{"title":"SegmentGeometry: A Tool for Measuring Second Moment of Area in 3D Slicer.","authors":"Jonathan M Huie, Adam P Summers, Sandy M Kawano","doi":"10.1093/iob/obac009","DOIUrl":"https://doi.org/10.1093/iob/obac009","url":null,"abstract":"<p><p>Second moment of area is a measure of how well the cross-section of a beam will resist bending because of its shape. Many have used second moment of area to investigate the mechanical adaptations of biological structures from stingray jaws to animal limb bones. In this context it is important to acknowledge the assumptions of beam theory, in which second moment of area plays a key role, if reasonable results are desired. For example, to minimize shear the structure should be at least 10 times longer than it is wide and deflection should be minimal. Analyzing the internal geometry of biological structures has never been easier or more accessible given the wide, and growing availability of micro-CT scans. Here, we offer a guide on the care that needs to be taken when interpreting second moment of area, and present open-access, open-source software that can process hundreds if not thousands of structures in a short time frame. <i>SegmentGeometry</i>, an extension for the open-source imaging platform 3D Slicer, iterates slice-by-slice through 3D structures to calculate second moment of area and other cross-sectional properties. We analyzed 2 case studies to demonstrate the power of this tool and to highlight interpretations that can be gleaned from second moment of area. Second moment of area is just one part of the Euler-Bernoulli beam theory and considering the full equation would greatly increase the number and diversity of questions that can be answered.</p>","PeriodicalId":13666,"journal":{"name":"Integrative Organismal Biology","volume":"4 1","pages":"obac009"},"PeriodicalIF":2.2,"publicationDate":"2022-02-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8919404/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142047729","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Vertebral Trabecular Bone Mechanical Properties Vary Among Functional Groups of Cetaceans.","authors":"D N Ingle, M E Porter","doi":"10.1093/iob/obab036","DOIUrl":"https://doi.org/10.1093/iob/obab036","url":null,"abstract":"<p><p>Since their appearance in the fossil record 34 million years ago, modern cetaceans (dolphins, whales, and porpoises) have radiated into diverse habitats circumglobally, developing vast phenotypic variations among species. Traits such as skeletal morphology and ecologically linked behaviors denote swimming activity; trade-offs in flexibility and rigidity along the vertebral column determine patterns of caudal oscillation. Here, we categorized 10 species of cetaceans (families Delphinidae and Kogiidae; <i>N</i> = 21 animals) into functional groups based on vertebral centra morphology, swimming speeds, diving behavior, and inferred swimming patterns. We quantified trabecular bone mechanical properties (yield strength, apparent stiffness, and resilience) among functional groups and regions of the vertebral column (thoracic, lumbar, and caudal). We extracted 6 mm<sup>3</sup> samples from vertebral bodies and tested them in compression in 3 orientations (rostrocaudal, dorsoventral, and mediolateral) at 2 mm min<sup>-1</sup>. Overall, bone from the pre-fluke/fluke boundary had the greatest yield strength and resilience, indicating that the greatest forces are translated to the tail during caudal oscillatory swimming. Group 1, composed of 5 shallow-diving delphinid species, had the greatest vertebral trabecular bone yield strength, apparent stiffness, and resilience of all functional groups. Conversely, Group 3, composed of 2 deep-diving kogiid species, had the least strong, stiff, and resilient bone, while Group 2 (3 deep-diving delphinid species) exhibited intermediate values. These data suggest that species that incorporate prolonged glides during deep descents in the water column actively swim less, and place relatively smaller loads on their vertebral columns, compared with species that execute shallower dives. We found that cetacean vertebral trabecular bone properties differed from the properties of terrestrial mammals; for every given bone strength, cetacean bone was less stiff by comparison. This relative lack of material rigidity within vertebral bone may be attributed to the non-weight-bearing locomotor modes of fully aquatic mammals.</p>","PeriodicalId":13666,"journal":{"name":"Integrative Organismal Biology","volume":" ","pages":"obab036"},"PeriodicalIF":1.5,"publicationDate":"2022-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8832228/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39622797","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Molly K Gabler-Smith, Dylan K Wainwright, Greta A Wong, George V Lauder
{"title":"Dermal Denticle Diversity in Sharks: Novel Patterns on the Interbranchial Skin.","authors":"Molly K Gabler-Smith, Dylan K Wainwright, Greta A Wong, George V Lauder","doi":"10.1093/iob/obab034","DOIUrl":"https://doi.org/10.1093/iob/obab034","url":null,"abstract":"<p><p>Shark skin is covered in dermal denticles-tooth-like structures consisting of enameloid, dentine, and a central pulp cavity. Previous studies have demonstrated differences in denticle morphology both among species and across different body regions within a species, including one report of extreme morphological variation within a 1 cm distance on the skin covering the branchial pouches, a region termed \"interbranchial skin.\" We used gel-based profilometry, histology, and scanning electron microscopy to quantify differences in denticle morphology and surface topography of interbranchial skin denticles among 13 species of sharks to better understand the surface structure of this region. We show that (1) interbranchial skin denticles differ across shark species, and (2) denticles on the leading edge of the skin covering each gill pouch have different morphology and surface topography compared with denticles on the trailing edge. Across all species studied, there were significant differences in denticle length (<i>P</i> = 0.01) and width (<i>P</i> = 0.002), with shorter and wider leading edge denticles compared with trailing edge denticles. Surface skew was also higher in leading edge denticles (<i>P</i> = 0.009), though most values were still negative, indicating a surface texture more dominated by valleys than peaks. Overall, leading edge denticles were smoother-edged than trailing edge denticles in all of the species studied. These data suggest two hypotheses: (1) smoother-edged leading edge denticles protect the previous gill flap from abrasion during respiration, and (2) ridged denticle morphology at the trailing edge might alter water turbulence exiting branchial pouches after passing over the gills. Future studies will focus on determining the relationship between denticle morphology and water flow by visualizing fluid motion over interbranchial denticles during <i>in vivo</i> respiration.</p>","PeriodicalId":13666,"journal":{"name":"Integrative Organismal Biology","volume":" ","pages":"obab034"},"PeriodicalIF":1.5,"publicationDate":"2021-12-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8694198/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39789116","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Thomas J Sanger, Laura Harding, Judith Kyrkos, Alexandrea J Turnquist, Lilian Epperlein, Sylvia A Nunez, Dryden Lachance, Seerat Dhindsa, James T Stroud, Raul E Diaz, Beata Czesny
{"title":"Environmental Thermal Stress Induces Neuronal Cell Death and Developmental Malformations in Reptiles.","authors":"Thomas J Sanger, Laura Harding, Judith Kyrkos, Alexandrea J Turnquist, Lilian Epperlein, Sylvia A Nunez, Dryden Lachance, Seerat Dhindsa, James T Stroud, Raul E Diaz, Beata Czesny","doi":"10.1093/iob/obab033","DOIUrl":"https://doi.org/10.1093/iob/obab033","url":null,"abstract":"<p><p>Every stage of organismal life history is being challenged by global warming. Many species are already experiencing temperatures approaching their physiological limits; this is particularly true for ectothermic species, such as lizards. Embryos are markedly sensitive to thermal insult. Here, we demonstrate that temperatures currently experienced in natural nesting areas can modify gene expression levels and induce neural and craniofacial malformations in embryos of the lizard <i>Anolis sagrei</i>. Developmental abnormalities ranged from minor changes in facial structure to significant disruption of anterior face and forebrain. The first several days of postoviposition development are particularly sensitive to this thermal insult. These results raise new concern over the viability of ectothermic species under contemporary climate change. Herein, we propose and test a novel developmental hypothesis that describes the cellular and developmental origins of those malformations: cell death in the developing forebrain and abnormal facial induction due to disrupted Hedgehog signaling. Based on similarities in the embryonic response to thermal stress among distantly related species, we propose that this developmental hypothesis represents a common embryonic response to thermal insult among amniote embryos. Our results emphasize the importance of adopting a broad, multidisciplinary approach that includes both lab and field perspectives when trying to understand the future impacts of anthropogenic change on animal development.</p>","PeriodicalId":13666,"journal":{"name":"Integrative Organismal Biology","volume":" ","pages":"obab033"},"PeriodicalIF":1.5,"publicationDate":"2021-12-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8643577/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39702592","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
D Rex Mitchell, Stephen Wroe, Matthew J Ravosa, Rachel A Menegaz
{"title":"More Challenging Diets Sustain Feeding Performance: Applications Toward the Captive Rearing of Wildlife.","authors":"D Rex Mitchell, Stephen Wroe, Matthew J Ravosa, Rachel A Menegaz","doi":"10.1093/iob/obab030","DOIUrl":"https://doi.org/10.1093/iob/obab030","url":null,"abstract":"<p><p>The rescue and rehabilitation of young fauna is of substantial importance to conservation. However, it has been suggested that incongruous diets offered in captive environments may alter craniofacial morphology and hinder the success of reintroduced animals. Despite these claims, to what extent dietary variation throughout ontogeny impacts intrapopulation cranial biomechanics has not yet been tested. Here, finite element models were generated from the adult crania of 40 rats (<i>n</i> = 10 per group) that were reared on 4 different diet regimes and stress magnitudes compared during incisor bite simulations. The diets consisted of (1) exclusively hard pellets from weaning, (2) exclusively soft ground pellet meal from weaning, (3) a juvenile switch from pellets to meal, and (4) a juvenile switch from meal to pellets. We hypothesized that a diet of exclusively soft meal would result in the weakest adult skulls, represented by significantly greater stress magnitudes at the muzzle, palate, and zygomatic arch. Our hypothesis was supported at the muzzle and palate, indicating that a diet limited to soft food inhibits bone deposition throughout ontogeny. This finding presents a strong case for a more variable and challenging diet during development. However, rather than the \"soft\" diet group resulting in the weakest zygomatic arch as predicted, this region instead showed the highest stress among rats that switched as juveniles from hard pellets to soft meal. We attribute this to a potential reduction in number and activity of osteoblasts, as demonstrated in studies of sudden and prolonged disuse of bone. A shift to softer foods in captivity, during rehabilitation after injury in the wild for example, can therefore be detrimental to healthy development of the skull in some growing animals, potentially increasing the risk of injury and impacting the ability to access full ranges of wild foods upon release. We suggest captive diet plans consider not just nutritional requirements but also food mechanical properties when rearing wildlife to adulthood for reintroduction.</p>","PeriodicalId":13666,"journal":{"name":"Integrative Organismal Biology","volume":" ","pages":"obab030"},"PeriodicalIF":1.5,"publicationDate":"2021-11-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8653637/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39710600","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Turtling the Salamander: Tail Movements Mitigate Need for Kinematic Limb Changes during Walking in Tiger Salamanders (<i>Ambystoma tigrinum)</i> with Restricted Lateral Movement.","authors":"Christine M Vega, Miriam A Ashley-Ross","doi":"10.1093/iob/obab029","DOIUrl":"https://doi.org/10.1093/iob/obab029","url":null,"abstract":"<p><p>Lateral undulation and trunk flexibility offer performance benefits to maneuverability, stability, and stride length (via speed and distance traveled). These benefits make them key characteristics of the locomotion of tetrapods with sprawling posture, with the exception of turtles. Despite their bony carapace preventing lateral undulations, turtles are able to improve their locomotor performance by increasing stride length via greater limb protraction. The goal of this study was to quantify the effect of reduced lateral flexibility in a generalized sprawling tetrapod, the tiger salamander (<i>Ambystoma tigrinum</i>). We had two potential predictions: (1) either salamanders completely compensate by changing their limb kinematics, or (2) their performance (i.e., speed) will suffer due to the reduced lateral flexibility. This reduction was performed by artificially limiting trunk flexibility by attaching a 2-piece shell around the body between the pectoral and pelvic girdles. Adult tiger salamanders (<i>n</i> = 3; SVL = 9-14.5 cm) walked on a 1-m trackway under three different conditions: unrestricted, flexible shell (Tygon tubing), and rigid shell (PVC tubing). Trials were filmed in a single, dorsal view, and kinematics of entire midline and specific body regions (head, trunk, tail), as well as the fore and hind limbs, were calculated. Tygon individuals had significantly higher curvature than both PVC and unrestricted individuals for the body, but this trend was primarily driven by changes in tail movements. PVC individuals had significantly lower curvature in the trunk region compared with unrestricted individuals or Tygon; however, there was no difference between unrestricted and Tygon individuals suggesting the shells performed as expected. PVC and Tygon individuals had significantly higher curvature in the tails compared with unrestricted individuals. There were no significant differences for any limb kinematic variables among treatments including average, minimum, and maximum angles. Thus, salamanders respond to decreased lateral movement in their trunk by increasing movements in their tail, without changes in limb kinematics. These results suggest that tail undulations may be a more critical component to sprawling-postured tetrapod locomotion than previously recognized.</p>","PeriodicalId":13666,"journal":{"name":"Integrative Organismal Biology","volume":" ","pages":"obab029"},"PeriodicalIF":1.5,"publicationDate":"2021-10-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8545788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39570482","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Sex Differences in How Territory Quality Affects Aggression in Convict Cichlids.","authors":"Joseph M Leese, T Blatt","doi":"10.1093/iob/obab028","DOIUrl":"https://doi.org/10.1093/iob/obab028","url":null,"abstract":"<p><p>In animal contests, the value an individual assigns to limited resources can directly impact the level of aggression it demonstrates. For territorial species, individuals often assess their territory quality and appropriately modify the time and energy invested in its defense. In this study, male and female convict cichlids, <i>Amatitlania nigrofasciata</i>, were acclimated to one of three territorial treatments representing either a low, medium, or high resource value. Territories with a \"Low Value\" included substrate alone, \"Medium Value\" territories included substrate and a nest site, and a \"High Value\" territory included substrate, a nest site, and constant food source. After three days of acclimation, a size-matched intruder was introduced to elicit territorial aggression and behaviors were observed. Territory quality affected one measure of low-intensity aggression (displays) in residents but had no effect on high-intensity aggression (bites and chases). Moreover, there was a significant effect of sex, with males and females differing in the types of aggressive behaviors demonstrated across all treatments. Females showed more low-intensity aggressive behaviors toward intruders than males did. Additionally, a significant interaction of sex and territory quality was observed on two measures of high-intensity aggressive behavior (bites and chases), with females more likely than males to increase aggressive behaviors along with increasing territory quality. This suggests that females may be more sensitive and/or responsive to changes in the quality of a territory, possibly due to the necessity of a suitable nest site for egg deposition within a territory.</p>","PeriodicalId":13666,"journal":{"name":"Integrative Organismal Biology","volume":" ","pages":"obab028"},"PeriodicalIF":1.5,"publicationDate":"2021-10-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8522484/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39535653","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"AutoBend: An Automated Approach for Estimating Intervertebral Joint Function from Bone-Only Digital Models.","authors":"K E Jones, R J Brocklehurst, S E Pierce","doi":"10.1093/iob/obab026","DOIUrl":"https://doi.org/10.1093/iob/obab026","url":null,"abstract":"<p><p>Deciphering the biological function of rare or extinct species is key to understanding evolutionary patterns across the tree of life. While soft tissues are vital determinants of joint function, they are rarely available for study. Therefore, extracting functional signals from skeletons, which are more widely available via museum collections, has become a priority for the field of comparative biomechanics. While most work has focused on the limb skeleton, the axial skeleton plays a critical role in body support, respiration, and locomotion, and is therefore of central importance for understanding broad-scale functional evolution. Here, we describe and experimentally validate AutoBend, an automated approach to estimating intervertebral joint function from bony vertebral columns. AutoBend calculates osteological range of motion (oROM) by automatically manipulating digitally articulated vertebrae while incorporating multiple constraints on motion, including both bony intersection and the role of soft tissues by restricting excessive strain in both centrum and zygapophyseal articulations. Using AutoBend and biomechanical data from cadaveric experiments on cats and tegus, we validate important modeling parameters required for oROM estimation, including the degree of zygapophyseal disarticulation, and the location of the center of rotation. Based on our validation, we apply a model with the center of rotation located within the vertebral disk, no joint translation, around 50% strain permitted in both zygapophyses and disks, and a small amount of vertebral intersection permitted. Our approach successfully reconstructs magnitudes and craniocaudal patterns of motion obtained from <i>ex vivo</i> experiments, supporting its potential utility. It also performs better than more typical methods that rely solely on bony intersection, emphasizing the importance of accounting for soft tissues. We estimated the sensitivity of the analyses to vertebral model construction by varying joint spacing, degree of overlap, and the impact of landmark placement. The effect of these factors was small relative to biological variation craniocaudally and between bending directions. We also present a new approach for estimating joint stiffness directly from oROM and morphometric measurements that can successfully reconstruct the craniocaudal patterns, but not magnitudes, derived from experimental data. Together, this work represents a significant step forward for understanding vertebral function in difficult-to-study (e.g., rare or extinct) species, paving the way for a broader understanding of patterns of functional evolution in the axial skeleton.</p>","PeriodicalId":13666,"journal":{"name":"Integrative Organismal Biology","volume":" ","pages":"obab026"},"PeriodicalIF":1.5,"publicationDate":"2021-10-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8514422/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39527610","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Differences in Mate Pairings of Hatchery- and Natural-Origin Coho Salmon Inferred from Offspring Genotypes.","authors":"H L Auld, D P Jacobson, A C Rhodes, M A Banks","doi":"10.1093/iob/obab020","DOIUrl":"https://doi.org/10.1093/iob/obab020","url":null,"abstract":"<p><p>Captive breeding can affect how sexual selection acts on subsequent generations. One context where this is important is in fish hatcheries. In many salmon hatcheries, spawning is controlled artificially and offspring are reared in captivity before release into the wild. While previous studies have suggested that hatchery- and natural-origin fish may make different mate choice decisions, it remains to be determined how hatchery fish may be making different mate choice decisions compared with natural-origin fish at a genetic level. Using genotyping-by-sequencing, we identify single-nucleotide polymorphisms (SNPs) associated with variation in mate pairings from a natural context involving hatchery- and natural-origin coho salmon (<i>Oncorhynchus kisutch</i>). In both natural-origin and hatchery mate pairs, we observed more SNPs with negative assortment than positive assortment. However, only 3% of the negative assortment SNPs were shared between the two mating groups, and 1% of the positive assortment SNPs were shared between the two mating groups, indicating divergence in mating cues between wild and hatchery-raised salmon. These findings shed light on mate choice in general and may have important implications in the conservation management of species as well as for improving other captive breeding scenarios. There remains much to discover about mate choice in salmon and research described here reflects our intent to test the potential of ongoing advances in population genomics to develop new hatchery practices that may improve the performance of hatchery offspring, lessening the differences and thus potential impacts upon wild stocks.</p>","PeriodicalId":13666,"journal":{"name":"Integrative Organismal Biology","volume":" ","pages":"obab020"},"PeriodicalIF":1.5,"publicationDate":"2021-08-14","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8363981/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39324301","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":4,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}