Differentiated appendages in Isoxys illuminate origin of arthropodization

Abstract The Cambrian fossil record has produced remarkable insights into the origin of euarthropods, particularly the evolution of their versatile body plan of segments bearing specialized, jointed appendages for different functions including feeding and locomotion [01, 02]. Early euarthropod evolution involved a major transition from lobopodian-like taxa [03, 04, 05] to organisms featuring a fully sclerotized trunk (arthrodization) and limbs (arthropodization) [02, 06, 07, 08]. However, the precise origin of arthropodization remains controversial because some of the earliest branching euarthropods possess a broad dorsal carapace that obscures critical details of the trunk and appendage organization [09, 10, 11, 12, 13, 14, 15]. Here, we demonstrate the presence of fully arthropodized ventral appendages in the upper stem-group euarthropod Isoxys curvirostratus from the early Cambrian Chengjiang biota in South China. Micro-computed tomography reveals the detailed three-dimensional structure of the biramous appendages in I. curvirostratus for the first time. In addition to the raptorial frontal appendages I. curvirostratus also possesses two batches of morphologically distinct biramous limbs, with the first batch consisting of four pairs of short cephalic appendages bearing prominent endites with a feeding function, followed by a second batch of elongate trunk appendages for locomotion. Each biramous limb bears an endopod with more than 12 well-defined podomeres, and an exopod consisting of a slender shaft carrying approximately a dozen paddle-shaped lamellae. Our findings clarify the enigmatic appendicular organization of Isoxys, one of the most ubiquitous euarthropods in Cambrian Burgess Shale-type deposits worldwide [01, 10, 11, 12, 14, 15, 16, 17, 18]. Critically, our new material shows that the trunk of I. curvirostratus was not arthrodized. The phylogenetic position of isoxyiids as possibly the earliest branching members of Deuteropoda [01, 02, 07, 15, 19], suggests that arthropodized biramous appendages evolved before the pattern of full trunk arthrodization that characterizes most extant and extinct members of this successful animal phylum.

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A bird-like skull in a Triassic diapsid reptile increases heterogeneity of the morphological and phylogenetic radiation of Diapsida

Royal Society Open Science ◽

10.1098/rsos.170499 ◽

2017 ◽

Vol 4 (10) ◽

pp. 170499 ◽

Cited By ~ 9

Author(s):

Adam C. Pritchard ◽

Sterling J. Nesbitt

Keyword(s):

Three Dimensional ◽

Total Body Length ◽

Phylogenetic Position ◽

Micro Computed Tomography ◽

Crown Group ◽

Chinle Formation ◽

Total Body ◽

Permian Mass Extinction ◽

First Time ◽

A New Species

The Triassic Period saw the first appearance of numerous amniote lineages (e.g. Lepidosauria, Archosauria, Mammalia) that defined Mesozoic ecosystems following the end Permian Mass Extinction, as well as the first major morphological diversification of crown-group reptiles. Unfortunately, much of our understanding of this event comes from the record of large-bodied reptiles (total body length > 1 m). Here we present a new species of drepanosaurid (small-bodied, chameleon-like diapsids) from the Upper Triassic Chinle Formation of New Mexico. Using reconstructions of micro-computed tomography data, we reveal the three-dimensional skull osteology of this clade for the first time. The skull presents many archaic anatomical traits unknown in Triassic crown-group reptiles (e.g. absence of bony support for the external ear), whereas other traits (e.g. toothless rostrum, anteriorly directed orbits, inflated endocranium) resemble derived avian theropods. A phylogenetic analysis of Permo-Triassic diapsids supports the hypothesis that drepanosaurs are an archaic lineage that originated in the Permian, far removed from crown-group Reptilia. The phylogenetic position of drepanosaurids indicates the presence of archaic Permian clades among Triassic small reptile assemblages and that morphological convergence produced a remarkably bird-like skull nearly 100 Myr before one is known to have emerged in Theropoda.

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Structure of the Lectin Mannose 6-Phosphate Receptor Homology (MRH) Domain of Glucosidase II, an Enzyme That Regulates Glycoprotein Folding Quality Control in the Endoplasmic Reticulum

Journal of Biological Chemistry ◽

10.1074/jbc.m113.450239 ◽

2013 ◽

Vol 288 (23) ◽

pp. 16460-16475 ◽

Cited By ~ 21

Author(s):

Linda J. Olson ◽

Ramiro Orsi ◽

Solana G. Alculumbre ◽

Francis C. Peterson ◽

Ivan D. Stigliano ◽

...

Keyword(s):

Endoplasmic Reticulum ◽

Three Dimensional ◽

Binding Pocket ◽

Dimensional Structure ◽

Mannose Residue ◽

Glucosidase Ii ◽

Mannose 6 Phosphate ◽

First Time ◽

Conserved Residue

Here we report for the first time the three-dimensional structure of a mannose 6-phosphate receptor homology (MRH) domain present in a protein with enzymatic activity, glucosidase II (GII). GII is involved in glycoprotein folding in the endoplasmic reticulum. GII removes the two innermost glucose residues from the Glc3Man9GlcNAc2 transferred to nascent proteins and the glucose added by UDP-Glc:glycoprotein glucosyltransferase. GII is composed of a catalytic GIIα subunit and a regulatory GIIβ subunit. GIIβ participates in the endoplasmic reticulum localization of GIIα and mediates in vivo enhancement of N-glycan trimming by GII through its C-terminal MRH domain. We determined the structure of a functional GIIβ MRH domain by NMR spectroscopy. It adopts a β-barrel fold similar to that of other MRH domains, but its binding pocket is the most shallow known to date as it accommodates a single mannose residue. In addition, we identified a conserved residue outside the binding pocket (Trp-409) present in GIIβ but not in other MRHs that influences GII glucose trimming activity.

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A fresh look at Cladarosymblema narrienense, a tetrapodomorph fish (Sarcopterygii: Megalichthyidae) from the Carboniferous of Australia, illuminated via X-ray tomography

PeerJ ◽

10.7717/peerj.12597 ◽

2021 ◽

Vol 9 ◽

pp. e12597

Author(s):

Alice M. Clement ◽

Richard Cloutier ◽

Jing Lu ◽

Egon Perilli ◽

Anton Maksimenko ◽

...

Keyword(s):

Original Description ◽

Sister Group ◽

Axial Skeleton ◽

Phylogenetic Position ◽

Micro Computed Tomography ◽

Holotype Specimen ◽

Freshwater Swamp ◽

The Family ◽

First Time ◽

Detailed Work

Background The megalichthyids are one of several clades of extinct tetrapodomorph fish that lived throughout the Devonian–Permian periods. They are advanced “osteolepidid-grade” fishes that lived in freshwater swamp and lake environments, with some taxa growing to very large sizes. They bear cosmine-covered bones and a large premaxillary tusk that lies lingually to a row of small teeth. Diagnosis of the family remains controversial with various authors revising it several times in recent works. There are fewer than 10 genera known globally, and only one member definitively identified from Gondwana. Cladarosymblema narrienense Fox et al. 1995 was described from the Lower Carboniferous Raymond Formation in Queensland, Australia, on the basis of several well-preserved specimens. Despite this detailed work, several aspects of its anatomy remain undescribed. Methods Two especially well-preserved 3D fossils of Cladarosymblema narrienense, including the holotype specimen, are scanned using synchrotron or micro-computed tomography (µCT), and 3D modelled using specialist segmentation and visualisation software. New anatomical detail, in particular internal anatomy, is revealed for the first time in this taxon. A novel phylogenetic matrix, adapted from other recent work on tetrapodomorphs, is used to clarify the interrelationships of the megalichthyids and confirm the phylogenetic position of C. narrienense. Results Never before seen morphological details of the palate, hyoid arch, basibranchial skeleton, pectoral girdle and axial skeleton are revealed and described. Several additional features are confirmed or updated from the original description. Moreover, the first full, virtual cranial endocast of any tetrapodomorph fish is presented and described, giving insight into the early neural adaptations in this group. Phylogenetic analysis confirms the monophyly of the Megalichthyidae with seven genera included (Askerichthys, Cladarosymblema, Ectosteorhachis, Mahalalepis, Megalichthys, Palatinichthys, and Sengoerichthys). The position of the megalichthyids as sister group to canowindrids, crownward of “osteolepidids” (e.g.,Osteolepis and Gogonasus), but below “tristichopterids” such as Eusthenopteron is confirmed, but our findings suggest further work is required to resolve megalichthyid interrelationships.

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Rational humanization of the powerful antithrombotic anti-GPIbα antibody: 6B4

Thrombosis and Haemostasis ◽

10.1160/th06-06-0297 ◽

2006 ◽

Vol 96 (11) ◽

pp. 671-684 ◽

Cited By ~ 21

Author(s):

Alexandre Fontayne ◽

Karen Vanhoorelbeke ◽

Inge Pareyn ◽

Isabel Van Rompaey ◽

Muriel Meiring ◽

...

Keyword(s):

Ex Vivo ◽

Three Dimensional ◽

Vector System ◽

Dimensional Structure ◽

Fab Fragment ◽

Variable Regions ◽

Significant Prolongation ◽

Von Willebrand ◽

First Time

SummaryFab-fragments of the monoclonal antibody 6B4, raised against human glycoprotein Ibα (GPIbα), have a powerful antithrombotic effect in baboons by blocking the GPIbα binding site for von Willebrand factor (VWF), without significant prolongation of the skin bleeding time. In order to bring this antibody to the clinic,we here humanized for the first time an anti-human GPIbα by variable-domain resurfacing guided by computer modeling. First, the genes coding for the variable regions of the heavy and light chains of 6B4 were cloned and sequenced. Based on this,a three-dimensional structure of the Fv-fragment was constructed by using homology-based modeling, and with this and comparison with antibodies with known structure,”murine” putative immunogenic residues which are exposed, were changed for “human-like” residues. The humanized Fab-fragment, h6B4-Fab, was constructed in the pKaneo vector system, expressed and purified and showed in vitro an unaltered, even slightly higher binding affinity for its antigen than the murine form as determined by different ELISA set-ups and surface plasmon resonance. Finally, injection of doses of 0.1 to 1.5 mg/kg of h6B4-Fab in baboons showed that both pharmacokinetics and ex-vivo bio-activity of the molecule were to a large extent preserved.In conclusion, the method used here to humanize 6B4 by resurfacing resulted in a fully active derivative, which is now ready for further development.

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Structural modeling and role of HAX-1 as a positive allosteric modulator of human serine protease HtrA2

Biochemical Journal ◽

10.1042/bcj20190569 ◽

2019 ◽

Vol 476 (20) ◽

pp. 2965-2980

Author(s):

Lalith K. Chaganti ◽

Shubhankar Dutta ◽

Raja Reddy Kuppili ◽

Mriganka Mandal ◽

Kakoli Bose

Keyword(s):

Pdz Domain ◽

Limited Proteolysis ◽

Three Dimensional ◽

Dimensional Structure ◽

Multifunctional Protein ◽

Promising Therapeutic Target ◽

Wide Range ◽

Structural Details ◽

Structural Architecture ◽

First Time

Abstract HAX-1, a multifunctional protein involved in cell proliferation, calcium homeostasis, and regulation of apoptosis, is a promising therapeutic target. It regulates apoptosis through multiple pathways, understanding of which is limited by the obscurity of its structural details and its intricate interaction with its cellular partners. Therefore, using computational modeling, biochemical, functional enzymology and spectroscopic tools, we predicted the structure of HAX-1 as well as delineated its interaction with one of it pro-apoptotic partner, HtrA2. In this study, three-dimensional structure of HAX-1 was predicted by threading and ab initio tools that were validated using limited proteolysis and fluorescence quenching studies. Our pull-down studies distinctly demonstrate that the interaction of HtrA2 with HAX-1 is directly through its protease domain and not via the conventional PDZ domain. Enzymology studies further depicted that HAX-1 acts as an allosteric activator of HtrA2. This ‘allosteric regulation’ offers promising opportunities for the specific control and functional modulation of a wide range of biological processes associated with HtrA2. Hence, this study for the first time dissects the structural architecture of HAX-1 and elucidates its role in PDZ-independent activation of HtrA2.

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Visualization of a pillar-shaped fiber bundle in a model needle-punched nonwoven fabric using X-ray micro-computed tomography

Textile Research Journal ◽

10.1177/0040517516652351 ◽

2016 ◽

Vol 87 (11) ◽

pp. 1387-1393 ◽

Cited By ~ 3

Author(s):

Tatsuya Ishikawa ◽

KyoungHou Kim ◽

Yutaka Ohkoshi

Keyword(s):

Fiber Bundle ◽

Three Dimensional ◽

Nonwoven Fabric ◽

Fiber Bundles ◽

Dimensional Structure ◽

Micro Computed Tomography ◽

X Ray ◽

Needle Punching ◽

Pet Fibers ◽

Polyethylene Fibers

In the needle-punching process, the barbs of a needle catch fibers and orient them along the thickness direction of the fabric. The oriented fibers form a pillar-shaped fiber bundle, which acts as a bonding point of the fabric. The structure of the pillar-shaped fiber bundle thus governs the mechanical properties of needle-punched nonwoven fabric, and both are largely affected by the needle-punching conditions. However, the three-dimensional structure of pillar-shaped fiber bundles and their development under different needle-punching conditions have not been revealed. In the present study, we visualized the three-dimensional structure of a pillar-shaped fiber bundle in needle-punched nonwoven fabric, employing X-ray micro-computed tomography (XCT) on the basis of the difference in the X-ray absorption coefficient between polyethylene terephthalate (PET) and polyethylene fibers. For a material density ratio of less than 1.4 and PET fibers having a diameter of 40 µm, the pillar-shaped bundles of PET fibers were visualized by erasing 20-µm polyethylene fibers in XCT images. Furthermore, we investigated the effects of the penetration depth of the needle on the development of pillar-shaped fiber bundles. The number of fibers constituting a pillar largely increased at a penetration depth of 19.0 mm, and pillars protruded from the bottom surface of the fabric and formed a stitch structure. The XCT applied in this study is thus effective in analyzing the structure of pillar-shaped fiber bundles quantitatively without affecting the structure of the nonwoven fabric.

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Morphological facilitators for vocal learning explored through the syrinx anatomy of a basal hummingbird

10.1101/2020.01.11.902734 ◽

2020 ◽

Cited By ~ 1

Author(s):

Amanda Monte ◽

Alexander F. Cerwenka ◽

Bernhard Ruthensteiner ◽

Manfred Gahr ◽

Daniel N. Düring

Keyword(s):

Sound Production ◽

Three Dimensional ◽

Vocal Learning ◽

Dimensional Structure ◽

Micro Computed Tomography ◽

Vocal Production ◽

Precise Control ◽

Acoustic Space ◽

Biomechanical Factors ◽

Intrinsic Musculature

AbstractVocal learning is a rare evolutionary trait that evolved independently in three avian clades: songbirds, parrots, and hummingbirds. Although the anatomy and mechanisms of sound production in songbirds are well understood, little is known about the hummingbird’s vocal anatomy. We use high-resolution micro-computed tomography (μCT) and microdissection to reveal the three-dimensional structure of the syrinx, the vocal organ of the black jacobin (Florisuga fusca), a phylogenetically basal hummingbird species. We identify three unique features of the black jacobin’s syrinx: (i) a shift in the position of the syrinx to the outside of the thoracic cavity and the related loss of the sterno-tracheal muscle, (ii) complex intrinsic musculature, oriented dorso-ventrally, and (iii) ossicles embedded in the medial vibratory membranes. Their syrinx morphology allows vibratory decoupling, precise control of complex acoustic parameters, and a large redundant acoustic space that may be key biomechanical factors facilitating the occurrence of vocal production learning.

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Three-dimensional wing structure attenuates aerodynamic efficiency in flapping fly wings

Journal of The Royal Society Interface ◽

10.1098/rsif.2019.0804 ◽

2020 ◽

Vol 17 (164) ◽

pp. 20190804 ◽

Cited By ~ 1

Author(s):

Thomas Engels ◽

Henja-Niniane Wehmann ◽

Fritz-Olaf Lehmann

Keyword(s):

Aerodynamic Force ◽

Three Dimensional ◽

Force Production ◽

Reynolds Numbers ◽

Dimensional Structure ◽

Micro Computed Tomography ◽

Venation Pattern ◽

Aerodynamic Pressure ◽

Inertial Loading ◽

External Forces

The aerial performance of flying insects ultimately depends on how flapping wings interact with the surrounding air. It has previously been suggested that the wing's three-dimensional camber and corrugation help to stiffen the wing against aerodynamic and inertial loading during flapping motion. Their contribution to aerodynamic force production, however, is under debate. Here, we investigated the potential benefit of three-dimensional wing shape in three different-sized species of flies using models of micro-computed tomography-scanned natural wings and models in which we removed either the wing's camber, corrugation, or both properties. Forces and aerodynamic power requirements during root flapping were derived from three-dimensional computational fluid dynamics modelling. Our data show that three-dimensional camber has no benefit for lift production and attenuates Rankine–Froude flight efficiency by up to approximately 12% compared to a flat wing. Moreover, we did not find evidence for lift-enhancing trapped vortices in corrugation valleys at Reynolds numbers between 137 and 1623. We found, however, that in all tested insect species, aerodynamic pressure distribution during flapping is closely aligned to the wing's venation pattern. Altogether, our study strongly supports the assumption that the wing's three-dimensional structure provides mechanical support against external forces rather than improving lift or saving energetic costs associated with active wing flapping.

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Exceptionally well-preserved silicified hippuritid rudist bivalves from the lower Maastrichtian of Puerto Rico

Carnets de géologie (Notebooks on geology) ◽

10.2110/carnets.2020.2018 ◽

2020 ◽

Vol 20 (18) ◽

pp. 333-366

Author(s):

Simon F. Mitchell

Keyword(s):

Puerto Rico ◽

New World ◽

Three Dimensional ◽

Acid Digestion ◽

Distinctive Morphology ◽

New Material ◽

Lower Maastrichtian ◽

Rudist Bivalves ◽

Left And Right ◽

First Time

Exceptionally well-preserved (silicified) hippuritid rudists occur in the El Rayo Formation (lower Maastrichtian) of south-western Puerto Rico. Three species belonging to three different genera are present: Caribbea muellerreidi (VERMUNT), Laluzia peruviana (GERTH) and Parastroma guitarti (PALMER). Acid digestion of the limestones has resulted in a collection with numerous three-dimensional left and right valves many with the preservation of the minute details of the pore system. The morphological features of each species are described, and many features are illustrated for the first time. The new material, coupled with descriptions from other studies, demonstrates that six genera of endemic hippuritids evolved in two separate radiations in the New World: an older radiation of forms that had pallial canals in their left valves (Barrettia, Whitfieldiella and Parastroma) and a younger radiation of forms lacking pallial canals in their left valves (Laluzia, Caribbea and Praebarrettia). The exquisite preservation also reveals that in these endemic New World hippuritids the sockets for the teeth consisted of slots into which ribs on the teeth fitted; this contrasts with Old World hippuritids that have true sockets formed from upfolds of the tabulae for the teeth. The distinctive morphology of the tooth sockets is here used to define a monophyletic subfamily for which the name Barrettiinae CHUBB is available.

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Enhanced macroboring and depressed calcification drive net dissolution at high-CO 2 coral reefs

Proceedings of The Royal Society B Biological Sciences ◽

10.1098/rspb.2016.1742 ◽

2016 ◽

Vol 283 (1842) ◽

pp. 20161742 ◽

Cited By ~ 39

Author(s):

Ian C. Enochs ◽

Derek P. Manzello ◽

Graham Kolodziej ◽

Sam H. C. Noonan ◽

Lauren Valentino ◽

...

Keyword(s):

Three Dimensional ◽

Skeletal Structure ◽

Global Ocean ◽

Biological Processes ◽

Micro Computed Tomography ◽

Dead Coral ◽

Intergovernmental Panel ◽

Three Dimensional Models ◽

First Time ◽

High Carbon Dioxide

Ocean acidification (OA) impacts the physiology of diverse marine taxa; among them corals that create complex reef framework structures. Biological processes operating on coral reef frameworks remain largely unknown from naturally high-carbon-dioxide (CO 2 ) ecosystems. For the first time, we independently quantified the response of multiple functional groups instrumental in the construction and erosion of these frameworks (accretion, macroboring, microboring, and grazing) along natural OA gradients. We deployed blocks of dead coral skeleton for roughly 2 years at two reefs in Papua New Guinea, each experiencing volcanically enriched CO 2 , and employed high-resolution micro-computed tomography (micro-CT) to create three-dimensional models of changing skeletal structure. OA conditions were correlated with decreased calcification and increased macroboring, primarily by annelids, representing a group of bioeroders not previously known to respond to OA. Incubation of these blocks, using the alkalinity anomaly methodology, revealed a switch from net calcification to net dissolution at a pH of roughly 7.8, within Intergovernmental Panel on Climate Change's (IPCC) predictions for global ocean waters by the end of the century. Together these data represent the first comprehensive experimental study of bioerosion and calcification from a naturally high-CO 2 reef ecosystem, where the processes of accelerated erosion and depressed calcification have combined to alter the permanence of this essential framework habitat.

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