Control of crystal size and lattice formation by starmaker in otolith biomineralization

HcN57, A Novel Unusual Acidic Silk-Like Matrix Protein from Hyriopsis cumingii, Participates in Framework Construction and Nacre Nucleation During Nacreous Layer Formation

In the classic molecular model of nacreous layer formation, unusual acidic matrix proteins rich in aspartic acid (Asp) residues are essential for nacre nucleation due to their great affinity for binding calcium. However, the acidic matrix proteins discovered in the nacreous layer so far have been weakly acidic with a high proportion of glutamate. In the present study, several silk-like matrix proteins, including the novel matrix protein HcN57, were identified in the ethylenediaminetetraacetic acid-soluble extracts of the nacreous layer of Hyriopsis cumingii. HcN57 is a highly repetitive protein that consists of a high proportion of alanine (Ala, 34.4%), glycine (Gly, 22.5%), and serine (Ser, 11.4%). It forms poly Ala blocks, GlynX repeats, an Ala-Gly repeat, and a Ser-Ala-rich region, exhibiting significant similarity to silk proteins found in spider species. The expression of HcN57 was specifically located in the dorsal epithelial cells of the mantle pallium and mantle center. Notably, expression of HcN57 was relatively high during nacreous layer regeneration and pearl nacre deposition, suggesting HcN57 is a silk matrix protein in the nacreous layer. Importantly, HcN57 also contains a certain content of Asp residues, making it an unusual acidic matrix protein present in the nacreous layer. These Asp residues are mainly distributed in three large hydrophilic acidic regions, which showed inhibitory activity against aragonite deposition and morphological regulation of calcite in vitro. Moreover, HcN57-dsRNA injection resulted in failure of nacre nucleation in vivo. Taken together, our results show that HcN57 is a bifunctional silk protein with poly Ala blocks and Gly-rich regions that serve as space fillers within the chitinous framework to prevent crystallization at unnecessary nucleation sites and Asp-rich regions that create a calcium ion supersaturated microenvironment for nucleation in the center of nacre tablets. These observations contribute to a better understanding of the mechanism by which silk proteins regulate framework construction and nacre nucleation during nacreous layer formation.

Immunohistochemical and ultrastructural characterization of the inner ear epithelial cells of splitnose rockfish (Sebastes diploproa)

The inner ear of teleost fish regulates the ionic and acid-base chemistry and secretes protein matrix into the endolymph to facilitate otolith biomineralization, which is used to maintain vestibular and auditory functions. The otolith is biomineralized in a concentric ring pattern corresponding to seasonal growth, and this calcium carbonate (CaCO3) polycrystal has become a vital aging and life-history tool for fishery managers, ecologists, and conservation biologists. Moreover, biomineralization patterns are sensitive to environmental variability including climate change, thereby threatening the accuracy and relevance of otolith-reliant toolkits. However, the cellular biology of the inner ear is poorly characterized, which is a hurdle for a mechanistic understanding of the underlying processes. This study provides a systematic characterization of the cell types in the inner ear of splitnose rockfish (Sebastes diploproa). Scanning electron microscopy revealed the apical morphologies of six inner ear cell types. In addition, immunostaining and confocal microscopy characterized the expression and subcellular localization of the proteins Na+-K+-ATPase, carbonic anhydrase, V-type H+-ATPase, Na+-K+-2Cl--cotransporter, otolith matrix protein 1, and otolin-1 in six inner ear cell types bordering the endolymph. This fundamental cytological characterization of the rockfish inner ear epithelium illustrates the intricate physiological processes involved in otolith biomineralization and highlights how greater mechanistic understanding is necessary to predict their multistressor responses to future climate change.

Chirality Supramolecular Systems: Helical Assemblies, Structure Designs, and Functions

Chirality, as one of the most striking characteristics, exists at various scales in nature. Originating from the interactions of host and guest molecules, supramolecular chirality possesses huge potential in the design of functional materials. Here, an overview of the recent progress in structure designs and functions of chiral supramolecular materials is present. First, three design routes of the chiral supramolecular structure are summarized. Compared with the template-induced and chemical synthesis strategies that depend on accurate molecular identification, the twisted-assembly technique creates chiral materials through the ordered stacking of the nanowire or films. Next, chirality inversion and amplification are reviewed to explain the chirality transfer from the molecular level to the macroscopic scale, where the available external stimuli on the chirality inversion are also given. Lastly, owing to the optical activity and the characteristics of the layer-by-layer stacking structure, the supramolecular chirality materials display various excellent performances, including smart response, shape-memorization, superior mechanical performance, and applications in biomedical fields. To sum up, this work provides a systematic review of the helical assemblies, structure design, and applications of supramolecular chirality systems.

Calcium carbonate polymorph selection in fish otoliths: A key role of phosphorylation of Starmaker-like protein

Fish otoliths are calcium carbonate biominerals found in the inner ear commonly used for tracking fish biochronologies and as a model system for biomineralization. The process of fish otolith formation is biologically controlled by numerous biomacromolecules which not only affect crystal size, shape, mechanical properties, but also selection of calcium carbonate polymorph (e.g., aragonite, vaterite). The proteinaceous control over calcium carbonate polymorph selection occurs in many other species (e.g., corals, mollusks, echinoderms) but the exact mechanism of protein interactions with calcium and carbonate ions - constituents of CaCO3 - are not fully elucidated. Herein, we focus on a native Starmaker-like protein isolated from vaterite asteriscus otoliths from Cyprinus carpio. The proteomic studies show the presence of the phosphorylated protein in vaterite otoliths. In a series of in vitro mineralization experiments with Starmaker-like, we show that native phosphorylation is a crucial determinant for the selection of a crystal's polymorphic form. This is the first report showing that the switch in calcium carbonate phase depends on the phosphorylation pattern of a single isolated protein. STATEMENT OF SIGNIFICANCE: Calcium carbonate has numerous applications in industry and medicine. However, we still do not understand the mechanism of biologically driven polymorph selection which results in specific biomineral properties. Previous work on calcium carbonate biominerals showed that either several macromolecular factors or high magnesium concentration (non-physiological) are required for proper polymorph selection (e.g., in mollusk shells, corals and otoliths). In this work, we showed for the first time that protein phosphorylation is a crucial factor for controlling the calcium carbonate crystal phase. This is important because a single protein from the otolith organic matrix could switch between polymorphs depending on the phosphorylation level. It seems that protein post-translational modifications (native, not artificial) are more important for biomolecular control of crystal growth than previously considered.

Single-cell RNA sequencing unravels the transcriptional network underlying zebrafish retina regeneration

In the lesioned zebrafish retina, Müller glia produce multipotent retinal progenitors that generate all retinal neurons, replacing lost cell types. To study the molecular mechanisms linking Müller glia reactivity to progenitor production and neuronal differentiation, we used single-cell RNA sequencing of Müller glia, progenitors and regenerated progeny from uninjured and light-lesioned retinae. We discover an injury-induced Müller glia differentiation trajectory that leads into a cell population with a hybrid identity expressing marker genes of Müller glia and progenitors. A glial self-renewal and a neurogenic trajectory depart from the hybrid cell population. We further observe that neurogenic progenitors progressively differentiate to generate retinal ganglion cells first and bipolar cells last, similar to the events observed during retinal development. Our work provides a comprehensive description of Müller glia and progenitor transcriptional changes and fate decisions in the regenerating retina, which are key to tailor cell differentiation and replacement therapies for retinal dystrophies in humans.

Genetic and Epigenetic Evidence for Nonestrogenic Disruption of Otolith Development by Bisphenol A in Zebrafish

Bisphenol A (BPA) is a well-known endocrine-disrupting chemical (EDC) that has estrogenic activities. In addition to disrupting reproductive development and function via estrogenic signaling pathways, BPA can also interfere with nonreproductive functions through nonestrogenic pathways; however, the mechanisms underlying such nonestrogenic activities are not well understood. In this study, we demonstrated that BPA could disrupt otolith formation during the early development of zebrafish with long-lasting ethological effects. Using multiple mutants of estrogen receptors, we provided strong genetic evidence that the BPA-induced otolith malformation was independent of estrogen signaling. Transcriptome analysis revealed that two genes related to otolith development, otopetrin 1 (otop1) and starmaker (stm), decreased their expression significantly after BPA exposure. Knockout of both otop1 and stm genes could phenocopy the BPA-induced otolith malformation, while microinjection of their mRNAs could rescue the BPA-induced abnormalities of otolith formation. Further experiments showed that BPA inhibited the expression of otop1 and stm by activating the MEK/ERK-EZH2-H3K27me3 signaling pathway. Taken together, our study provided comprehensive genetic and molecular evidence that BPA induced the otolith malformation through nonestrogenic pathway during zebrafish early development and its activities involved epigenetic control of key genes (e.g., otop1 and stm) participating in otolith formation.

Nonclassical mechanisms to irreversibly suppress β-hematin crystal growth

Hematin crystallization is an essential element of heme detoxification of malaria parasites and its inhibition by antimalarial drugs is a common treatment avenue. We demonstrate at biomimetic conditions in vitro irreversible inhibition of hematin crystal growth due to distinct cooperative mechanisms that activate at high crystallization driving forces. The evolution of crystal shape after limited-time exposure to both artemisinin metabolites and quinoline-class antimalarials indicates that crystal growth remains suppressed after the artemisinin metabolites and the drugs are purged from the solution. Treating malaria parasites with the same agents reveals that three- and six-hour inhibitor pulses inhibit parasite growth with efficacy comparable to that of inhibitor exposure during the entire parasite lifetime. Time-resolved in situ atomic force microscopy (AFM), complemented by light scattering, reveals two molecular-level mechanisms of inhibitor action that prevent β-hematin growth recovery. Hematin adducts of artemisinins incite copious nucleation of nonextendable nanocrystals, which incorporate into larger growing crystals, whereas pyronaridine, a quinoline-class drug, promotes step bunches, which evolve to engender abundant dislocations. Both incorporated crystals and dislocations are known to induce lattice strain, which persists and permanently impedes crystal growth. Nucleation, step bunching, and other cooperative behaviors can be amplified or curtailed as means to control crystal sizes, size distributions, aspect ratios, and other properties essential for numerous fields that rely on crystalline materials.

Rearing in strontium-enriched water induces vaterite otoliths in the Japanese rice fish, Oryzias latipes

Sagittal otoliths, typically composed of aragonite, are frequently laid down rather as vaterite during growth in hatchery-reared fish populations. Sagittal vateritization is believed to impair individual hearing/balancing abilities, but the causal mechanism remains unclear. Here we experimentally demonstrated that rearing in Sr-rich water induces sagittal vateritization in the HdrR-II1 inbred strain of the Japanese rice fish, Oryzias latipes. Both sagittae were partly vateritized in 70% of individuals subjected to the Sr²⁺ treatment (n = 10), whereas fish reared in normal tap water showed no sagittal vateritization (n = 8). Our result is consistent with the theoretical prediction that vaterite becomes thermodynamically more stable than aragonite as the Sr²⁺ concentration in solution increases. A vateritic layer develops surrounding the original aragonitic sagitta in vateritized otoliths, some of which take on a comma-like shape. Electron probe microanalysis demonstrates that the vateritized phase is characterized by lower Sr²⁺ and higher Mg²⁺ concentrations than the aragonitic phase. It is unlikely that increased environmental Sr²⁺ is responsible for the sagittal vateritization in farmed fish. However, our findings likely help to establish an in vivo assay using O. latipes to understand the physiological process underlying the sagittal vateritization in farmed fish.

Oxide- and Silicate-Water Interfaces and Their Roles in Technology and the Environment

Interfacial reactions drive all elemental cycling on Earth and play pivotal roles in human activities such as agriculture, water purification, energy production and storage, environmental contaminant remediation, and nuclear waste repository management. The onset of the 21st century marked the beginning of a more detailed understanding of mineral aqueous interfaces enabled by advances in techniques that use tunable high-flux focused ultrafast laser and X-ray sources to provide near-atomic measurement resolution, as well as by nanofabrication approaches that enable transmission electron microscopy in a liquid cell. This leap into atomic- and nanometer-scale measurements has uncovered scale-dependent phenomena whose reaction thermodynamics, kinetics, and pathways deviate from previous observations made on larger systems. A second key advance is new experimental evidence for what scientists hypothesized but could not test previously, namely, interfacial chemical reactions are frequently driven by "anomalies" or "non-idealities" such as defects, nanoconfinement, and other nontypical chemical structures. Third, progress in computational chemistry has yielded new insights that allow a move beyond simple schematics, leading to a molecular model of these complex interfaces. In combination with surface-sensitive measurements, we have gained knowledge of the interfacial structure and dynamics, including the underlying solid surface and the immediately adjacent water and aqueous ions, enabling a better definition of what constitutes the oxide- and silicate-water interfaces. This critical review discusses how science progresses from understanding ideal solid-water interfaces to more realistic systems, focusing on accomplishments in the last 20 years and identifying challenges and future opportunities for the community to address. We anticipate that the next 20 years will focus on understanding and predicting dynamic transient and reactive structures over greater spatial and temporal ranges as well as systems of greater structural and chemical complexity. Closer collaborations of theoretical and experimental experts across disciplines will continue to be critical to achieving this great aspiration.

First paleoproteome study of fossil fish otoliths and the pristine preservation of the biomineral crystal host

Otoliths are calcium carbonate components of the stato-acoustical organ responsible for hearing and maintenance of the body balance in teleost fish. During their formation, control over, e.g., morphology and carbonate polymorph is influenced by complex insoluble collagen-like protein and soluble non-collagenous protein assemblages; many of these proteins are incorporated into their aragonite crystal structure. However, in the fossil record these proteins are considered lost through diagenetic processes, hampering studies of past biomineralization mechanisms. Here we report the presence of 11 fish-specific proteins (and several isoforms) in Miocene (ca. 14.8-14.6 Ma) phycid hake otoliths. These fossil otoliths were preserved in water-impermeable clays and exhibit microscopic and crystallographic features indistinguishable from modern representatives, consistent with an exceptionally pristine state of preservation. Indeed, these fossil otoliths retain ca. 10% of the proteins sequenced from modern counterparts, including proteins specific to inner ear development, such as otolin-1-like proteins involved in the arrangement of the otoliths into the sensory epithelium and otogelin/otogelin-like proteins that are located in the acellular membranes of the inner ear in modern fish. The specificity of these proteins excludes the possibility of external contamination. Identification of a fraction of identical proteins in modern and fossil phycid hake otoliths implies a highly conserved inner ear biomineralization process through time.

Single-cell transcriptomic profiling of the zebrafish inner ear reveals molecularly distinct hair cell and supporting cell subtypes

A major cause of human deafness and vestibular dysfunction is permanent loss of the mechanosensory hair cells of the inner ear. In non-mammalian vertebrates such as zebrafish, regeneration of missing hair cells can occur throughout life. While a comparative approach has the potential to reveal the basis of such differential regenerative ability, the degree to which the inner ears of fish and mammals share common hair cells and supporting cell types remains unresolved. Here, we perform single-cell RNA sequencing of the zebrafish inner ear at embryonic through adult stages to catalog the diversity of hair cells and non-sensory supporting cells. We identify a putative progenitor population for hair cells and supporting cells, as well as distinct hair and supporting cell types in the maculae versus cristae. The hair cell and supporting cell types differ from those described for the lateral line system, a distributed mechanosensory organ in zebrafish in which most studies of hair cell regeneration have been conducted. In the maculae, we identify two subtypes of hair cells that share gene expression with mammalian striolar or extrastriolar hair cells. In situ hybridization reveals that these hair cell subtypes occupy distinct spatial domains within the three macular organs, the utricle, saccule, and lagena, consistent with the reported distinct electrophysiological properties of hair cells within these domains. These findings suggest that primitive specialization of spatially distinct striolar and extrastriolar hair cells likely arose in the last common ancestor of fish and mammals. The similarities of inner ear cell type composition between fish and mammals validate zebrafish as a relevant model for understanding inner ear-specific hair cell function and regeneration.

Otoliths of Caspian gobies (Teleostei: Gobiidae): Morphological diversity and phylogenetic implications

Otoliths (ear stones) of the inner ears of teleost fishes, which develop independently from the skeleton and are functionally associated with hearing and the sense of equilibrium, have significantly contributed to contemporary understanding of teleost fish systematics and evolutionary diversity. The sagittal otolith is of particular interest, since it often possesses distinctive morphological features that differ significantly among species, and have been shown to be species- and genus-specific, making it an informative taxonomic tool for ichthyologists. The otolith morphology of the Caspian Sea gobiids has not been thoroughly studied yet, with data available for only a few species. The aim of the present paper is to examine the qualitative and quantitative taxonomic and phylogenetic information in the sagittal otoliths of these species. A total of 118 otoliths representing 30 gobiid species (including 53.5% of the Caspian gobiofauna) in three gobiid lineages (i.e., Gobius, Pomatoschistus, and Acanthogobius) and 11 genera (i.e., all Ponto-Caspian gobiid genera except Babka) were analysed at taxonomic levels using an integrated descriptive and morphometric approach. The results indicated high taxonomic efficiency of otolith morphology and morphometry at taxonomic levels for the Ponto-Caspian gobiids. Our qualitative and quantitative otolith data also (i) support the monophyly of neogobiin gobies, (ii) along with other morphological and ecological data, offer a new perspective on the systematics of Neogobius bathybius, (iii) suggest the reassignment of Hyrcanogobius bergi to the genus Knipowitschia, and (iv) question the phylogenetic integrity of the four phenotypic groups previously defined in the tadpole-goby genus Benthophilus; however, more studies are needed to complete these evaluations and confirm our otolith study findings.

Visual, spectral, and microchemical quantification of crystalline anomalies in otoliths of wild and cultured delta smelt

Developmental abnormalities in otoliths can impact growth and survival in teleost fishes. Here, we quantified the frequency and severity of developmental anomalies in otoliths of delta smelt (Hypomesus transpacificus), a critically endangered estuarine fish that is endemic to the San Francisco Estuary. Left-right asymmetry and anomalous crystalline polymorphs (i.e., vaterite) were quantified and compared between wild and cultured populations using digital image analysis. Visual estimates of vaterite were validated using X-ray diffraction, Raman spectroscopy, laser ablation ICPMS, and electron probe microanalysis. Results indicated that cultured delta smelt were 80 times more likely to contain a vateritic otolith and 18 times more likely to contain relatively large (≥ 15%) amounts of vaterite. Similarly, cultured fish exhibited 30% greater asymmetry than wild fish. These results indicate that cultured delta smelt exhibit a significantly higher frequency of vestibular abnormalities which are known to reduce fitness and survival. Such hatchery effects on otolith development could have important implications for captive culture practices and the supplementation of wild fish populations with cultured individuals.

The Role of Intrinsically Disordered Proteins in Liquid–Liquid Phase Separation during Calcium Carbonate Biomineralization

Some animal organs contain mineralized tissues. These so-called hard tissues are mostly deposits of calcium salts, usually in the form of calcium phosphate or calcium carbonate. Examples of this include fish otoliths and mammalian otoconia, which are found in the inner ear, and they are an essential part of the sensory system that maintains body balance. The composition of ear stones is quite well known, but the role of individual components in the nucleation and growth of these biominerals is enigmatic. It is sure that intrinsically disordered proteins (IDPs) play an important role in this aspect. They have an impact on the shape and size of otoliths. It seems probable that IDPs, with their inherent ability to phase separate, also play a role in nucleation processes. This review discusses the major theories on the mechanisms of biomineral nucleation with a focus on the importance of protein-driven liquid–liquid phase separation (LLPS). It also presents the current understanding of the role of IDPs in the formation of calcium carbonate biominerals and predicts their potential ability to drive LLPS.

Presence of chondroitin sulphate and requirement for heparan sulphate biosynthesis in the developing zebrafish inner ear

Epithelial morphogenesis to form the semicircular canal ducts of the zebrafish inner ear depends on the production of the large glycosaminoglycan hyaluronan, which is thought to contribute to the driving force that pushes projections of epithelium into the lumen of the otic vesicle. Proteoglycans are also implicated in otic morphogenesis: several of the genes coding for proteoglycan core proteins, together with enzymes that synthesise and modify their polysaccharide chains, are expressed in the developing zebrafish inner ear. In this study, we demonstrate the highly specific localisation of chondroitin sulphate to the sites of epithelial projection outgrowth in the ear, present before any morphological deformation of the epithelium. Staining for chondroitin sulphate is also present in the otolithic membrane, whereas the otoliths are strongly positive for keratan sulphate. We show that heparan sulphate biosynthesis is critical for normal epithelial projection outgrowth, otolith growth and tethering. In the ext2 mutant ear, which has reduced heparan sulphate levels, but continues to produce hyaluronan, epithelial projections are rudimentary, and do not grow sufficiently to meet and fuse to form the pillars of tissue that normally span the otic lumen. Staining for chondroitin sulphate and expression of versican b, a chondroitin sulphate proteoglycan core protein gene, persist abnormally at high levels in the unfused projections of the ext2 mutant ear. We propose a model for wild-type epithelial projection outgrowth in which hyaluronan and proteoglycans are linked to form a hydrated gel that fills the projection core, with both classes of molecule playing essential roles in zebrafish semicircular canal morphogenesis.

Retinoic acid signaling regulates late stages of semicircular canal morphogenesis and otolith maintenance in the zebrafish inner ear

BACKGROUND

The vitamin A derivative all-trans retinoic acid (RA) regulates early stages of inner ear development. As the early disruption of the RA pathway results in profound mispatterning of the developing inner ear, this confounds analyses of specific roles in later stages. Therefore, we used the temporal-specific exposure of all-trans RA or diethylaminobenzaldehyde to evaluate RA functions in late otic development.

RESULTS

Perturbing late RA signaling causes behavioral defects analogous to those expected in larvae suffering from vestibular dysfunction. These larvae also demonstrate malformations of the semi-circular canals, as visualized through (a) use of the transgenic strain nkhspdmc12a, a fluorescent reporter expressed in otic epithelium; and (b) injection of the fluorescent lipophilic dye DiI. We also noted the altered expression of genes encoding ECM proteins or modifying enzymes. Other malformations of the inner ear observed in our work include the loss or reduced size of the utricular and saccular otoliths, suggesting a role for RA in otolith maintenance.

CONCLUSION

Our work has identified a previously undescribed late phase of RA activity in otic development, demonstrating that vestibular defects observed in human patients in relation to perturbed RA signaling are not solely due to its early disruption in otic development.

Single-cell transcriptome reveals insights into the development and function of the zebrafish ovary

Zebrafish are an established research organism that has made many contributions to our understanding of vertebrate tissue and organ development, yet there are still significant gaps in our understanding of the genes that regulate gonad development, sex, and reproduction. Unlike the development of many organs, such as the brain and heart that form during the first few days of development, zebrafish gonads do not begin to form until the larval stage (≥5 dpf). Thus, forward genetic screens have identified very few genes required for gonad development. In addition, bulk RNA sequencing studies which identify genes expressed in the gonads do not have the resolution necessary to define minor cell populations that may play significant roles in development and function of these organs. To overcome these limitations, we have used single-cell RNA sequencing to determine the transcriptomes of cells isolated from juvenile zebrafish ovaries. This resulted in the profiles of 10,658 germ cells and 14,431 somatic cells. Our germ cell data represents all developmental stages from germline stem cells to early meiotic oocytes. Our somatic cell data represents all known somatic cell types, including follicle cells, theca cells and ovarian stromal cells. Further analysis revealed an unexpected number of cell subpopulations within these broadly defined cell types. To further define their functional significance, we determined the location of these cell subpopulations within the ovary. Finally, we used gene knockout experiments to determine the roles of foxl2l and wnt9b for oocyte development and sex determination and/or differentiation, respectively. Our results reveal novel insights into zebrafish ovarian development and function and the transcriptome profiles will provide a valuable resource for future studies.

Biomineralization: Integrating mechanism and evolutionary history

Calcium carbonate (CaCO₃) biomineralizing organisms have played major roles in the history of life and the global carbon cycle during the past 541 Ma. Both marine diversification and mass extinctions reflect physiological responses to environmental changes through time. An integrated understanding of carbonate biomineralization is necessary to illuminate this evolutionary record and to understand how modern organisms will respond to 21st century global change. Biomineralization evolved independently but convergently across phyla, suggesting a unity of mechanism that transcends biological differences. In this review, we combine CaCO₃ skeleton formation mechanisms with constraints from evolutionary history, omics, and a meta-analysis of isotopic data to develop a plausible model for CaCO₃ biomineralization applicable to all phyla. The model provides a framework for understanding the environmental sensitivity of marine calcifiers, past mass extinctions, and resilience in 21st century acidifying oceans. Thus, it frames questions about the past, present, and future of CaCO₃ biomineralizing organisms.

Quantifying fish otolith mineralogy for trace-element chemistry studies

Otoliths are frequently used to infer environmental conditions or fish life history events based on trace-element concentrations. However, otoliths can be comprised of any one or combination of the three most common polymorphs of calcium carbonate—aragonite, calcite, and vaterite—which can affect the ecological interpretation of otolith trace-element results. Previous studies have reported heterogeneous calcium carbonate compositions between left and right otoliths but did not provide quantitative assessments of polymorph abundances. In this study, neutron diffraction and Raman spectroscopy were used to identify and quantify mineralogical compositions of Chinook salmon Oncorhynchus tshawytscha otolith pairs. We found mineralogical compositions frequently differed between otoliths in a pair and accurate calcium carbonate polymorph identification was rarely possible by visual inspection alone. The prevalence of multiple polymorphs in otoliths is not well-understood, and future research should focus on identifying otolith compositions and investigate how variations in mineralogy affect trace-element incorporation and potentially bias environmental interpretations.

Zebrafish stm is involved in the development of otoliths and of the fertilization envelope

Using an in vivo assay, we selected 11 genes that were highly upregulated during the induction of ovulation in zebrafish using microarray analysis and RNA sequencing. The starmaker gene (stm) was one of these genes. Although stm has been previously reported to be involved in otolith formation during the early development of zebrafish, we detected its expression in eggs and showed that stm was related to fertilization by establishing an stm gene knockout strain using the CRISPR/Cas9 system. Further phenotypic analysis of stm knockout fish was conducted in this study. With a higher nonfertilization rate, the stm mutant strain showed an extremely low survival rate. Otoliths of stm homozygous mutant zebrafish showed abnormal morphology in embryos and adult fish. However, fish did not show any abnormalities in swimming behaviour in either embryos or adults. Stm proteins were detected on the chorion of ovulated eggs before spawning. Fibre-supported knob-like structures on the fertilization envelope (FE) also showed abnormal structures in stm mutants. The Stm protein is necessary for otolith formation, and a lack of Stm causes abnormal otolith formation. The partial defect of otolith formation does not cause defects in swimming behaviour. The Stm protein is expressed in the chorion and is responsible for the formation of fibre-supported knob-like structures on the FE. It was suggested that a lack of Stm caused a lower fertilization rate due to inadequate formation of the FE.

Lay summary

In zebrafish, the protein Starmaker (Stm) was identified as having a role in ovulation. Stm is also known to be required for the formation of ear stones (otoliths) which are needed to keep the body in balance. Zebrafish lacking Stm were produced by genome editing. As expected, Stm-deficient fish formed abnormal otoliths. To investigate the role of Stm in ovulation, fertilization and early development, we tried mating of Stm mutants and observed their juveniles. Although no problem found in ovulation, we found low fertilization rate and abnormal structure of knob-like structure (small pit) on the egg membrane. Survival rate of embryos with abnormal egg membrane was extremely low. It was demonstrated that Stm protein is necessary to form the functional egg membrane to protect embryos from the outside environment.

Whole-Genome Sequencing and Genome-Wide Studies of Spiny Head Croaker (Collichthys lucidus) Reveals Potential Insights for Well-Developed Otoliths in the Family Sciaenidae

Spiny head croaker (Collichthys lucidus), belonging to the family Sciaenidae, is a small economic fish with a main distribution in the coastal waters of Northwestern Pacific. Here, we constructed a nonredundant chromosome-level genome assembly of spiny head croaker and also made genome-wide investigations on genome evolution and gene families related to otolith development. A primary genome assembly of 811.23 Mb, with a contig N50 of 74.92 kb, was generated by a combination of 49.12-Gb Illumina clean reads and 35.24 Gb of PacBio long reads. Contigs of this draft assembly were further anchored into chromosomes by integration with additional 185.33-Gb Hi-C data, resulting in a high-quality chromosome-level genome assembly of 817.24 Mb, with an improved scaffold N50 of 26.58 Mb. Based on our phylogenetic analysis, we observed that C. lucidus is much closer to Larimichthys crocea than Miichthys miiuy. We also predicted that many gene families were significantly expanded (p-value <0.05) in spiny head croaker; among them, some are associated with "calcium signaling pathway" and potential "inner ear functions." In addition, we identified some otolith-related genes (such as otol1a that encodes Otolin-1a) with critical deletions or mutations, suggesting possible molecular mechanisms for well-developed otoliths in the family Sciaenidae.

Proceedings of the 2020 Classic Examples in Toxicologic Pathology XXVII

The histopathology slide seminar "Classic Examples in Toxicologic Pathology XXVII" was held on February 21 and 22, 2020, at the Department of Pathology at the University of Veterinary Medicine in Hannover, Germany, with joint organization by the European Society of Toxicologic Pathology. The goal of this annual seminar is to present and discuss classical and actual cases of toxicologic pathology. This article summarizes the presentations given during the seminar, including images of representative lesions. Ten actual and classical cases of toxicologic pathology, mostly induced by a test article, were presented. These included small intestine pathology and transcriptomics induced by a γ-secretase modulator, liver findings in nonhuman primates induced by gene therapy, drug-induced neutropenia in dogs, device-induced growth plate lesions, polycystic lesions in CAR/PXR double knockout mice, inner ear lesions in transgenic mice, findings in Beagle dogs induced by an inhibitor of the myeloid leukemia cell differentiation protein MCL1, findings induced by a monovalent fibroblast growth factor receptor 1 antagonist, kidney lesions induced by a mammalian target of rapamycin inhibitor in combination therapy, and findings in mutation-specific drugs.

Ciliopathy genes are required for apical secretion of Cochlin, an otolith crystallization factor

Here, we report that important regulators of cilia formation and ciliary compartment-directed protein transport function in secretion polarity. Mutations in cilia genes cep290 and bbs2, involved in human ciliopathies, affect apical secretion of Cochlin, a major otolith component and a determinant of calcium carbonate crystallization form. We show that Cochlin, defective in human auditory and vestibular disorder, DFNA9, is secreted from small specialized regions of vestibular system epithelia. Cells of these regions secrete Cochlin both apically into the ear lumen and basally into the basal lamina. Basally secreted Cochlin diffuses along the basal surface of vestibular epithelia, while apically secreted Cochlin is incorporated into the otolith. Mutations in a subset of ciliopathy genes lead to defects in Cochlin apical secretion, causing abnormal otolith crystallization and behavioral defects. This study reveals a class of ciliary proteins that are important for the polarity of secretion and delineate a secretory pathway that regulates biomineralization.

Influence of ontogenetic development, temperature, and pCO2 on otolith calcium carbonate polymorph composition in sturgeons

Changes to calcium carbonate (CaCO₃) biomineralization in aquatic organisms is among the many predicted effects of climate change. Because otolith (hearing/orientation structures in fish) CaCO₃ precipitation and polymorph composition are controlled by genetic and environmental factors, climate change may be predicted to affect the phenotypic plasticity of otoliths. We examined precipitation of otolith polymorphs (aragonite, vaterite, calcite) during early life history in two species of sturgeon, Lake Sturgeon, (Acipenser fulvescens) and White Sturgeon (A. transmontanus), using quantitative X-ray microdiffraction. Both species showed similar fluctuations in otolith polymorphs with a significant shift in the proportions of vaterite and aragonite in sagittal otoliths coinciding with the transition to fully exogenous feeding. We also examined the effect of the environment on otolith morphology and polymorph composition during early life history in Lake Sturgeon larvae reared in varying temperature (16/22 °C) and pCO₂ (1000/2500 µatm) environments for 5 months. Fish raised in elevated temperature had significantly increased otolith size and precipitation of large single calcite crystals. Interestingly, pCO₂ had no statistically significant effect on size or polymorph composition of otoliths despite blood pH exhibiting a mild alkalosis, which is contrary to what has been observed in several studies on marine fishes. These results suggest climate change may influence otolith polymorph composition during early life history in Lake Sturgeon.

Molecular mechanism of calcium induced trimerization of C1q-like domain of otolin-1 from human and zebrafish

The C1q superfamily includes proteins involved in innate immunity, insulin sensitivity, biomineralization and more. Among these proteins is otolin-1, which is a collagen-like protein that forms a scaffold for the biomineralization of inner ear stones in vertebrates. The globular C1q-like domain (gC1q), which is the most conserved part of otolin-1, binds Ca²⁺ and stabilizes its collagen-like triple helix. The molecular details of the assembly of gC1q otolin-1 trimers are not known. Here, we substituted putative Ca²⁺-binding acidic residues of gC1q otolin-1 with alanine to analyse how alanine influences the formation of gC1q trimers. We used human and zebrafish gC1q otolin-1 to assess how evolutionary changes affected the function of the protein. Surprisingly, the mutated forms of gC1q otolin-1 trimerized even in the absence of Ca²⁺, although they were less stable than native proteins saturated with Ca²⁺. We also found that the zebrafish gC1q domain was less stable than the human homologue under all tested conditions and became stabilized at higher concentrations of Ca²⁺, which showed that specific interactions leading to the neutralization of the negative charge at the axis of a gC1q trimer by Ca²⁺ are required for the trimers to form. Moreover, human gC1q otolin-1 seems to be optimized to function at lower concentrations of Ca²⁺, which is consistent with reported Ca²⁺ concentrations in the endolymphs of fish and mammals. Our results allow us to explain the molecular mechanism of assembly of proteins from the C1q superfamily, the modulating role of Ca²⁺ and expand the knowledge of biomineralization of vertebrate inner ear stones: otoliths and otoconia.

The role of Niemann-Pick type C2 in zebrafish embryonic development

Niemann-Pick disease type C (NPC) is a rare, fatal, neurodegenerative lysosomal disease caused by mutations of either NPC1 or NPC2. NPC2 is a soluble lysosomal protein that functions in coordination with NPC1 to efflux cholesterol from the lysosomal compartment. Mutations of either gene result in the accumulation of unesterified cholesterol and other lipids in the late endosome/lysosome, and reduction of cellular cholesterol bioavailability. Zygotic null npc2m/m zebrafish showed significant unesterified cholesterol accumulation at larval stages, a reduction in body size, and motor and balance defects in adulthood. However, the phenotype at embryonic stages was milder than expected, suggesting a possible role of maternal Npc2 in embryonic development. Maternal-zygotic npc2m/m zebrafish exhibited significant developmental defects, including defective otic vesicle development/absent otoliths, abnormal head/brain development, curved/twisted body axes and no circulating blood cells, and died by 72 hpf. RNA-seq analysis conducted on 30 hpf npc2+/m and MZnpc2m/m embryos revealed a significant reduction in the expression of notch3 and other downstream genes in the Notch signaling pathway, suggesting that impaired Notch3 signaling underlies aspects of the developmental defects observed in MZnpc2m/m zebrafish.

Mantle Modularity Underlies the Plasticity of the Molluscan Shell: Supporting Data From Cepaea nemoralis

Molluscs have evolved the capacity to fabricate a wide variety of shells over their 540+ million-year history. While modern sequencing and proteomic technologies continue to expand the catalog of molluscan shell-forming proteins, a complete functional understanding of how any mollusc constructs its shell remains an ambitious goal. This lack of understanding also constrains our understanding of how evolution has generated a plethora of molluscan shell morphologies. Taking advantage of a previous expression atlas for shell-forming genes in Lymnaea stagnalis, I have characterized the spatial expression patterns of seven shell-forming genes in the terrestrial gastropod Cepaea nemoralis, with the aim of comparing and contrasting their expression patterns between the two species. Four of these genes were selected from a previous proteomic screen of the C. nemoralis shell, two were targeted by bioinformatics criteria designed to identify likely shell-forming gene products, and the final one was a clear homolog of a peroxidase sequence in the L. stagnalis dataset. While the spatial expression patterns of all seven C. nemoralis genes could be recognized as falling into distinct zones within the mantle tissue similar to those established in L. stagnalis, some zones have apparently been modified. These similarities and differences hint at a modularity to the molluscan mantle that may provide a mechanistic explanation as to how evolution has efficiently generated a diversity of molluscan shells.

The skeletome of the red coral Corallium rubrum indicates an independent evolution of biomineralization process in octocorals

Background

The process of calcium carbonate biomineralization has arisen multiple times during metazoan evolution. In the phylum Cnidaria, biomineralization has mostly been studied in the subclass Hexacorallia (i.e. stony corals) in comparison to the subclass Octocorallia (i.e. red corals); the two diverged approximately 600 million years ago. The precious Mediterranean red coral, Corallium rubrum, is an octocorallian species, which produces two distinct high-magnesium calcite biominerals, the axial skeleton and the sclerites. In order to gain insight into the red coral biomineralization process and cnidarian biomineralization evolution, we studied the protein repertoire forming the organic matrix (OM) of its two biominerals.

Results

We combined High-Resolution Mass Spectrometry and transcriptome analysis to study the OM composition of the axial skeleton and the sclerites. We identified a total of 102 OM proteins, 52 are found in the two red coral biominerals with scleritin being the most abundant protein in each fraction. Contrary to reef building corals, the red coral organic matrix possesses a large number of collagen-like proteins. Agrin-like glycoproteins and proteins with sugar-binding domains are also predominant. Twenty-seven and 23 proteins were uniquely assigned to the axial skeleton and the sclerites, respectively. The inferred regulatory function of these OM proteins suggests that the difference between the two biominerals is due to the modeling of the matrix network, rather than the presence of specific structural components. At least one OM component could have been horizontally transferred from prokaryotes early during Octocorallia evolution.

Conclusion

Our results suggest that calcification of the red coral axial skeleton likely represents a secondary calcification of an ancestral gorgonian horny axis. In addition, the comparison with stony coral skeletomes highlighted the low proportion of similar proteins between the biomineral OMs of hexacorallian and octocorallian corals, suggesting an independent acquisition of calcification in anthozoans.

Emx2 regulates hair cell rearrangement but not positional identity within neuromasts

Each hair cell (HC) precursor of zebrafish neuromasts divides to form two daughter HCs of opposite hair bundle orientations. Previously, we showed that transcription factor Emx2, expressed in only one of the daughter HCs, generates this bidirectional HC pattern (Jiang et al., 2017). Here, we asked whether Emx2 mediates this effect by changing location of hair bundle establishment or positions of HCs since daughter HCs are known to switch positions with each other. We showed this HC rearrangement, redefined as two processes named Rock and Roll, is required for positional acquisition of HCs. Apical protrusion formation of nascent HCs and planar polarity signaling are both important for the Rock and Roll. Emx2 facilitates Rock and Roll by delaying apical protrusion of its nascent HCs but it does not determine HCs' ultimate positions, indicating that Emx2 mediates bidirectional HC pattern by changing the location where hair bundle is established in HCs.

Pax2a is expressed in oocytes and is responsible for early development and oogenesis in zebrafish

Eleven genes, including pax2a, were selected as candidate ovulation-inducing genes on the basis of microarray analysis and RNA sequencing in our previous study. The purpose of this study was to investigate the role of the pax2a gene in the ovulation-inducing process. F2 pax2a homozygous mutant zebrafish possessing a deletion of 6 nucleotides were established in this study. However, the deletion included the start codon (ATG) of the pax2a gene, and the Pax2a protein was still detected, which indicated that the deletion caused a shift in the start codon to the next ATG, resulting in a 12-amino acid deletion. F2 pax2a homozygous mutant zebrafish showed ovulation. However, the embryos showed an abnormal oval shape at the epiboly stage that resulted in yolk and tail formation abnormalities and heart edema. The surviving F3 homozygous mutants did not develop ovaries. Pax2a was detected in oocytes and eggs but not after the Prim-22 stage. It is suggested that pax2a is expressed as a maternal gene in oocytes and is necessary for oogenesis and early development.

Systematic characterization of the branch point binding protein, splicing factor 1, gene family in plant development and stress responses

BACKGROUND

Among eukaryotic organisms, alternative splicing is an important process that can generate multiple transcripts from one same precursor messenger RNA, which greatly increase transcriptome and proteome diversity. This process is carried out by a super-protein complex defined as the spliceosome. Specifically, splicing factor 1/branchpoint binding protein (SF1/BBP) is a single protein that can bind to the intronic branchpoint sequence (BPS), connecting the 5' and 3' splice site binding complexes during early spliceosome assembly. The molecular function of this protein has been extensively investigated in yeast, metazoa and mammals. However, its counterpart in plants has been seldomly reported.

RESULTS

To this end, we conducted a systematic characterization of the SF1 gene family across plant lineages. In this work, a total of 92 sequences from 59 plant species were identified. Phylogenetic relationships of these sequences were constructed, and subsequent bioinformatic analysis suggested that this family likely originated from an ancient gene transposition duplication event. Most plant species were shown to maintain a single copy of this gene. Furthermore, an additional RNA binding motif (RRM) existed in most members of this gene family in comparison to their animal and yeast counterparts, indicating that their potential role was preserved in the plant lineage.

CONCLUSION

Our analysis presents general features of the gene and protein structure of this splicing factor family and will provide fundamental information for further functional studies in plants.

Functional effect of vaterite - the presence of an alternative crystalline structure in otoliths alters escape kinematics of the brown trout

The fast-start escape response is the main locomotor behaviour observed in fish to evade predatory attacks and thereby increase their probability of survival. Thus far, this high-speed sensory motor control has been extensively studied in relation to extrinsic factors. In contrast, there has been surprisingly little consideration of intrinsic individual factors that can mediate sensorial perception, such as inter-individual variability in mechanosensory systems. The inner ear of teleost fishes is composed of otoliths that play an important role in hearing and balance functions. While sagittal otoliths are normally composed of aragonite in many fish species, the inclusion of vaterite (an abnormal crystalline structure) has been reported in a number of individuals from different environments. There is currently strong theoretical and empirical evidence that vaterite deposition has a negative impact on auditory sensitivity in fishes. While the functional/behavioural implications of this defect on otolith-related hearing function has been hypothesised, it has remained largely untested experimentally. Here, using juvenile (0+ years) Salmo trutta originating from the wild in experimental conditions, we report for the first time that the deposition of calcium carbonate in its crystalline vateritic polymorph has significant pervasive effects on the escape kinematics of fish. The presence of an alternative crystalline structure in otoliths is likely to alter fish behaviour in ways that decrease survival. We also report that altered behaviour in individuals with vateritic otoliths is partially compensated for by the presence of a functional lateral line. Such functional compensation suggests more slight consequences, if any, in the wild.

Functional derivatives of human dentin matrix protein 1 modulate morphology of calcium carbonate crystals

Dentin matrix protein 1 (DMP1) is an acidic, extracellular matrix protein essential for biomineralization of calcium phosphate, in bone and dentin. It is proteolytically processed into two fragments, 44K and 56K. Recently, the presence of DMP1 was noticed in inner ear, specifically in otoconia, which are calcium carbonate biominerals involved in sensing of balance. In this study, the solution structure and biomineralization activity of otoconial 44K and 56K fragments toward calcium carbonate were investigated. The results of analytical ultracentrifugation, circular dichroism, and gel filtration indicated that DMP1 fragments are disordered in solution. Notably, 56K formed oligomers in the presence of calcium ions. It was also observed that both fragments influenced the crystal growth by in vitro biomineralization assay and scanning electron microscopy. In addition, they sequester the calcium ions during the calcite formation. Calcium carbonate crystals precipitated in vitro changed their size and shape in the presence of DMP1 fragments. Oligomerization propensity of 56K may significantly enhance this function. Our study indicates that intrinsically disordered DMP1 has a previously unknown regulatory function for biomineralization of otoconia.

In situ 3D visualization of biomineralization matrix proteins

Calcium biominerals occur in all major animal phyla, and through biomolecular control, exhibit such diverse structures as exoskeletons, shells, bones, teeth and earstones (otoliths). Determining the three-dimensional expression of key biomineral proteins, however, has proven challenging as typical protein identification methods either lose spatial resolution during dissolution of the mineral phase or are costly and limited to two-dimensional expression of high abundance proteins. Here we present a modification of the CLARITY and ACT-PRESTO protocols to visualize and confirm, for the first time, the timing of expression and function of two key regulators of biomineralization.

Cilia in the developing zebrafish ear

The inner ear, which mediates the senses of hearing and balance, derives from a simple ectodermal vesicle in the vertebrate embryo. In the zebrafish, the otic placode and vesicle express a whole suite of genes required for ciliogenesis and ciliary motility. Every cell of the otic epithelium is ciliated at early stages; at least three different ciliary subtypes can be distinguished on the basis of length, motility, genetic requirements and function. In the early otic vesicle, most cilia are short and immotile. Long, immotile kinocilia on the first sensory hair cells tether the otoliths, biomineralized aggregates of calcium carbonate and protein. Small numbers of motile cilia at the poles of the otic vesicle contribute to the accuracy of otolith tethering, but neither the presence of cilia nor ciliary motility is absolutely required for this process. Instead, otolith tethering is dependent on the presence of hair cells and the function of the glycoprotein Otogelin. Otic cilia or ciliary proteins also mediate sensitivity to ototoxins and coordinate responses to extracellular signals. Other studies are beginning to unravel the role of ciliary proteins in cellular compartments other than the kinocilium, where they are important for the integrity and survival of the sensory hair cell. This article is part of the Theo Murphy meeting issue 'Unity and diversity of cilia in locomotion and transport'.

Lattice Shrinkage by Incorporation of Recombinant Starmaker-Like Protein within Bioinspired Calcium Carbonate Crystals

The biological mediation of mineral formation (biomineralization) is realized through diverse organic macromolecules that guide this process in a spatial and temporal manner. Although the role of these molecules in biomineralization is being gradually revealed, the molecular basis of their regulatory function is still poorly understood. In this study, the incorporation and distribution of the model intrinsically disordered starmaker-like (Stm-l) protein, which is active in fish otoliths biomineralization, within calcium carbonate crystals, is revealed. Stm-l promotes crystal nucleation and anisotropic tailoring of crystal morphology. Intracrystalline incorporation of Stm-l protein unexpectedly results in shrinkage (and not expansion, as commonly described in biomineral and bioinspired crystals) of the crystal lattice volume, which is described herein, for the first time, for bioinspired mineralization. A ring pattern was observed in crystals grown for 48 h; this was composed of a protein-enriched region flanked by protein-depleted regions. It can be explained as a result of the Ostwald-like ripening process and intrinsic properties of Stm-l, and bears some analogy to the daily growth layers of the otolith.

Otoliths of sub-adult Lake Sturgeon Acipenser fulvescens contain aragonite and vaterite calcium carbonate polymorphs

In this study we quantified the percent CaCO₃ polymorph composition in otoliths of larval and juvenile Lake Sturgeon Acipenser fulvescens via X-ray microdiffraction. Sagittal otoliths of sub-adults were primarily composed of aragonite (> 90%) while the lapilli otoliths were 100% vaterite. This is the first time the presence of aragonite in otoliths has been reported in an acipenseriform and is surprising given that the ability to form aragonite otoliths was not thought to have evolved until the separation of teleost and holostean species from other Actinopterygian fishes (e.g., sturgeon, paddlefish, gar).

Zebrafish otolith biomineralization requires polyketide synthase

Deflecting biomineralized crystals attached to vestibular hair cells are necessary for maintaining balance. Zebrafish (Danio rerio) are useful organisms to study these biomineralized crystals called otoliths, as many required genes are homologous to human otoconial development. We sought to identify and characterize the causative gene in a trio of homozygous recessive mutants, no content (nco) and corkscrew (csr), and vanished (vns), which fail to develop otoliths during early ear development. We show that nco, csr, and vns have potentially deleterious mutations in polyketide synthase (pks1), a multi-modular protein that has been previously implicated in biomineralization events in chordates and echinoderms. We found that Otoconin-90 (Oc90) expression within the otocyst is diffuse in nco and csr; therefore, it is not sufficient for otolith biomineralization in zebrafish. Similarly, normal localization of Otogelin, a protein required for otolith tethering in the otolithic membrane, is not sufficient for Oc90 attachment. Furthermore, eNOS signaling and Endothelin-1 signaling were the most up- and down-regulated pathways during otolith agenesis in nco, respectively. Our results demonstrate distinct processes for otolith nucleation and biomineralization in vertebrates and will be a starting point for models that are independent of Oc90-mediated seeding. This study will serve as a basis for investigating the role of eNOS signaling and Endothelin-1 signaling during otolith formation.

In vivo and in vitro analysis of starmaker activity in zebrafish otolith biomineralization

Otoliths are one of the biominerals whose formation is highly controlled by proteins. The first protein discovered to be involved in otolith biomineralization in zebrafish was starmaker (Stm). Previously, Stm was shown to be responsible for the preferential formation of aragonite, a polymorph of calcium carbonate, in otoliths. In this work, proteomic analysis of adult zebrafish otoliths was performed. Stm is the only highly phosphorylated protein found in our studies. Besides previously studied otolith proteins, we discovered several dozens of unknown proteins that reveal the likely mechanism of biomineralization. A comparison of aragonite and vaterite otoliths showed similarities in protein composition. We observed the presence of Stm in both types of otoliths. In vitro studies of 2 characteristic Stm fragments indicated that the DS-rich region has a special biomineralization activity, especially after phosphorylation.-Kalka, M., Markiewicz, N., Ptak, M., Sone, E. D., Ożyhar, A., Dobryszycki, P., Wojtas, M. In vivo and in vitro analysis of starmaker activity in zebrafish otolith biomineralization.

Solid-State NMR and MD Study of the Structure of the Statherin Mutant SNa15 on Mineral Surfaces

Elucidation of the structure and interactions of proteins at native mineral interfaces is key to understanding how biological systems regulate the formation of hard tissue structures. In addition, understanding how these same proteins interact with non-native mineral surfaces has important implications for the design of medical and dental implants, chromatographic supports, diagnostic tools, and a host of other applications. Here, we combine solid-state NMR spectroscopy, isotherm measurements, and molecular dynamics simulations to study how SNa15, a peptide derived from the hydroxyapatite (HAP) recognition domain of the biomineralization protein statherin, interacts with HAP, silica (SiO₂), and titania (TiO₂) mineral surfaces. Adsorption isotherms are used to characterize the binding affinity of SNa15 to HAP, SiO₂, and TiO₂. We also apply 1D ¹³C CP MAS, 1D ¹⁵N CP MAS, and 2D ¹³C-¹³C DARR experiments to SNa15 samples with uniformly ¹³C- and ¹⁵N-enriched residues to determine backbone and side-chain chemical shifts. Different computational tools, namely TALOS-N and molecular dynamics simulations, are used to deduce secondary structure from backbone and side-chain chemical shift data. Our results show that SNa15 adopts an α-helical conformation when adsorbed to HAP and TiO₂, but the helix largely unravels upon adsorption to SiO₂. Interactions with HAP are mediated in general by acidic and some basic amino acids, although the specific amino acids involved in direct surface interaction vary with surface. The integrated experimental and computational approach used in this study is able to provide high-resolution insights into adsorption of proteins on interfaces.

SW, Honig A, Johnston AE, San Antonio CM, Bourque B, Hannigan RE. Ocean acidification alters morphology of all otolith types in Clark's anemonefish (Amphiprion clarkii)

Ocean acidification, the ongoing decline of surface ocean pH and [CO3 2 - ] due to absorption of surplus atmospheric CO2, has far-reaching consequences for marine biota, especially calcifiers. Among these are teleost fishes, which internally calcify otoliths, critical elements of the inner ear and vestibular system. There is evidence in the literature that ocean acidification increases otolith size and alters shape, perhaps impacting otic mechanics and thus sensory perception. Here, larval Clark's anemonefish, Amphiprion clarkii (Bennett, 1830), were reared in various seawater pCO2/pH treatments analogous to future ocean scenarios. At the onset of metamorphosis, all otoliths were removed from each individual fish and analyzed for treatment effects on morphometrics including area, perimeter, and circularity; scanning electron microscopy was used to screen for evidence of treatment effects on lateral development, surface roughness, and vaterite replacement. The results corroborate those of other experiments with other taxa that observed otolith growth with elevated pCO2, and provide evidence that lateral development and surface roughness increased as well. Both sagittae exhibited increasing area, perimeter, lateral development, and roughness; left lapilli exhibited increasing area and perimeter while right lapilli exhibited increasing lateral development and roughness; and left asterisci exhibited increasing perimeter, roughness, and ellipticity with increasing pCO2. Right lapilli and left asterisci were only impacted by the most extreme pCO2 treatment, suggesting they are resilient to any conditions short of aragonite undersaturation, while all other impacted otoliths responded to lower concentrations. Finally, fish settlement competency at 10 dph was dramatically reduced, and fish standard length marginally reduced with increasing pCO2. Increasing abnormality and asymmetry of otoliths may impact inner ear function by altering otolith-maculae interactions.

Chiral switching in biomineral suprastructures induced by homochiral l-amino acid

How homochiral l-biomolecules in nature induce a chiral switch in biomineralized architectures is unknown, although chiral switching is common in many calcium carbonate-hardened structures found in marine and terrestrial organisms. We created hierarchically organized, chiral biomineral structures of calcium carbonate, whose chirality can be switched by a single l-enantiomer of an amino acid. The control of this chiral switching involves two stages: a calcium carbonate (vaterite) platelet layer inclination stage, followed by a platelet layer rotation stage, the latter stage being responsible for successional chiral switching events within the biomineralized structures. The morphology of the synthesized chiral vaterite structures remarkably resembles pathologic chiral vaterite otoconia found in the human inner ear. In general, these findings describe how a single-enantiomer amino acid might contribute to biomineral architectures having more than one chirality as is commonly seen in biology, and more specifically, they suggest how pathologic chiral malformations may arise in humans.

Full-section otolith microtexture imaged by local-probe X-ray diffraction

An optimized synchrotron-based X-ray diffraction method is described for the direct and efficient measurement of crystallite phase and orientation at micrometre resolution across textured polycrystalline samples of millimetre size (high scale dynamics) within a reasonable time frame. The method is demonstrated by application to biomineral fish otoliths. Otoliths are calcium carbonate accretions formed in the inner ears of vertebrates. Fish otoliths are essential biological archives, providing information for individual age estimation, the study of population dynamics and fish stock management, as well as past environmental and climatic conditions from archaeological specimens. Here, X-ray diffraction mapping is discussed as a means of describing the mineralogical structure and microtexture of otoliths. Texture maps could be generated with a fewa priorihypotheses on the aragonitic system. Full-section imaging allows quantitative intercomparison of crystal orientation coupled to microstructural description, across the zones of the otoliths that represent distinctive mineral organization. It reveals the extents of these regions and their internal textural structure. Characterization of structural and textural correlations across whole images is therefore proposed as a complementary approach to investigate and validate the local in-depth nanometre-scale study of biominerals. The estimation of crystallite size and orientational distribution points to diffracting domains intermediate in size between the otolith nanogranules and the crystalline units, in agreement with recently reported results.

Calcium-Binding Proteins with Disordered Structure and Their Role in Secretion, Storage, and Cellular Signaling

Calcium is one of the most important second messengers and its intracellular signaling regulates many aspects of cell physiology. Calcium ions, like phosphate ions, are highly charged and thus are able to alter protein conformation upon binding; thereby they constitute key factors in signal transduction. One of the most common calcium-binding structural motifs is the EF-hand, a well-defined helix-loop-helix structural domain, present in many calcium-binding proteins (CBPs). Nonetheless, some CBPs contain non-canonical, disordered motifs, which usually bind calcium with high capacity and low affinity, and which represent a subset of proteins with specific functions, but these functions rarely involve signaling. When compared with phosphorylation-mediated signal transduction, the role of intrinsic disorder in calcium signaling is significantly less prominent and not direct. The list of known examples of intrinsically disordered CBPs is relatively short and the disorder in these examples seems to be linked to secretion and storage. Calcium-sensitive phosphatase calcineurin is an exception, but it represents an example of transient disorder, which is, nevertheless, vital to the functioning of this protein. The underlying reason for the different role of disordered proteins in the two main cellular signaling systems appears to be linked to the gradient of calcium concentration, present in all living cells.

Ocean acidification promotes otolith growth and calcite deposition in gilthead sea bream (Sparus aurata) larvae

The effects of ocean acidification on otolith crystallization and growth rates were investigated in gilthead sea bream (Sparus aurata) larvae. Larvae were exposed to three different pH levels: pH8.2, pH7.7 and pH7.3 for a period of 18 days post-fertilization. For the first time, we demonstrate that pH has a significant impact on the carbonate polymorph composition, showing calcite in a significant percentage of individuals at low pH. Around 21% of the larvae exposed to pH7.3 showed irregular calcitic otoliths rather than commonly found round aragonitic otoliths. Calcitic otoliths showed a moderate level of heritability suggesting an important role of genetic factors. We also observed significantly larger otoliths in larvae reared at pH7.7 and pH7.3 compared to pH8.2 in both sagittae and lapilli. Our results demonstrate that otolith growth rates in gilthead sea bream larvae increase at low pH while a significant proportion of larvae are prone to the formation of calcitic otoliths at pH7.3.