Morphology Of Organisms Research Articles

Deep silicification–assisted long-term preservation of structural and genomic information across biospecies: From micro to macro

The concurrent preservation of morphological, structural, and genomic attributes within biological samples is paramount for comprehensive insights into biological phenomena and disease mechanisms. However, current preservation methodologies (e.g., cryopreservation, chemical reagent fixation, and bioplasticization) exhibit limitations in simultaneously achieving these critical combined goals. To address this gap, inspired by natural fossilization, here we propose "deep silicification," a room temperature technology that eliminates fixation requirements and overcomes the cold chain problem. By harnessing the synergy between ethanol and dimethyl sulfoxide, deep silicification significantly enhances silica penetration and accumulation within bioorganisms, thereby reinforcing structural integrity. This versatile and cost-effective approach demonstrates remarkable efficacy in preserving organismal morphology across various scales. Accelerated aging experiments underscore a 4,723-fold enhancement in genomic information storage over millennia, with whole-genome sequencing confirming nearly 100% fidelity. With its simplicity and reliability, "deep silicification" represents a paradigm shift in biological sample storage.

Ediacaran marine animal forests and the ventilation of the oceans

The rise of animals across the Ediacaran-Cambrian transition marked a step-change in the history of life, from a microbially dominated world to the complex macroscopic biosphere we see today.1,2,3 While the importance of bioturbation and swimming in altering the structure and function of Earth systems is well established,4,5,6 the influence of epifaunal animals on the hydrodynamics of marine environments is not well understood. Of particular interest are the oldest "marine animal forests,"7 which comprise a diversity of sessile soft-bodied organisms dominated by the fractally branching rangeomorphs.8,9 Typified by fossil assemblages from the Ediacaran of Mistaken Point, Newfoundland,8,10,11 these ancient communities might have played a pivotal role in structuring marine environments, similar to modern ecosystems,7,12,13 but our understanding of how they impacted fluid flow in the water column is limited. Here, we use ecological modeling and computational flow simulations to explore how Ediacaran marine animal forests influenced their surrounding environment. Our results reveal how organism morphology and community structure and composition combined to impact vertical mixing of the surrounding water. We find that Mistaken Point communities were capable of generating high-mixing conditions, thereby likely promoting gas and nutrient transport within the "canopy." This mixing could have served to enhance local-scale oxygen concentrations and redistribute resources like dissolved organic carbon. Our work suggests that Ediacaran marine animal forests may have contributed to the ventilation of the oceans over 560 million years ago, well before the Cambrian explosion of animals.

Nonspecificity of Immunohistochemistry for Mycobacteria Species Using a Rabbit Polyclonal Antibody.

Recent publications have featured immunohistochemistry (IHC) as a sensitive tool for detecting Mycobacterium tuberculosis and nontuberculous mycobacteria, but performance is limited to cases suspected to have mycobacterial infection. To examine cross-reactivity of a polyclonal antimycobacterial antibody with various types of pathogens, tissues, and inflammatory patterns. Surgical pathology files during a period of 6 years were searched, and 40 cases representing a variety of pathogens, tissue types, and inflammatory responses were retrieved. Cases were stained with a rabbit polyclonal antimycobacterial antibody (Biocare Medical, Pacheco, California). The cases and associated histochemical stains, culture, and molecular results were reviewed by 3 pathologists. All 8 cases of mycobacterial infection previously diagnosed by other methods were positive for mycobacteria by IHC. In addition, multiple bacterial and fungal organisms and 1 case of Leishmania amastigotes were also immunoreactive with the mycobacterial IHC. Although highly sensitive for mycobacteria, the polyclonal antibody shows significant cross-reactivity with other organisms. This is a sensitive but nonspecific stain that can be used as an alternative confirmation method for mycobacteria, but attention should be paid to inflammatory reaction and organism morphology when IHC is positive to avoid misdiagnosis.

Phylogeography and phenotypic wing shape variation in a damselfly across populations in Europe.

Describing geographical variation in morphology of organisms in combination with data on genetic differentiation and biogeography can provide important information on how natural selection shapes such variation. Here we study genetic structure using ddRAD seq and wing shape variation using geometric morphometrics in 14 populations of the damselfly Lestes sponsa along its latitudinal range in Europe. The genetic analysis showed a significant, yet relatively weak population structure with high genetic heterozygosity and low inbreeding coefficients, indicating that neutral processes contributed very little to the observed wing shape differences. The genetic analysis also showed that some regions of the genome (about 10%) are putatively shaped by selection. The phylogenetic analysis showed that the Spanish and French populations were the ancestral ones with northern Swedish and Finnish populations being the most derived ones. We found that wing shape differed significantly among populations and showed a significant quadratic (but weak) relationship with latitude. This latitudinal relationship was largely attributed to allometric effects of wing size, but non-allometric variation also explained a portion of this relationship. However, wing shape showed no phylogenetic signal suggesting that lineage-specific variation did not contribute to the variation along the latitudinal gradient. In contrast, wing size, which is correlated with body size in L. sponsa, had a strong negative correlation with latitude. Our results suggest a relatively weak population structure among the sampled populations across Europe, but a clear differentiation between south and north populations. The observed geographic phenotypic variation in wing shape may have been affected by different local selection pressures or environmental effects.

3D Morphological Scanning and Environmental Correlates of Bufo gargarizans in the Yellow River Basin

Morphology plays a crucial role in understanding the intricacies of biological forms. Traditional morphometric methods, focusing on one- or two-dimensional geometric levels, often fall short of accurately capturing the three-dimensional (3D) structure of organisms. The advent of 3D scanning techniques has revolutionized the study of organismal morphology, enabling comprehensive and accurate measurements. This study employs a 3D structured light scanning system to analyze the morphological variations in the Chinese toad (Bufo gargarizans Cantor, 1842) along the Yellow River Basin. The 3D digital model obtained from the scan was used to calculate various morphological parameters including body surface area, volume, fractal dimensions, and limb size. The research explores geographic variability patterns and identifies environmental drivers affecting the 3D phenotypic variation of B. gargarizans. Results reveal a bimodal pattern of variation in the toad population, with higher elevations exhibiting smaller body sizes, greater appendage proportions, and more complex body structures. Linear regression analyses highlight the influence of elevation and annual mean temperature on the morphological variation of B. gargarizans, with elevation playing a significant role. This study underscores the significance of 3D morphometric analysis in unraveling the intricacies of organismal morphology and understanding the adaptive strategies of species in diverse environments.

Precise bulk density measurement of planktonic foraminiferal test by X-ray microcomputed tomography

X-ray Microcomputed Tomography (µCT) is rapidly becoming an important analytical technique for examining the precise morphometry of small objects. The most notable feature of this technique is that it enables nondestructive, highly accurate morphometric measurements at micrometer-order resolution. In the Earth sciences, this makes µCT extremely useful for clarifying how genetic associations and the surrounding environment affect the morphology of micro-sized organisms. However, the actual analytical methods and the points that must be considered to produce reliable data have rarely been discussed in detail. Here, to address this lack of discussion, we describe in detail our methodology for precise µCT-based morphometry by using a test of the planktonic foraminifer and marine calcifier Globorotalia inflata. In addition to demonstrating the long-term stability of our µCT setup and analytical approach, we also propose a new methodology for test bulk density calibration using artificial carbonate phantoms. We expect that µCT together with our artificial phantom-based methodology will be useful for calculating accurate test bulk densities of micro-sized marine calcifiers.

Estimation of seafloor burrow length and inclination using underwater ultrasound

There are many benthic organisms on the seafloor. Then, Some benthic organisms form burrows beneath the seafloor. These burrows have a considerable influence on the surrounding environment providing shelter for symbionts other than the main organisms and promoting water circulation in seafloor sediments. Therefore, the investigation of the burrow morphology of benthic organisms can be valid for marine environment conservation. Several methods already exist that can estimate the burrow shape and the organisms within the burrows. However, there is a need for a method suitable for screening surveys to measure many burrows. In this study, a novel method to estimate the morphology of the burrow interior, such as the total length and slope, using underwater ultrasound was proposed. By using this method, it is expected to enable quick and nondestructive measurement of the internal conditions of a burrow. This paper discusses the feasibility of using the proposed method to estimate the length and inclination of the burrow based on the results of laboratory experiments and field surveys. It was confirmed that the inclination angle and the length of the actual burrow can be accurately estimated on the order of 4 deg. and up to 18 cm, respectively.

Morphological diversity increases with decreasing resources along a zooplankton time series.

Biodiversity is studied notably because of its reciprocal relationship with ecosystem functions such as production. Diversity is traditionally described from a taxonomic, genetic or functional point of view but the diversity in organism morphology is seldom explicitly considered, except for body size. We describe morphological diversity of marine zooplankton seasonally and over 12 years using quantitative imaging of weekly plankton samples, in the northwestern Mediterranean Sea. We extract 45 morphological features on greater than 800 000 individuals, which we summarize into four main morphological traits (size, transparency, circularity and shape complexity). In this morphological space, we define objective morphological groups and, from those, compute morphological diversity indices (richness, evenness and divergence) using metrics originally defined for functional diversity. On both time scales, morphological diversity increased when nutritive resources and plankton concentrations were low, thus matching the theoretical reciprocal relationship. Over the long term at least, this diversity increase was not fully attributable to taxonomic diversity changes. The decline in the most common plankton forms and the increase in morphological variance and in extreme morphologies suggest a mechanism akin to specialization under low production, with likely consequences for trophic structure and carbon flux.

Systematic review of free and open source software (FOSS) employed in ecomorphological studies with recommendations for user-friendly developments

Morphometrics is an important aspect of biological research that integrates in various ways with other branches of biology like genetics, ecology, and evolution to determine an organism's form and function. It is one of the most frequently used methods to study ecomorphology (the interaction of morphological features of organisms with environmental variables). In recent years, research in the field of morphometrics has achieved revolutionary developments from studying simple morphological variations to visualizing shape differences, thanks to free and open source software (FOSS). These FOSS not only incorporate various steps of morphometric methods such as image processing, digitization, data acquisition and statistical analyses but also help in determining the influence of ecological factors on an organism's morphology. In this article, we discussed the applications, benefits, and drawbacks of FOSS frequently employed in current ecomorphological studies. We observed that in many morphological studies, the integration of ecological data is completely missing, which is a prerequisite in determining the influential factors influencing an organism's morphology. We believe that the main reason behind the lack of integration of ecological information in these studies is the dearth of proper knowledge about the usage of presently available FOSS. To move forward, we, therefore, propose software developers to design user-friendly FOSS which will be compatible with all operating systems and can integrate all maneuvers of ecomorphological methods with common data file formats. This will help researchers to employ an ecomorphological approach to resolve various questions in biological research.

Adverse developmental impacts in progeny of zebrafish exposed to the agricultural herbicide atrazine during embryogenesis

Atrazine (ATZ) is an herbicide commonly used on crops in the Midwestern US and other select global regions. The US Environmental Protection Agency ATZ regulatory limit is 3 parts per billion (ppb; µg/L), but this limit is often exceeded. ATZ has a long half-life, is a common contaminant of drinking water sources, and is indicated as an endocrine disrupting chemical in multiple species. The zebrafish was used to test the hypothesis that an embryonic parental ATZ exposure alters protein levels leading to modifications in morphology and behavior in developing progeny. Zebrafish embryos (F1) were collected from adults (F0) exposed to 0, 0.3, 3, or 30 ppb ATZ during embryogenesis. Differential proteomics, morphology, and behavior assays were completed with offspring aged 120 or 144 h with no additional chemical treatment. Proteomic analysis identified differential expression of proteins associated with neurological development and disease; and organ and organismal morphology, development, and injury, specifically the skeletomuscular system. Head length and ratio of head length to total length was significantly increased in the F1 of 0.3 and 30 ppb ATZ groups (p < 0.05). Based on molecular pathway alterations, further craniofacial morphology assessment found decreased distance for cartilaginous structures, decreased surface area and distance between saccular otoliths, and a more posteriorly positioned notochord (p < 0.05), indicating delayed ossification and skeletal growth. The visual motor response assay showed hyperactivity in progeny of the 30 ppb treatment group for distance moved and of the 0.3 and 30 ppb treatment groups for time spent moving (p < 0.05). Due to the changes in saccular otoliths, an acoustic startle assay was completed and showed decreased response in the 0.3 and 30 ppb treatments (p < 0.05). These findings suggest that a single embryonic parental exposure alters cellular pathways in their progeny that lead to perturbations in craniofacial development and behavior.

Vascular optimality dictates plant morphology away from Leonardo’s rule

Metabolic scaling theory (MST) provides an understanding of scaling in organismal morphology. Empirical data on the apparently universal pattern of tip-to-base conduit widening across vascular plants motivate a set of generalized MST (gMST) relationships allowing for variable rates of conduit coalescence and taper and a transition between transport and diffusive domains. Our model, with coalescence limited to the distalmost part of the conductive system, reconciles previous MST-based models and extends their applicability to the entire plant. We derive an inverse relationship between stem volume taper and conduit widening, which implies that plant morphology is dictated by vascular optimality and not the assumption of constant sapwood area across all branching levels, contradicting Leonardo's rule. Thus, energy efficiency controls conduit coalescence rate, lowering the carbon cost needed to sustain the vascular network. Our model shows that as a plant grows taller, it must increase conduit widening and coalescence, which may make it more vulnerable to drought. We calculated how our gMST model implies a lower carbon cost to sustain a similar network compared to previous MST-based models. We also show that gMST predicts the cross-sectional area of vessels and their frequency along the relative length better than previous MST models for a range of plant types. We encourage further research obtaining data that would allow testing other gMST predictions that remain unconfirmed empirically, such as conduit coalescence rate in stems. The premise of energy efficiency can potentially become instrumental to our understanding of plant carbon allocation.

Biostratinomy of the enigmatic tubular organism Aulozoon soliorum, the Rawnsley Quartzite, South Australia

The Ediacaran fauna (574–539 Ma) are the first macroscopic community forming organisms on Earth, thus providing unique insight into the origins and evolution of complex life. However, the assignment of most Ediacaran organisms to specific phyla and kingdoms remains difficult due to their commonly non-analogous body plans and soft-bodied nature, which often results in the loss of diagnostic features through the processes of death and fossilization. Notably, this taphonomic overprint is not imparted equally to all Ediacaran organisms and is particularly exaggerated for the morphotypic grouping of tubular organisms. This morphogroup is comprised of macroscopic organisms with elongate, hollow, and simple body plans and is the most abundant Ediacaran morphogroup. However, the simple and hollow morphology of tubular organisms results in a broadly low preservation potential. In turn, this commonly limits the reconstruction of in vivo morphology, muddles taxonomic assignment, obfuscates phylogenetic affinities, and inhibits understanding of their broader significance. Fortunately, previous studies of abundant tubular taxa have demonstrated that taxon-level biostratinomic investigations can, in part, account for this low preservation potential. Such studies inform a more complete understanding of the morphogroup, providing novel insight into the paleobiology, paleoecology, and biomaterials of tubular taxa. To contribute to this biostratinomically-geared assessment of Ediacaran tubular organisms, this study analyzes the preservation of Aulozoon soliorum, an abundant tubular organism from the Rawnsley Quartzite of South Australia. This investigation demonstrates that Aulozoon is preserved via five preservational modes, which inform a novel in vivo reconstruction of Aulozoon as a sessile, fluid-filled, cylindrical organism with a holdfast and a thin, organic, and featureless body wall. The preservational modes identified here additionally inform a taphonomic framework under which Aulozoon fossils can be interpreted, thus furthering holistic understanding of the morphogroup-specific preservational variability of Ediacaran tubular organisms.

Sex analysis in marine biological systems: insights and opportunities

The ocean is facing unprecedented challenges due to the escalating impacts of climate change and other pressures threatening ecosystems and the many benefits they provide. Effective strategies for reversing the loss of biodiversity rely on knowledge of how marine organisms, populations, and communities respond to environmental change. A fundamental but often overlooked biological characteristic of organisms is sex, which is distinct from sociocultural gender. Here, we examined how sex influences marine organisms, populations, and communities, through a review of sex analysis applications in marine biological research. We found that sex broadly affects the morphology, physiology, behavior, and distribution of organisms and populations across taxa, with evidence of sex‐specific differences in survival to thermal stress, timing of biological mechanisms, and energetics. To facilitate further integration of sex into marine biological research, we synthesize current approaches, discuss methodological and logistical challenges, and lay out guidelines for future research.

A Middle Ordovician Burgess Shale-type fauna from Castle Bank, Wales (UK).

Burgess Shale-type faunas are critical to our understanding of animal evolution during the Cambrian, giving an unrivalled view of the morphology of ancient organisms and the ecology of the earliest animal-dominated communities. Rare examples in Lower Ordovician strata such as the Fezouata Biota illustrate the subsequent evolution of ecosystems but only from before the main phase of the Great Ordovician Biodiversification Event. Later Ordovician Konservat-Lagerstätten are not directly comparable with the Burgess Shale-type faunas as they do not represent diverse, open-shelf communities, limiting our ability to track ecological development through the critical Ordovician biodiversification interval. Here we present the Castle Bank fauna: a highly diverse Middle Ordovician Burgess Shale-type fauna from Wales (UK) that is directly comparable with the Burgess Shale and Chengjiang biotas in palaeoenvironment and preservational style. The deposit includes animals with morphologies similar to the iconic Cambrian taxa Opabinia, Yohoia and Wiwaxia, combined with early examples of more derived groups such as barnacles. Many taxa such as kinorhynchs show the small sizes typical of modern faunas, illustrating post-Cambrian miniaturization. Castle Bank provides a new perspective on early animal evolution, revealing the next chapter in ecosystem development following the Chengjiang, Burgess Shale and Fezouata biotas.

The rangeomorph Pectinifrons abyssalis: Hydrodynamic function at the dawn of animal life

Rangeomorphs are among the oldest putative eumetazoans known from the fossil record. Establishing how they fed is thus key to understanding the structure and function of the earliest animal ecosystems. Here, we use computational fluid dynamics to test hypothesized feeding modes for the fence-like rangeomorph Pectinifrons abyssalis, comparing this to the morphologically similar extant carnivorous sponge Chondrocladia lyra. Our results reveal complex patterns of flow around P.abyssalis unlike those previously reconstructed for any other Ediacaran taxon. Comparisons with C. lyra reveal substantial differences between the two organisms, suggesting they converged on a similar fence-like morphology for different functions. We argue that the flow patterns recovered for P.abyssalis do not support either a suspension feeding or osmotrophic feeding habit. Instead, our results indicate that rangeomorph fronds may represent organs adapted for gas exchange. If correct, this interpretation could require a dramatic reinterpretation of the oldest macroscopic animals.

Luciferase-Based High-Throughput Screen with Aspergillus fumigatus to Identify Antifungal Small Molecules.

Only three classes of contemporary antifungal drugs are routinely utilized in the clinic against filamentous fungal pathogens such as Aspergillus fumigatus. High-throughput phenotypic screens to identify small molecules with activity against filamentous fungi remain challenging due to the hyphal, biofilm-like growth morphology of these important organisms. In this chapter, we describe a protocol for utilizing a bioluminescent A. fumigatus strain for identifying small molecules that potentiate the activity of the triazole antifungal drug fluconazole. The assay holds great promise for identifying small molecules with activity against filamentous fungal pathogens.

Ten (mostly) simple rules to future‐proof trait data in ecological and evolutionary sciences

Abstract Traits have become a crucial part of ecological and evolutionary sciences, helping researchers understand the function of an organism's morphology, physiology, growth and life history, with effects on fitness, behaviour, interactions with the environment and ecosystem processes. However, measuring, compiling and analysing trait data comes with data‐scientific challenges. We offer 10 (mostly) simple rules, with some detailed extensions, as a guide in making critical decisions that consider the entire life cycle of trait data. This article is particularly motivated by its last rule, that is, to propagate good practice. It has the intention of bringing awareness of how data on the traits of organisms can be collected and managed for reuse by the research community. Trait observations are relevant to a broad interdisciplinary community of field biologists, synthesis ecologists, evolutionary biologists, computer scientists and database managers. We hope these basic guidelines can be useful as a starter for active communication in disseminating such integrative knowledge and in how to make trait data future‐proof. We invite the scientific community to participate in this effort at http://opentraits.org/best‐practices.html.

A forgotten element of the blue economy: marine biomimetics and inspiration from the deep sea.

The morphology, physiology, and behavior of marine organisms have been a valuable source of inspiration for solving conceptual and design problems. Here, we introduce this rich and rapidly expanding field of marine biomimetics, and identify it as a poorly articulated and often overlooked element of the ocean economy associated with substantial monetary benefits. We showcase innovations across seven broad categories of marine biomimetic design (adhesion, antifouling, armor, buoyancy, movement, sensory, stealth), and use this framing as context for a closer consideration of the increasingly frequent focus on deep-sea life as an inspiration for biomimetic design. We contend that marine biomimetics is not only a "forgotten" sector of the ocean economy, but has the potential to drive appreciation of nonmonetary values, conservation, and stewardship, making it well-aligned with notions of a sustainable blue economy. We note, however, that the highest ambitions for a blue economy are that it not only drives sustainability, but also greater equity and inclusivity, and conclude by articulating challenges and considerations for bringing marine biomimetics onto this trajectory.

Repeated computed tomography scanning reveals morphological development of burrows produced by the tiger pistol shrimp Alpheus bellulus.

The burrow morphology of endobenthic organisms reflects their subsurface ecology. In this study, we observed the three-dimensional development of burrows produced by the tiger pistol shrimp Alpheus bellulus in a tank using an X-ray computed tomography (CT) scanner. CT scanning was performed at 10–30 min intervals immediately after the start of burrow construction. The three-dimensional morphology (surface area, volume, depth, length, and diameter) of burrows at each observation time was imaged and measured. In addition, the rate of increase of each parameter was calculated. Surface area, volume, length, and depth rapidly increased immediately after the start of the experiment in all burrows. Subsequently, there was a reduction in the rate of increase at 40 min after the start of excavation for burrow depth, at 75 min for length, and at 90 min for surface area and volume. Although there were large differences in burrow diameter among the burrows immediately after the start of the experiment, all burrows reached nearly identical diameters after 90 min. Changes in burrow morphology were not observed in most of the burrows more than 210 min after the start of the experiment, meaning that A. bellulus can create burrows that are sufficient for survival within this time period. The use of CT scans in this study clarified the developmental process of the three-dimensional structure of A. bellulus burrows and is applicable to various burrow-producing organisms. Our results provide new insights into the development of burrow structures.

Integration of Histopathology and Clinical Microbiology in the Diagnosis of Infectious Diseases: Focus on Mycoses

Identification and interpretation of microorganisms on histopathology is a skill set critical for both anatomic pathologists and clinical microbiologists. Microorganisms, and fungi in particular, develop structural properties differently within tissue than on an agar plate. For proper diagnoses the interpreter must be familiar with both phenotypes. Here, we review the specifics of fungal growth in tissue, including organism morphology, host reaction, and limitations for accurate histology identification.