decreased with storage duration. Residual yolk weight (Δ = +1.09 g) and liver percentage (Δ = +0.18%) were higher in old breeders than in younger breeders. At day 6, chicken BW, yolk free body mass, liver percentage, and intestine percentage interacted between egg storage duration and breeder age with the strongest effects in chickens from older breeder after 19 D of storage. Heart percentage was lower after 19 D compared with 5 and 12 D of storage (Δ = -0.05% on average). Feed intake and feed conversion ratio were higher between day 0 to 7 and 0 to 35 after 19 D than after 5 D egg storage (Δ19-5 D = +12 g and +199 g; +0.11 points and +0.09 points, respectively). It can be concluded that when it is needed, eggs from younger breeders should be stored for a prolonged period (≥12 D) rather than those from older breeders.

The Potential Role of Schistosome-Associated Factors as Therapeutic Modulators of the Immune System.

The parasites and eggs of helminths, including schistosomes, are associated with factors that can modulate the nature and outcomes of host immune responses, particularly enhancing type 2 immunity and impairing the effects of type 1 and type 17 immunity. The main species of schistosomes that cause infection in humans are capable of generating a microenvironment that allows survival of the parasite by evasion of the immune response. Schistosome infections are associated with beneficial effects on chronic immune disorders, including allergies, autoimmune diseases, and alloimmune responses. Recently, there has been increasing research interest in the role of schistosomes in immunoregulation during human infection, and the mechanisms underlying these roles continue to be investigated. Further studies may identify potential opportunities to develop new treatments for immune disease. In this review, we provide an update on the advances in our understanding of schistosome-associated modulation of the cells of the innate and adaptive immune systems as well as the potential role of schistosome-associated factors as therapeutic modulators of immune disorders, including allergies, autoimmune diseases, and transplant immunopathology. We also discuss potential opportunities for targeting schistosome-induced immunoregulation for future translation to the clinical setting.

Lipid Droplet Composition Varies Based on Medaka Fish Eggs Development as Revealed by NIR-, MIR-, and Raman Imaging.

In fertilized fish eggs, lipids are an energy reservoir for the embryo development and substrate for organogenesis. They occur in the cytoplasmic area and form lipid droplets (LDs), but also the yolk egg is composed of lipids and proteins. Insight on the LD formation and distribution and their interactions with other cellular organelles could provide information about the role based on the egg development. For non-destructive, macro-scale visualization of biochemical components of fish eggs, such as lipids proteins and water, near-infrared (NIR) imaging is the method of choice. Mid-infrared (MIR) and Raman spectroscopy imaging were used to provide details on chemical composition of LDs and other egg organelles. NIR imaging illustrated main compartments of the egg including membrane, LDs, yolk, relative protein, and lipid content in well-localized egg structures and their interactions with water molecules. In the yolk, a co-existence of lipids and proteins with carotenoids and carbohydrates was detected by Raman spectroscopy. Results showed a prominent decrease of unsaturated fatty acids, phospholipids, and triglycerides/cholesteryl esters content in the eggs due to the embryo development. An opposite trend of changes was observed by MIR spectroscopy for the glycogen, suggesting that consumption of lipids occurred with production of this carbohydrate. The comprehensive vibrational spectroscopic analysis based on NIR, MIR, and Raman imaging is a unique tool in studying in situ dynamic biological processes.

Females adjust maternal hormone concentration in eggs according to male condition in a burying beetle.

In birds and other vertebrates, there is good evidence that females adjust the allocation of hormones in their eggs in response to prenatal environmental conditions, such as food availability or male phenotype, with profound consequences for life history traits of offspring. In insects, there is also evidence that females deposit juvenile hormones (JH) and ecdysteroids (ESH) in their eggs, hormones that play a key role in regulating offspring growth and metamorphosis. However, it is unclear whether females adjust their hormonal deposition in eggs in response to prenatal environmental conditions. Here we address this gap by conducting an experiment on the burying beetle Nicrophorus vespilloides, in which we manipulated the presence of the male parent and the size of the carcass used for breeding at the time of laying. We also tested for effects of the condition (i.e., body mass) of the parents. We then recorded subsequent effects on JH and ESH concentrations in the eggs. We found no evidence for an effect of these prenatal environmental conditions (male presence and carcass size) on hormonal concentration in the eggs. However, we found that females reduced their deposition of JH when mated with heavier males. This finding is consistent with negative differential allocation of maternal hormones in response to variation in the body mass of the male parent. We encourage further work to investigate the role of maternally derived hormones in insect eggs.

Production of Recombinant Monoclonal Antibodies in the Egg White of Gene-Targeted Transgenic Chickens.

Increased commercial demand for monoclonal antibodies (mAbs) has resulted in the urgent need to establish efficient production systems. We previously developed a transgenic chicken bioreactor system that effectively produced human cytokines in egg whites using genome-edited transgenic chickens. Here, we describe the application of this system to mAb production. The genes encoding the heavy and light chains of humanized anti-HER2 mAb, linked by a 2A peptide sequence, were integrated into the chicken ovalbumin gene locus using a CRISPR/Cas9 protocol. The knock-in hens produced a fully assembled humanized mAb in their eggs. The mAb expression level in the egg white was 1.4-1.9 mg/mL, as determined by ELISA. Furthermore, the antigen binding affinity of the anti-HER2 mAb obtained was estimated to be equal to that of the therapeutic anti-HER2 mAb (trastuzumab). In addition, antigen-specific binding by the egg white mAb was demonstrated by immunofluorescence against HER2-positive and -negative cells. These results indicate that the chicken bioreactor system can efficiently produce mAbs with antigen binding capacity and can serve as an alternative production system for commercial mAbs.

Zygote Electroporation for CRISPR/Cas9 Delivery to Generate Genetically Modified Mice.

The CRISPR/Cas9 system is a powerful tool for generation of genetically modified mice. In conventional protocols, Cas9 protein (or mRNA) and sgRNA are introduced into zygotes by microinjection. However, microinjection requires special skill and is too time-consuming to treat zygotes on a large scale. Recently, we have developed a simple electroporation method which generates genetically modified mice with high efficiency. Here, we describe our method GEEP (genome editing by electroporation of Cas9 protein). This method facilitates high-throughput genetic analysis of the mouse. This chapter describes the GEEP method to generate genetically modified mice.

Human oocytes and zygotes are ready for ultra-fast vitrification after 2 minutes of exposure to standard CPA solutions.

Vitrification of human oocytes and embryos in different stages of development is a key element of daily clinical practice of in vitro fertilization treatments. Despite the cooling and warming of the cells is ultra-fast, the procedure as a whole is time consuming. Most of the duration is employed in a long (8-15 minutes), gradual or direct exposure to a non-vitrifying cryoprotectant solution, which is followed by a short exposure to a more concentrated vitrifying solution. A reduction in the duration of the protocols is desirable to improve the workflow in the IVF setting and reduce the time of exposure to suboptimal temperature and osmolarity, as well as potentially toxic cryoprotectants. In this work it is shown that this reduction is feasible. In silico (MatLab program using two-parameter permeability model) and in vitro observations of the oocytes' osmotic behaviour indicate that the dehydration upon exposure to standard cryoprotectant solutions occurs very fast: the point of minimum volume of the shrink-swell curve is reached within 60 seconds. At that point, intracellular water ejection is complete, which coupled with the permeation of low molecular weight cryoprotectants results in similar intracellular and extracellular solute concentrations. This shows that prolonging the exposure to the cryoprotectant solutions does not improve the cytosolic glass forming tendency and could be avoided. To test this finding, human oocytes and zygotes that were donated for research were subjected to a shortened, dehydration-based protocol, consisting of two consecutive exposures of one-minute to two standard cryoprotectant solutions, containing ethylene glycol, dimethyl sulfoxide and sucrose. At the end of this two-minute dehydration protocol, the critical intracellular solute concentration necessary for successful vitrification was attained, confirmed by the post-warming survival and ability to resume cytokinesis of the cells. Further studies of the developmental competency of oocytes and embryos would be necessary to determine the suitability of this specific dehydration protocol for clinical practice, but based on our results, short times of exposure to increasingly hypertonic solutions could be a more time-efficient strategy to prepare human oocytes and embryos for vitrification.

Toxic Flatworm Egg Plates Serve as a Possible Source of Tetrodotoxin for Pufferfish.

The pufferfish Takifugu niphobles (at present Takifugu alboplumbeus) possesses highly concentrated tetrodotoxin (TTX), an extremely potent neurotoxin that provides effective protection from predators, at least at the larval stages. However, the source of the toxin has remained unclear. Recently, DNA from the toxic flatworm Planocera multitentaculata was detected in the intestinal contents of juveniles and young of the pufferfish, suggesting that the flatworm contributes to its toxification at various stages of its life. In this study, we describe the behavior of the pufferfish in the intertidal zone that appears to contribute to its toxification before and during its spawning period: pufferfish were found to aggregate and ingest flatworm egg plates by scraping them off the surface of rocks. DNA analysis based on 28S rRNA and cytochrome c oxidase subunit I (COI) genes identified the egg plates as those of P. multitentaculata. Liquid chromatography with tandem mass spectrometry analysis revealed that the egg plates contain highly concentrated TTX. The feeding behavior of the pufferfish on the flatworm egg plates was also observed in the aquarium. These results suggest that pufferfish feed on the flatworm egg plate, which enables them to acquire toxicity themselves while providing their offspring with the protective shield of TTX.

Shorter than short-chain: Very short-chain chlorinated paraffins (vSCCPs) found in wildlife from the Yangtze River Delta.

Very short-chain chlorinated paraffins (vSCCPs, C6-9) occurred in 94% of wildlife samples from the Yangtze River Delta (YRD), China, with CnClm comparable to that of a local CP product, CP-52. Therefore, we determined the content of vSCCPs in CP-52 using a mathematical deconvolution technique. Then with CP-52 and several other reference standards, vSCCPs together with short-, medium-, and long-chain CPs were quantified in 21 wildlife species from an artificial wetland ecosystem and a freshwater ecosystem in the YRD. Concentrations of vSCCPs ranged from 2.6 to 8400 ng/g lipid. These concentrations were 1.2-380 fold lower than SCCPs, but were significantly correlated with those of SCCPs. vSCCP concentrations were comparable to or higher than reported for brominated flame retardants in the same samples. Bioaccumulation tendency of vSCCPs was identified in two benthic species, indicating congener-specific accumulation of vSCCPs in the environment.

Genetic Markers of Benzimidazole Resistance among Human Hookworms (Necator americanus) in Kintampo North Municipality, Ghana.

Hookworm infection causes anemia, malnutrition, and growth delay, especially in children living in sub-Saharan Africa. The World Health Organization recommends periodic mass drug administration (MDA) of anthelminthics to school-age children (SAC) as a means of reducing morbidity. Recently, questions have been raised about the effectiveness of MDA as a global control strategy for hookworms and other soil-transmitted helminths (STHs). Genomic DNA was extracted from Necator americanus hookworm eggs isolated from SAC enrolled in a cross-sectional study of STH epidemiology and deworming response in Kintampo North Municipality, Ghana. A polymerase chain reaction (PCR) assay was then used to identify single-nucleotide polymorphisms (SNPs) associated with benzimidazole resistance within the N. americanus ß-tubulin gene. Both F167Y and F200Y resistance-associated SNPs were detected in hookworm samples from infected study subjects. Furthermore, the ratios of resistant to wild-type SNP at these two loci were increased in posttreatment samples from subjects who were not cured by albendazole, suggesting that deworming drug exposure may enrich resistance-associated mutations. A previously unreported association between F200Y and a third resistance-associated SNP, E198A, was identified by sequencing of F200Y amplicons. These data confirm that markers of benzimidazole resistance are circulating among hookworms in central Ghana, with unknown potential to impact the effectiveness and sustainability of chemotherapeutic approaches to disease transmission and control.

Chromatin Characterization in Xenopus laevis Cell-Free Egg Extracts and Embryos.

Xenopus laevis development is marked by accelerated cell division solely supported by the proteins maternally deposited in the egg. Oocytes mature to eggs with concomitant transcriptional silencing. The unique maternal chromatin state contributing to this silencing and subsequent zygotic activation is likely established by histone posttranslational modifications and histone variants. Therefore, tools for understanding the nature and function of maternal and embryonic histones are essential to deciphering mechanisms of regulation of development, chromatin assembly, and transcription. Here we describe protocols for isolating pronuclear sperm chromatin from Xenopus egg extracts and hydroxyapatite-based histone purification from this chromatin. The histones purified through this method can be directly assembled into chromatin through in vitro assembly reactions, providing a unique opportunity to biochemically dissect the effect of histone variants, histone modifications, and other factors in chromatin replication and assembly. We also describe how to isolate chromatin from staged embryos and analyze the proteins to reveal dynamic developmental histone modifications. Finally, we present protocols to measure chromatin assembly in extracts, including supercoiling and micrococcal nuclease assays. Using these approaches, analysis of maternal and zygotic histone posttranslational modifications concomitant with cell-cycle and developmental transitions can be tested.

Persistent organic pollutants in sediments, intertidal crabs, and the threatened Olrog's gull in a northern Patagonia salt marsh, Argentina.

Persistent organic pollutants (POPs) are of great concern for the environment. In this study we (a) determine levels and distribution of OCPs, PCBs, and PBDEs in sediments and two crab species (Neohelice granulata and Cyrtograpsus altimanus), (b) assess bioaccumulation in crabs, and (c) explore the occurrence of POPs in the Near Threatened Olrog's gull (Larus atlanticus) chicks and eggs in one of the most important salt marsh environments in the South West Atlantic. Sediments, crabs, and gull chicks and eggs showed POPs presence at low levels; being α-endosulfan, PCB-153, and BDE-47 the most represented compounds. In sediments, pollutant concentrations were lower than those reported in Canadian guidelines for the protection of the aquatic life. POP bioaccumulation was recorded in crabs, suggesting a risk to upper trophic level predators. Further studies are needed to understand the trophic effects of POPs in San Blas bay, particularly on the threatened Olrog's gull.

Mitotic entry drives replisome disassembly at stalled replication forks.

The disassembly of eukaryotic replisome during replication termination is mediated by CRL-dependent poly-ubiquitylation of Mcm7 and p97 segregase. The replisome also disassembles at stalled or collapsed replication forks under certain stress conditions, but the underlying mechanism is poorly understood. Here, we discovered a novel pathway driving stepwise disassembly of the replisome at stalled replication forks after forced entry into M-phase using Xenopus egg extracts. This pathway was dependent on M-CDK activity and K48- and K63-linked poly-ubiquitylation but not on CRL and p97, which is different from known pathways. Furthermore, this pathway could not disassemble converged replisomes whose Mcm7 subunit had been poly-ubiquitylated without p97. These results suggest that there is a distinctive pathway for replisome disassembly when stalled replication forks persist into M-phase.

Trace elements in biomaterials and soils from a Yellow-legged gull (Larus michahellis) colony in the Atlantic Islands of Galicia National Park (NW Spain).

Seabird colonies drastically transform the sites that they inhabit. Although the influence of seabirds on nutrient cycling has been investigated in numerous studies, the effects on trace elements has scarcely been considered. In this study, we determined the total contents of 9 trace elements in biomaterials (excrement, pellets, feathers and eggs) and soils in relation to the presence the Yellow-legged gull Larus michahellis. The concentrations of Zn, Cu and As were particularly high in the pellets and excrement. The total contents of the trace elements were significantly higher in the soils in the sub-colonies in which Yellow-legged gulls predominate than in soil from the control zone (with no gulls). The difference was even higher for the most reactive geochemical fractions. We observed that the oxidizable fraction was the most relevant fraction for almost all trace elements, indicating the importance of organic matter in trace element retention in sandy soils.

Conceptus Coats of Marsupials and Monotremes.

Mammals evolved from oviparous reptiles that laid eggs in a dry, terrestrial environment, thus requiring large amounts of yolk to support development and tough, outer coats to protect them. Eutherian mammals such as humans and mice exhibit an "extreme" form of viviparity in which yolk and conceptus coats have become largely redundant. However, the "other" mammals-monotremes and marsupials-have retained and modified some features of reptilian development that provide valuable insights into the evolution of viviparity in mammals. Most striking of these are the conceptus coats, which include the zona pellucida, the mucoid coat, and the shell coat. We discuss current knowledge of these coats in monotremes and marsupials, their possible roles, and recently identified components such as the zona pellucida protein ZPAX, conceptus coat mucin (CCM), and nephronectin (NPNT).

Annual variation in polychlorinated biphenyl (PCB) exposure in tree swallow (Tachycineta bicolor) eggs and nestlings at Great Lakes Restoration Initiative (GLRI) study sites.

Tree swallow (Tachycineta bicolor) eggs and nestlings were collected from 16 sites across the Great Lakes to quantify normal annual variation in total polychlorinated biphenyl (PCB) exposure and to validate the sample size choice in earlier work. A sample size of five eggs or five nestlings per site was adequate to quantify exposure to PCBs in tree swallows given the current exposure levels and variation. There was no difference in PCB exposure in two randomly selected sets of five eggs collected in the same year, but analyzed in different years. Additionally, there was only modest annual variation in exposure, with between 69% (nestlings) and 73% (eggs) of sites having no differences between years. There was a tendency, both statistically and qualitatively, for there to be less exposure in the second year compared to the first year.

Production of Wilson Disease Model Rabbits with Homology-Directed Precision Point Mutations in the ATP7B Gene Using the CRISPR/Cas9 System.

CRISPR/Cas9 has recently been developed as an efficient genome engineering tool. The rabbit is a suitable animal model for studies of metabolic diseases. In this study, we generated ATP7B site-directed point mutation rabbits to simulate a major mutation type in Asians (p. Arg778Leu) with Wilson disease (WD) by using the CRISPR/Cas9 system combined with single-strand DNA oligonucleotides (ssODNs). The efficiency of the precision point mutation was 52.94% when zygotes were injected 14 hours after HCG treatment and was significantly higher than that of zygotes injected 19 hours after HCG treatment (14.29%). The rabbits carrying the allele with mutant ATP7B died at approximately three months of age. Additionally, the copper content in the livers of rabbits at the onset of WD increased nine-fold, a level similar to the five-fold increase observed in humans with WD. Thus, the efficiency of precision point mutations increases when RNAs are injected into zygotes at earlier stages, and the ATP7B mutant rabbits are a potential model for human WD disease with applications in pathological analysis, clinical treatment and gene therapy research.