Multicellular Research Articles

Discoidal carbonaceous compressions from the Early Mesoproterozoic Gaoyuzhuang Formation: a fossil example of microbial biofilm

Discoidal carbonaceous compressions are the most common type of Precambrian macrofossils with a long temporal range starting from the late Paleoproterozoic. However, their unsolved biological nature restricts our understanding of the early evolution of macroscopic life. Here we report an assemblage of well-preserved discoidal carbonaceous macrofossils from the early Mesoproterozoic Gaoyuzhuang Formation in North China, which provides insights into this problem. They are preserved in round to elliptical shapes with sizes ranging from millimeters to several centimeters. Petrographic thin sections show that the macrofossils consist of laminated structures with alternating organic matter along with clay minerals and dolomites. Neither cellular structures nor individual microfossils were identified within them, but their regular shape, internal structures, and associated mineral constituents suggest that they are probably remains of the microbial biofilms, rather than multicellular organisms. It presents a well-preserved fossil example of microbial biofilms with macroscopic size and regular overall morphology. It further implies a possible origin of microbial biofilm for some of the early carbonaceous macrofossils and calls for detailed reexaminations of those macrofossils to exclude such possibilities. Our finding is consistent with previous studies that biofilms may have played an important role in survival for early microorganisms in the Precambrian ecosystem. Thematic collection: This article is part of the The North China Craton as a window to Earth’s middle age collection available at: https://www.lyellcollection.org/topic/collections/the-north-china-craton-as-a-window-to-earths-middle-age

Mapping the Human Cell Surface Interactome: A Key to Decode Cell-to-Cell Communication.

Proteins on the surfaces of cells serve as physical connection points to bridge one cell with another, enabling direct communication between cells and cohesive structure. As biomedical research makes the leap from characterizing individual cells toward understanding the multicellular organization of the human body, the binding interactions between molecules on the surfaces of cells are foundational both for computational models and for clinical efforts to exploit these influential receptor pathways. To achieve this grander vision, we must assemble the full interactome of ways surface proteins can link together. This review investigates how close we are to knowing the human cell surface protein interactome. We summarize the current state of databases and systematic technologies to assemble surface protein interactomes, while highlighting substantial gaps that remain. We aim for this to serve as a road map for eventually building a more robust picture of the human cell surface protein interactome.

Shape Evolution in Two Acts: Morphological Diversity of Larval and Adult Neoaustraranan Frogs

Phenotypic traits can evolve independently at different stages of ontogeny, optimizing adaptation to distinct ecological contexts and increasing morphological diversity in species with complex life cycles. Given the relative independence resulting from the profound changes induced by metamorphosis, niche occupation and resource utilization in tadpoles may prompt evolutionary responses that do not necessarily affect the adults. Consequently, diversity patterns observed in the larval shape may not necessarily correspond to those found in the adult shape for the same species, a premise that can be tested through the Adaptive Decoupling Hypothesis (ADH). Herein, we investigate the ADH for larval and adult shape differentiation in Neoaustrarana frogs. Neoaustrarana frogs, particularly within the Cycloramphidae family, exhibit remarkable diversity in tadpole morphology, making them an ideal model for studying adaptive decoupling. By analyzing 83 representative species across four families (Alsodidae, Batrachylidae, Cycloramphidae, and Hylodidae), we generate a morphological dataset for both larval and adult forms. We found a low correlation between larval and adult shapes, species with a highly distinct larval shape having relatively similar shape when adults. Larval morphological disparity is not a good predictor for adult morphological disparity within the group, with distinct patterns observed among families. Differences between families are notable in other aspects as well, such as the role of allometric components influencing shape and morphospace occupancy. The larval shape has higher phylogenetic structure than the adult. Evolutionary convergence emerges as a mechanism of diversification for both larval and adult shapes in the early evolution of neoaustraranans, with shape disparity of tadpoles reaching stable levels since the Oligocene. The widest occupation in morphospace involves families associated with dynamically changing environments over geological time. Our findings support the ADH driving phenotypic diversity in Neoaustrarana, underscoring the importance of considering ontogenetic stages in evolutionary studies.

Group-selection via aggregative propagule-formation enables cooperative multicellularity in an individual based, spatial model.

The emergence of multicellularity is one of the major transitions in evolution that happened multiple times independently. During aggregative multicellularity, genetically potentially unrelated lineages cooperate to form transient multicellular groups. Unlike clonal multicellularity, aggregative multicellular organisms do not rely on kin selection instead other mechanisms maintain cooperation against cheater phenotypes that benefit from cooperators but do not contribute to groups. Spatiality with limited diffusion can facilitate group selection, as interactions among individuals are restricted to local neighbourhoods only. Selection for larger size (e.g. avoiding predation) may facilitate the emergence of aggregation, though it is unknown, whether and how much role such selection played during the evolution of aggregative multicellularity. We have investigated the effect of spatiality and the necessity of predation on the stability of aggregative multicellularity via individual-based modelling on the ecological timescale. We have examined whether aggregation facilitates the survival of cooperators in a temporally heterogeneous environment against cheaters, where only a subset of the population is allowed to periodically colonize a new, resource-rich habitat. Cooperators constitutively produce adhesive molecules to promote aggregation and propagule-formation while cheaters spare this expense to grow faster but cannot aggregate on their own, hence depending on cooperators for long-term survival. We have compared different population-level reproduction modes with and without individual selection (predation) to evaluate the different hypotheses. In a temporally homogeneous environment without propagule-based colonization, cheaters always win. Predation can benefit cooperators, but it is not enough to maintain the necessary cooperator amount in successive dispersals, either randomly or by fragmentation. Aggregation-based propagation however can ensure the adequate ratio of cooperators-to-cheaters in the propagule and is sufficient to do so even without predation. Spatiality combined with temporal heterogeneity helps cooperators via group selection, thus facilitating aggregative multicellularity. External stress selecting for larger size (e.g. predation) may facilitate aggregation, however, according to our results, it is neither necessary nor sufficient for aggregative multicellularity to be maintained when there is effective group-selection.

DNA Reaction Circuits to Establish Designated Biological Functions in Multicellular Community.

In multicellular organisms, individual cells are coordinated through complex communication networks to accomplish various physiological tasks. Aiming to establish new biological functions in the multicellular community, we used DNA as the building block to develop a cascade of nongenetic reaction circuits to establish a dynamic cell-cell communication network. Utilizing membrane-anchored amphiphilic DNA tetrahedra (TDN) as the nanoscaffold, reaction circuits were incorporated into three unrelated cells in order to uniquely regulate their sense-and-response behaviors. As a proof-of-concept, this step enabled these cells to simulate significant biological events involved in T cell-mediated anticancer immunity. Such events included cancer-associated antigen recognition and the presentation of antigen-presenting cells (APCs), APC-facilitated T cell activation and dissociation, and T cell-mediated cancer targeting and killing. By combining the excellent programmability and molecular recognition ability of DNA, our cell-surface reaction circuits hold promise for mimicking and manipulating many biological processes.

Engineering Cell Instructive Microenvironments for In Vitro Replication of Functional Barrier Organs.

Multicellular organisms exhibit synergistic effects among their components, giving rise to emergent properties crucial for their genesis and overall functionality and survival. Morphogenesis involves and relies upon intricate and biunivocal interactions among cells and their environment, that is, the extracellular matrix (ECM). Cells secrete their own ECM, which in turn, regulates their morphogenetic program by controlling time and space presentation of matricellular signals. The ECM, once considered passive, is now recognized as an informative space where both biochemical and biophysical signals are tightly orchestrated. Replicating this sophisticated and highly interconnected informative media in a synthetic scaffold for tissue engineering is unattainable with current technology and this limits the capability to engineer functional human organs in vitro and in vivo. This review explores current limitations to in vitro organ morphogenesis, emphasizing the interplay of gene regulatory networks, mechanical factors, and tissue microenvironment cues. In vitro efforts to replicate biological processes for barrier organs such as the lung and intestine, are examined. The importance of maintaining cells within their native microenvironmental context is highlighted to accurately replicate organ-specific properties. The review underscores the necessity for microphysiological systems that faithfully reproduce cell-native interactions, for advancing the understanding of developmental disorders and disease progression.

Hypothesized life cycle of the snow algae Chlainomonas sp. (Chlamydomonadales, Chlorophyta) from the Cascade Mountains, USA.

Chlainomonas (Chlamydomonadales, Chlorophyta) is one of the four genera of snow algae known to produce annual pink or red blooms in alpine snow. No Chlainomonas species have been successfully cultured in the laboratory, but diverse cell types have been observed from many field-collected samples, from multiple species. The diversity of morphologies suggests these algae have complex life cycles with changes in ploidy. Over 7 years (2017-2023), we observed seasonal blooms dominated by a Chlainomonas species from late spring through the summer months on a snow-on-lake habitat in an alpine basin in the North Cascade Mountains of Washington, USA. The Bagley Lake Chlainomonas is distinct from previously reported species based on morphology and sequence data. We observed a similar collection of cell types observed in other Chlainomonas species, with the addition of swarming biflagellate cells that emerged from sporangia. We present a life cycle hypothesis for this species that links cell morphologies observed in the field to seasonally available habitat. The progression of cell types suggests cells are undergoing both meiosis and fertilization in the life cycle. Since the life cycle is the most fundamental biological feature of an organism, with direct consequences for evolutionary processes, it is critical to understand how snow algal life cycles will influence their responses to changes in their habitat driven by climate warming. For microbial taxa that live in extreme environments and are difficult to culture, temporal field studies, such as we report here, may be key to creating testable hypotheses for life cycles.

Combined effect of seasons and life history in an anuran strengthens the response and relationship between their physiology and gut microbiota

Gut microbiota impact host physiology, though simultaneous investigations in ectothermic vertebrates are rare. Particularly, amphibians may exhibit more complex interactions between host physiology and the effects of gut microbiota due to the combination of seasonal changes and complex life histories. In this study, we assessed the relationships among food resources, gut bacterial communities, and host physiology in frogs (Phelophylax nigromaculatus), taking into account seasonal and life history variations. We found that food sources were not correlated with physiological parameters but had some relationships with the gut bacterial community. Variations in gut bacterial community and host physiology were influenced by the combined effects of seasonal differences and life history, though mostly driven by seasonal differences. An increase in Firmicutes was associated with higher fat content, reflecting potential fat storage in frogs during the non-breeding season. The increase in Bacteroidetes resulted in lower fat content in adult frogs and decreased immunity in juvenile frogs during the breeding season, demonstrating a direct link. Our results suggest that the gut microbiome may act as a link between food conditions and physiological status, and that the combined effect of seasons and life history could reinforce the relationship between gut microbiota and physiological status in ectothermic animals. While food sources may influence the gut microbiota of ectotherms, we contend that temperature-correlated seasonal variation, which predominately influences most ectotherms, is a significant factor.

Effects of flowing water stimulation on hormone regulation during the maturation process of Conger myriaster ovaries

Conger eel (Conger myriaster) is an economically important species in China. Due to the complex life history of the conger eel, achieving artificial reproduction has remained elusive. This study aimed to explore the effect of water stimulation on hormonal regulation during the artificial reproduction of conger eel. The experiment was divided into four groups: A1 (no hormone injection, still water), A2 (no hormone injection, flowing water), B1 (hormone injection, still water), and B2 (hormone injection, flowing water). The flowing water group maintained a flow velocity of 0.4 ± 0.05 m/s for 12 h daily throughout the 60-day period. Steroid hormone levels in the serum and ovaries of conger eels were analyzed using UPLC-MS/MS and ELISA on the 30th and 60th days of the experiment. The relative expression levels of follicle-stimulating hormone (FSHβ) and luteinizing hormone (LHβ) in the pituitary were determined by quantitative PCR. The results showed a significantly lower gonadosomatic index (GSI) in B2 compared to B1 (p < 0.05) on the 30th day. FSH was found to act only in the early stages of ovarian development, with water stimulation significantly enhancing FSH synthesis (p < 0.05), while FSHβ gene was not expressed after hormone injection. Conversely, LH was highly expressed in late ovarian development, with flowing water stimulation significantly promoting LH synthesis (p < 0.05). Serum cortisol (COR) levels were significantly higher in the flowing water group than in the still water group (p < 0.05). Furthermore, estradiol (E2) content of B2 was significantly lower than that of B1 on the 30th and 60th day. Overall, flowing water stimulation enhanced the synthesis of FSH in early ovarian development and LH in late ovarian development, while reducing E2 accumulation in the ovaries. In this study, the effect of flowing water stimulation on hormone regulation during the artificial reproduction of conger eel was initially investigated to provide a theoretical basis for optimizing artificial reproduction techniques.

Assessing the hydromechanical control of plant growth.

Multicellular organisms grow and acquire their shapes through the differential expansion and deformation of their cells. Recent research has addressed the role of cell and tissue mechanical properties in these processes. In plants, it is believed that growth rate is a function of the mechanical stress exerted on the cell wall, the thin polymeric layer surrounding cells, involving an effective viscosity. Nevertheless, recent studies have questioned this view, suggesting that cell wall elasticity sets the growth rate or that uptake of water is limiting for plant growth. To assess these issues, we developed a microfluidic device to quantify the growth rates, elastic properties and hydraulic conductivity of individual Marchantia polymorpha plants in a controlled environment with a high throughput. We characterized the effect of osmotic treatment and abscisic acid on growth and hydromechanical properties. Overall, the instantaneous growth rate of individuals is correlated with both bulk elastic modulus and hydraulic conductivity. Our results are consistent with a framework in which the growth rate is determined primarily by the elasticity of the wall and its remodelling, and secondarily by hydraulic conductivity. Accordingly, the coupling between the chemistry of the cell wall and the hydromechanics of the cell appears as key to set growth patterns during morphogenesis.

Precise Structural Analysis of Neutral Glycans Using Aerolysin Mutant T240R Nanopore.

Glycans play vital roles in nearly all life processes of multicellular organisms, and understanding these activities is inseparable from elucidating the biological significance of glycans. However, glycan research has lagged behind that of DNA and protein due to the challenges posed by structural heterogeneity and isomerism (i.e., structures with equal molecular weights) the lack of high-efficiency structural analysis techniques. Nanopore technology has emerged as a sensitive single-molecule biosensor, shining a light on glycan analysis. However, a significant number of glycans are small and uncharged, making it challenging to elicit identifiable nanopore signals. Here we introduce a R-binaphthyl tag into glycans, which enhances the cation-π interaction between the derivatized glycan molecules and the nanopore interface, enabling the detection of neutral glycans with an aerolysin nanopore. This approach allows for the distinction of di-, tri-, and tetrasaccharides with monosaccharide resolution and has the potential for group discrimination, the monitoring of enzymatic transglycosylation reactions. Notably, the aerolysin mutant T240R achieves unambiguous identification of six disaccharide isomers, trisaccharide and tetrasaccharide linkage isomers. Molecular docking simulations reveal that multiple noncovalent interactions occur between residues R282, K238, and R240 and the glycans and R-binaphthyl tag, significantly slowing down their translocation across the nanopore. Importantly, we provide a demonstration of the kinetic translocation process of neutral glycan isomers, establishing a solid theoretical foundation for glycan nanopore analysis. The development of our technology could promote the analysis of glycan structural isomers and has the potential for nanopore-based glycan structural determination and sequencing.

Hierarchical Symmetry-Breaking Model for Stem Cell Differentiation

Waddington envisioned stem cell differentiation as a marble rolling down a hill, passing through hierarchically branched valleys representing the cell’s temporal state. The terminal valleys at the bottom of the hill indicate the possible committed cells of the multicellular organism. Although originally proposed as a metaphor, Waddington’s hypothesis establishes the fundamental principles for characterizing the differentiation process as a dynamic system: the generated equilibrium points must exhibit hierarchical branching, robustness to perturbations (homeorhesis), and produce the appropriate number of cells for each cell type. This article aims to capture these characteristics using a mathematical model based on two fundamental hypotheses. First, it is assumed that the gene regulatory network consists of hierarchically coupled subnetworks of genes (modules), each modeled as a dynamical system exhibiting supercritical pitchfork or cusp bifurcation. Second, the gene modules are spatiotemporally regulated by feedback mechanisms originating from epigenetic factors. Analytical and numerical results show that the proposed model exhibits self-organized multistability with hierarchical branching. Moreover, these branches of equilibrium points are robust to perturbations, and the number of different cells produced can be determined by the system parameters.

The paleoredox context of early eukaryotic evolution: insights from the Tonian Mackenzie Mountains Supergroup, Canada.

Tonian (ca. 1000-720 Ma) marine environments are hypothesised to have experienced major redox changes coinciding with the evolution and diversification of multicellular eukaryotes. In particular, the earliest Tonian stratigraphic record features the colonisation of benthic habitats by multicellular macroscopic algae, which would have been powerful ecosystem engineers that contributed to the oxygenation of the oceans and the reorganisation of biogeochemical cycles. However, the paleoredox context of this expansion of macroalgal habitats in Tonian nearshore marine environments remains uncertain due to limited well-preserved fossils and stratigraphy. As such, the interdependent relationship between early complex life and ocean redox state is unclear. An assemblage of macrofossils including the chlorophyte macroalga Archaeochaeta guncho was recently discovered in the lower Mackenzie Mountains Supergroup in Yukon (Canada), which archives marine sedimentation from ca. 950-775 Ma, permitting investigation into environmental evolution coincident with eukaryotic ecosystem evolution and expansion. Here we present multi-proxy geochemical data from the lower Mackenzie Mountains Supergroup to constrain the paleoredox environment within which these large benthic macroalgae thrived. Two transects show evidence for basin-wide anoxic (ferruginous) oceanic conditions (i.e., high FeHR/FeT, low Fepy/FeHR), with muted redox-sensitive trace metal enrichments and possible seasonal variability. However, the weathering of sulfide minerals in the studied samples may obscure geochemical signatures of euxinic conditions. These results suggest that macroalgae colonized shallow environments in an ocean that remained dominantly anoxic with limited evidence for oxygenation until ca. 850 Ma. Collectively, these geochemical results provide novel insights into the environmental conditions surrounding the evolution and expansion of benthic macroalgae and the eventual dominance of oxygenated oceanic conditions required for the later emergence of animals.

Design and analysis of novel microelectromechanical system based microgripper for manipulating microbiological species and micro objects

Design and analysis of a pair of novel microelectromechanical system (MEMS) microgrippers having single and multiple sets of jaws respectively, incorporated with displacement amplification mechanism and electrostatic force sensor is presented in this research work. The novelty of the proposed microgrippers is their unique and efficient designs, having the versatility of gripping ranges. The size of the microgripper is 3.2 × 3.7 mm2 in both cases and has one and three sets of jaws with gripping ranges of 30–64 µm, 175–200 µm, and 350–380 µm respectively. The three jaw sets are application-specific to the multicellular small organism, eukaryotic cells, and microcells, respectively. The microgrippers are being actuated by an optimized V-shaped thermal chevron actuator whose input is amplified by using a pantograph displacement amplification mechanism with an amplification factor of 54. The force applied to the gripping object is sensed by a rotary comb electrostatic force sensor. Special attention has been paid to the structural design, and detailed stress analysis has been discussed. This research work includes static, electrostatic, parametric, and electrothermal analysis carried out using Finite Element Method (FEM) techniques and analytical modeling. The results show that the operating voltage range of the devices is from 4 to 9.25 V, having a maximum operational temperature of 380 °C with a factor of safety of 1.026. The maximum capacitance change with the full operational range of microgrippers is 0.63 µf, having a capacitive sensitivity of 19.6 nf/µm. The microgrippers can be used as an instrument to grip not only the microbiological species but also can be beneficial to carry out manipulations at the micro-level like micro-assembly. The proposed microgripper has a substantial structural stability, has a high amplification factor and accommodates manipulation of a wide range of microorganism.

Transforming perspectives on gender through imagined futures: A speculative design inquiry

This paper will present a second-year Fashion Design Theory project, ‘Imagining Gender Equality in 100 Years’. The project outcomes were based on the critical design approach of speculative design (SD), exploring the intersectional issues of gender relevant to a South African context. SD thrives on imagination to create scenarios that change perspectives, beliefs, and values related to social problems. The following questions were posed to the students in developing the project guidelines. Firstly, what will the change in values, beliefs, and attitudes related to issues of gender look like in the future? And how can students use design to imagine spaces in the present for discussion and debate about alternative ways of being in an imagined future? With the application of action research, the paper discusses and analyses a selection of student projects completed in 2020 and 2021. In doing this, the paper aims to reflect on the transformation of a design theory assessment by applying critical design approaches culminating in creative and conceptual outcomes for complex life problems. In addition, reflections and lessons learnt on the blended teaching and learning methods amidst Covid-19 will be imparted.

Disruption of metazoan gene regulatory networks in cancer alters the balance of co-expression between genes of unicellular and multicellular origins

BackgroundMetazoans inherited genes from unicellular ancestors that perform essential biological processes such as cell division, metabolism, and protein translation. Multicellularity requires careful control and coordination of these unicellular genes to maintain tissue integrity and homeostasis. Gene regulatory networks (GRNs) that arose during metazoan evolution are frequently altered in cancer, resulting in over-expression of unicellular genes. We propose that an imbalance in co-expression of unicellular (UC) and multicellular (MC) genes is a driving force in cancer.ResultsWe combine gene co-expression analysis to infer changes to GRNs in cancer with protein sequence conservation data to distinguish genes with UC and MC origins. Co-expression networks created using RNA sequencing data from 31 tumor types and normal tissue samples are divided into modules enriched for UC genes, MC genes, or mixed UC-MC modules. The greatest differences between tumor and normal tissue co-expression networks occur within mixed UC-MC modules. MC and UC genes not commonly co-expressed in normal tissues form distinct co-expression modules seen only in tumors. The degree of rewiring of genes within mixed UC-MC modules increases with tumor grade and stage. Mixed UC-MC modules are enriched for somatic mutations in cancer genes, particularly amplifications, suggesting an important driver of the rewiring observed in tumors is copy number changes.ConclusionsOur study shows the greatest changes to gene co-expression patterns during tumor progression occur between genes of MC and UC origins, implicating the breakdown and rewiring of metazoan gene regulatory networks in cancer development and progression.

The impact of developmental stage, tissue type, and sex on DNA double-strand break repair in Drosophila melanogaster.

Accurate repair of DNA double-strand breaks (DSBs) is essential for the maintenance of genome integrity, as failure to repair DSBs can result in cell death. The cell has evolved two main mechanisms for DSB repair: non-homologous end-joining (NHEJ) and homology-directed repair (HDR), which includes single-strand annealing (SSA) and homologous recombination (HR). While certain factors like age and state of the chromatin are known to influence DSB repair pathway choice, the roles of developmental stage, tissue type, and sex have yet to be elucidated in multicellular organisms. To examine the influence of these factors, DSB repair in various embryonic developmental stages, larva, and adult tissues in Drosophila melanogaster was analyzed through molecular analysis of the DR-white assay using Tracking across Indels by DEcomposition (TIDE). The proportion of HR repair was highest in tissues that maintain the canonical (G1/S/G2/M) cell cycle and suppressed in both terminally differentiated and polyploid tissues. To determine the impact of sex on repair pathway choice, repair in different tissues in both males and females was analyzed. When molecularly examining tissues containing mostly somatic cells, males and females demonstrated similar proportions of HR and NHEJ. However, when DSB repair was analyzed in male and female premeiotic germline cells utilizing phenotypic analysis of the DR-white assay, there was a significant decrease in HR in females compared to males. This study describes the impact of development, tissue-specific cycling profile, and, in some cases, sex on DSB repair outcomes, underscoring the complexity of repair in multicellular organisms.

Diversity of genome size and chromosome number in homothallic and heterothallic strains of the Closterium peracerosum-strigosum-littorale complex (Desmidiales, Zygnematophyceae, Streptophyta).

The evolutionary transitions of mating systems between outcrossing and self-fertilization are often suggested to associate with the cytological and genomic changes, but the empirical reports are limited in multicellular organisms. Here we used the unicellular zygnematophycean algae, the Closterium peracerosum-strigosum-littorale (C. psl.) complex, to address whether genomic properties such as genome sizes and chromosome numbers are associated with mating system transitions between homothallism (self-fertility) and heterothallism (self-sterility). Phylogenetic analysis revealed the polyphyly of homothallic strains, suggesting multiple transitions between homothallism and heterothallism in the C. psl. complex. Flow cytometry analysis identified a more than 2-fold genome size variation, ranging from 0.53 to 1.42 Gbp, which was positively correlated with chromosome number variation between strains. Although we did not find consistent trends in genome size change and mating system transitions, the mean chromosome sizes tend to be smaller in homothallic strains than in their relative heterothallic strains. This result suggests that homothallic strains possibly have more fragmented chromosomes, which is consistent with the argument that self-fertilizing populations may tolerate more chromosomal rearrangements.

Positive-unlabeled learning identifies vaccine candidate antigens in the malaria parasite Plasmodium falciparum

Malaria vaccine development is hampered by extensive antigenic variation and complex life stages of Plasmodium species. Vaccine development has focused on a small number of antigens, many of which were identified without utilizing systematic genome-level approaches. In this study, we implement a machine learning-based reverse vaccinology approach to predict potential new malaria vaccine candidate antigens. We assemble and analyze P. falciparum proteomic, structural, functional, immunological, genomic, and transcriptomic data, and use positive-unlabeled learning to predict potential antigens based on the properties of known antigens and remaining proteins. We prioritize candidate antigens based on model performance on reference antigens with different genetic diversity and quantify the protein properties that contribute most to identifying top candidates. Candidate antigens are characterized by gene essentiality, gene ontology, and gene expression in different life stages to inform future vaccine development. This approach provides a framework for identifying and prioritizing candidate vaccine antigens for a broad range of pathogens.

Effect of Helichrysum italicum in Promoting Collagen Deposition and Skin Regeneration in a New Dynamic Model of Skin Wound Healing.

Natural products have many healing effects on the skin with minimal or no adverse effects. In this study, we analyzed the regenerative properties of a waste product (hydrolate) derived from Helichrysum italicum (HH) on scratch-tested skin cell populations seeded on a fluidic culture system. Helichrysum italicum has always been recognized in the traditional medicine of Mediterranean countries for its wide pharmacological activities. We recreated skin physiology with a bioreactor that mimics skin stem cell (SSCs) and fibroblast (HFF1) communication as in vivo skin layers. Dynamic culture models represent an essential instrument for recreating and preserving the complex multicellular organization and interactions of the cellular microenvironment. Both cell types were exposed to two different concentrations of HH after the scratch assay and were compared to untreated control cells. Collagen is the constituent of many wound care products that act directly on the damaged wound environment. We analyzed the role played by HH in stimulating collagen production during tissue repair, both in static and dynamic culture conditions, by a confocal microscopic analysis. In addition, we performed a gene expression analysis that revealed the activation of a molecular program of stemness in treated skin stem cells. Altogether, our results indicate a future translational application of this natural extract to support skin regeneration and define a new protocol to recreate a dynamic process of healing.