Organ Mapping Antibody Panels: a community resource for standardized multiplexed tissue imaging.

Multiplexed antibody-based imaging enables the detailed characterization of molecular and cellular organization in tissues. Advances in the field now allow high-parameter data collection (>60 targets); however, considerable expertise and capital are needed to construct the antibody panels employed by these methods. Organ mapping antibody panels are community-validated resources that save time and money, increase reproducibility, accelerate discovery and support the construction of a Human Reference Atlas.

Single Cell Analysis of Proteoforms.

We introduce single cell Proteoform imaging Mass Spectrometry (scPiMS), which realizes the benefit of direct solvent extraction and MS detection of intact proteins from single cells dropcast onto glass slides. Sampling and detection of whole proteoforms by individual ion mass spectrometry enable a scalable approach to single cell proteomics. This new scPiMS platform addresses the throughput bottleneck in single cell proteomics and boosts the cell processing rate by several fold while accessing protein composition with higher coverage.

Mapping the KRAS proteoform landscape in colorectal cancer identifies truncated KRAS4B that decreases MAPK signaling.

The KRAS gene is one of the most frequently mutated oncogenes in human cancer and gives rise to two isoforms, KRAS4A and KRAS4B. KRAS post-translational modifications (PTMs) have the potential to influence downstream signaling. However, the relationship between KRAS PTMs and oncogenic mutations remains unclear, and the extent of isoform-specific modification is unknown. Here, we present the first top-down proteomics study evaluating both KRAS4A and KRAS4B, resulting in 39 completely characterized proteoforms across colorectal cancer cell lines and primary tumor samples. We determined which KRAS PTMs are present, along with their relative abundance, and that proteoforms of KRAS4A versus KRAS4B are differentially modified. Moreover, we identified a subset of KRAS4B proteoforms lacking the C185 residue and associated C-terminal PTMs. By confocal microscopy, we confirmed that this truncated GFP-KRAS4BC185∗ proteoform is unable to associate with the plasma membrane, resulting in a decrease in mitogen-activated protein kinase signaling pathway activation. Collectively, our study provides a reference set of functionally distinct KRAS proteoforms and the colorectal cancer contexts in which they are present.

Development of Ln(III) Derivatives as 19F Parashift Probes.

19F parashift probes with paramagnetically shifted reporter nuclei provide attractive platforms to develop molecular imaging probes. These probes enable ratiometric detection of molecular disease markers using a direct detection technique. Here, we describe a series of trivalent lanthanide (Ln(III)) complexes that are structural analogues of the clinically approved MR contrast agent (CA) ProHance to obtain LnL 19F parashift probes. We evaluated trans-gadolinium paramagnetic lanthanides compared to diamagnetic YL for 19F chemical shift and relaxation rate enhancement. The paramagnetic contribution to chemical shift (δPCS) for paramagnetic LnL exhibited either shifts to lower frequency (δPCS < 0 for TbL, DyL, and HoL) or shifts to higher frequency (δPCS > 0 for ErL, TmL, and YbL) compared to YL 19F spectroscopic signal. Zero-echo time pulse sequences achieved 56-fold sensitivity enhancement for DyL over YL, while developing probe-specific pulse sequences with fast delay times and acquisition times achieved 0.6-fold enhancement in limit of detection for DyL. DyL provides an attractive platform to develop 19F parashift probes for ratiometric detection of enzymatic activity.

The origin of squamates revealed by a Middle Triassic lizard from the Italian Alps.

Modern squamates (lizards, snakes and amphisbaenians) are the world's most diverse group of tetrapods along with birds 1 and have a long evolutionary history, with the oldest known fossils dating from the Middle Jurassic period-168 million years ago2-4. The evolutionary origin of squamates is contentious because of several issues: (1) a fossil gap of approximately 70 million years exists between the oldest known fossils and their estimated origin5-7; (2) limited sampling of squamates in reptile phylogenies; and (3) conflicts between morphological and molecular hypotheses regarding the origin of crown squamates6,8,9. Here we shed light on these problems by using high-resolution microfocus X-ray computed tomography data from the articulated fossil reptile Megachirella wachtleri (Middle Triassic period, Italian Alps 10 ). We also present a phylogenetic dataset, combining fossils and extant taxa, and morphological and molecular data. We analysed this dataset under different optimality criteria to assess diapsid reptile relationships and the origins of squamates. Our results re-shape the diapsid phylogeny and present evidence that M. wachtleri is the oldest known stem squamate. Megachirella is 75 million years older than the previously known oldest squamate fossils, partially filling the fossil gap in the origin of lizards, and indicates a more gradual acquisition of squamatan features in diapsid evolution than previously thought. For the first time, to our knowledge, morphological and molecular data are in agreement regarding early squamate evolution, with geckoes-and not iguanians-as the earliest crown clade squamates. Divergence time estimates using relaxed combined morphological and molecular clocks show that lepidosaurs and most other diapsids originated before the Permian/Triassic extinction event, indicating that the Triassic was a period of radiation, not origin, for several diapsid lineages.

Striatal brain volume linked to severity of substance use in high-risk incarcerated youth.

Substance use disorders among juveniles are a major public health concern and are often intertwined with other psychosocial risk factors including antisocial behavior. Identifying etiological risks and mechanisms promoting substance use disorders remains a high priority for informing more focused interventions in high-risk populations. The present study examined brain gray matter structure in relation to substance use severity among n = 152 high-risk, incarcerated boys (aged 14-20). Substance use severity was positively associated with gray matter volume across several frontal/striatal brain regions including amygdala, pallidum, putamen, insula, and orbitofrontal cortex. Effects were apparent when using voxel-based-morphometric analysis, as well as in whole-brain, data-driven, network-based approaches (source-based morphometry). These findings support the hypothesis that elevated gray matter volume in striatal reward circuits may be an endogenous marker for vulnerability to severe substance use behaviors among youth.

Beyond sound: bimodal acoustic calls used in mate-choice and aggression by red-eyed treefrogs.

Airborne sound signals function as key mediators of mate-choice, aggression and other social interactions in a wide range of vertebrate and invertebrate animals. Calling animals produce more than sound, however. When displaying on or near a solid substrate, such as vegetation or soil, they also unavoidably excite substrate vibrations because of the physics of sound production and of acoustic propagation, and these vibrations can propagate to receivers. Despite their near ubiquity, these vibrational signal components have received very little research attention and in vertebrates it is unknown whether they are relevant to mate-choice, an important driver of evolutionary divergence. Here, we show that female red-eyed treefrogs are more than twice as likely to choose a male mating call when airborne sound is paired with its corresponding substrate vibrations. Furthermore, males of the same species are more aggressive towards and display a greater range of aggressive behaviors in response to bimodal (sound and vibration) versus unimodal (sound or vibration alone) calls. In aggressive contexts, at least, air- and substrate-borne signal components function non-redundantly. These results are a clear demonstration that vibrations produced by a calling animal can function together with airborne sound to markedly enhance the function of a signal. If this phenomenon proves widespread, this finding has the potential to substantially influence our understanding of the function and evolution of acoustic signals.

Plicidentine and the repeated origins of snake venom fangs.

Snake fangs are an iconic exemplar of a complex adaptation, but despite striking developmental and morphological similarities, they probably evolved independently in several lineages of venomous snakes. How snakes could, uniquely among vertebrates, repeatedly evolve their complex venom delivery apparatus is an intriguing question. Here we shed light on the repeated evolution of snake venom fangs using histology, high-resolution computed tomography (microCT) and biomechanical modelling. Our examination of venomous and non-venomous species reveals that most snakes have dentine infoldings at the bases of their teeth, known as plicidentine, and that in venomous species, one of these infoldings was repurposed to form a longitudinal groove for venom delivery. Like plicidentine, venom grooves originate from infoldings of the developing dental epithelium prior to the formation of the tooth hard tissues. Derivation of the venom groove from a large plicidentine fold that develops early in tooth ontogeny reveals how snake venom fangs could originate repeatedly through the co-option of a pre-existing dental feature even without close association to a venom duct. We also show that, contrary to previous assumptions, dentine infoldings do not improve compression or bending resistance of snake teeth during biting; plicidentine may instead have a role in tooth attachment.

Insights into skull evolution in fossorial snakes, as revealed by the cranial morphology of Atractaspis irregularis (Serpentes: Colubroidea).

Comparative osteological analyses of extant organisms provide key insight into major evolutionary transitions and phylogenetic hypotheses. This is especially true for snakes, given their unique morphology relative to other squamates and the persistent controversy regarding their evolutionary origins. However, the osteology of several major snake groups remains undescribed, thus hindering efforts to accurately reconstruct the phylogeny of snakes. One such group is the Atractaspididae, a family of fossorial colubroids. We herein present the first detailed description of the atractaspidid skull, based on fully segmented micro-computed tomography (micro-CT) scans of Atractaspis irregularis. The skull of Atractaspis presents a highly unique morphology influenced by both fossoriality and paedomorphosis. This paedomorphosis is especially evident in the jaws, palate, and suspensorium, the major elements associated with macrostomy (large-gaped feeding in snakes). Comparison to scolecophidians-a group of blind, fossorial, miniaturized snakes-in turn sheds light on current hypotheses of snake phylogeny. Features of both the naso-frontal joint and the morphofunctional system related to macrostomy refute the traditional notion that scolecophidians are fundamentally different from alethinophidians (all other extant snakes). Instead, these features support the controversial hypothesis of scolecophidians as "regressed alethinophidians," in contrast to their traditional placement as the earliest-diverging snake lineage. We propose that Atractaspis and scolecophidians fall along a morphological continuum, characterized by differing degrees of paedomorphosis. Altogether, a combination of heterochrony and miniaturization provides a mechanism for the derivation of the scolecophidian skull from an ancestral fossorial alethinophidian morphotype, exemplified by the nonminiaturized and less extreme paedomorph Atractaspis.

Tooth attachment and pleurodont implantation in lizards: Histology, development, and evolution.

Squamates present a unique challenge to the homology and evolution of tooth attachment tissues. Their stereotypically pleurodont teeth are fused in place by a single "bone of attachment", with seemingly dubious homology to the three-part tooth attachment system of mammals and crocodilians. Despite extensive debate over the interpretations of squamate pleurodonty, its phylogenetic significance, and the growing evidence from fossil amniotes for the homology of tooth attachment tissues, few studies have defined pleurodonty on histological grounds. Using a sample of extant squamate teeth that we organize into three broad categories of implantation, we investigate the histological and developmental properties of their dental tissues in multiple planes of section. We use these data to demonstrate the specific soft- and hard-tissue features of squamate teeth that produce their disparate tooth implantation modes. In addition, we describe cementum, periodontal ligaments, and alveolar bone in pleurodont squamates, dental tissues that were historically thought to be restricted to extant mammals and crocodilians. Moreover, we show how the differences between pleurodonty and thecodonty do not relate to the identity of the tooth attachment tissues, but rather the arrangements of homologous tissues around the teeth.

Sphenodontian phylogeny and the impact of model choice in Bayesian morphological clock estimates of divergence times and evolutionary rates.

BACKGROUND: The vast majority of all life that ever existed on earth is now extinct and several aspects of their evolutionary history can only be assessed by using morphological data from the fossil record. Sphenodontian reptiles are a classic example, having an evolutionary history of at least 230 million years, but currently represented by a single living species (Sphenodon punctatus). Hence, it is imperative to improve the development and implementation of probabilistic models to estimate evolutionary trees from morphological data (e.g., morphological clocks), which has direct benefits to understanding relationships and evolutionary patterns for both fossil and living species. However, the impact of model choice on morphology-only datasets has been poorly explored. RESULTS: Here, we investigate the impact of a wide array of model choices on the inference of evolutionary trees and macroevolutionary parameters (divergence times and evolutionary rates) using a new data matrix on sphenodontian reptiles. Specifically, we tested different clock models, clock partitioning, taxon sampling strategies, sampling for ancestors, and variations on the fossilized birth-death (FBD) tree model parameters through time. We find a strong impact on divergence times and background evolutionary rates when applying widely utilized approaches, such as allowing for ancestors in the tree and the inappropriate assumption of diversification parameters being constant through time. We compare those results with previous studies on the impact of model choice to molecular data analysis and provide suggestions for improving the implementation of morphological clocks. Optimal model combinations find the radiation of most major lineages of sphenodontians to be in the Triassic and a gradual but continuous drop in morphological rates of evolution across distinct regions of the phenotype throughout the history of the group. CONCLUSIONS: We provide a new hypothesis of sphenodontian classification, along with detailed macroevolutionary patterns in the evolutionary history of the group. Importantly, we provide suggestions to avoid overestimated divergence times and biased parameter estimates using morphological clocks. Partitioning relaxed clocks offers methodological limitations, but those can be at least partially circumvented to reveal a detailed assessment of rates of evolution across the phenotype and tests of evolutionary mosaicism.

The iliosacral joint in lizards: an osteological and histological analysis.

The development of the iliosacral joint (ISJ) in tetrapods represented a crucial step in the evolution of terrestrial locomotion. This structure is responsible for transferring forces between the vertebral column and appendicular skeleton, thus supporting the bodyweight on land. However, most research dealing with the water-to-land transition and biomechanical studies in general has focused exclusively on the articulation between the pelvic girdle and femur. Our knowledge about the contact between the pelvic girdle and vertebral column (i.e. the ISJ) at a tissue level is restricted so far to human anatomy, with little to no information available on other tetrapods. This lack of data limits our understanding of the development and evolution of such a key structure, and thus on the pattern and processes of the evolution of terrestrial locomotion. Therefore, we investigated the macro- and microanatomy of the ISJ in limb-bearing squamates that, similar to most non-mammalian, non-avian tetrapods, possess only two sacral ribs articulating with the posterior process of the ilium. Using a combination of osteology, micro-computed tomography and histology, we collected data on the ISJ apparatus of numerous specimens, sampling different taxa and different ontogenetic stages. Osteologically, we recorded consistent variability in all three processes of the ilium (preacetabular, supracetabular and posterior) and sacral ribs that correlate with posture and locomotion. The presence of a cavity between the ilium and sacral ribs, abundant articular cartilage and fibrocartilage, and a surrounding membrane of dense fibrous connective tissue allowed us to define this contact as a synovial joint. By comparison, the two sacral ribs are connected to each other mostly by dense fibrous tissue, with some cartilage found more distally along the margins of the two ribs, defining this joint as a combination of a syndesmosis and synchondrosis. Considering the intermediary position of the ISJ between the axial and appendicular skeletons, the shape of the articular surfaces of the sacral ribs and ilium, and the characteristics of the muscles associated with this structure, we argue that the mobility of the ISJ is primarily driven by the movements of the hindlimb during locomotion. We hypothesize that limited torsion of the ilium at the ISJ happens when the hip is abducted, and the joint is likely able to absorb the compressional and extensional forces related to the protraction and retraction of the femur. The mix of fibres and cartilage between the two sacral ribs instead serves primarily as a shock absorber, with the potential for limited vertical translation during locomotion.

The morphological diversity of the quadrate bone in squamate reptiles as revealed by high-resolution computed tomography and geometric morphometrics.

We examined the morphological diversity of the quadrate bone in squamate reptiles (i.e. lizards, snakes, amphisbaenians). The quadrate is the principal splanchnocranial element involved in suspending the lower jaw from the skull, and its shape is of particular interest because it is potentially affected by several factors, such as phylogenetic history, allometry, ecology, skull kinesis and hearing capabilities (e.g. presence or absence of a tympanic ear). Due to its complexity, the quadrate bone is also considered one of the most diagnostic elements in fragmentary fossil taxa. We describe quadrates from 38 species spread across all major squamate clades, using qualitative and quantitative (e.g. geometric morphometrics) methods. We test for possible correlations between shape variation and factors such as phylogeny, size, ecology and presence/absence of a tympanum. Our results show that the shape of the quadrate is highly evolutionarily plastic, with very little of the diversity explained by phylogenetic history. Size variation (allometric scaling) is similarly unable to explain much shape diversity in the squamate quadrate. Ecology (terrestrial/fossorial/aquatic) and presence of a tympanic ear are more significant, but together explain only about 20% of the diversity observed. Other unexplored and more analytically complex factors, such as skull biomechanics, likely play additional major roles in shaping the quadrates of lizards and snakes.

Self-Immolative Activation of ß-Galactosidase-Responsive Probes for In Vivo MR Imaging in Mouse Models.

Our lab has developed a new series of self-immolative MR agents for the rapid detection of enzyme activity in mouse models expressing ß-galactosidase (ß-gal). We investigated two molecular architectures to create agents that detect ß-gal activity by modulating the coordination of water to GdIII . The first is an intermolecular approach, wherein we designed several structural isomers to maximize coordination of endogenous carbonate ions. The second involves an intramolecular mechanism for q modulation. We incorporated a pendant coordinating carboxylate ligand with a 2, 4, 6, or 8 carbon linker to saturate ligand coordination to the GdIII ion. This renders the agent ineffective. We show that one agent in particular (6-C pendant carboxylate) is an extremely effective MR reporter for the detection of enzyme activity in a mouse model expressing ß-gal.

Water-Soluble Nanoconjugate for Enhanced Cellular Delivery of Receptor-Targeted Magnetic Resonance Contrast Agents.

ProGlo is an efficient steroid receptor-targeted magnetic resonance (MR) imaging contrast agent (CA). It has been shown to bind to the progesterone receptor (PR) and produce enhanced image contrast in PR-positive cells and tissues in vitro and in vivo. However, the hydrophobicity of the steroid targeting domain of ProGlo (logP = 1.4) limits its formulation and delivery at clinically relevant doses. In this work, a hydrophobic moiety was utilized to drive efficient adsorption onto nanodiamond (ND) clusters to form a water-soluble nanoconstruct (logP = -2.4) with 80% release in 8 h under biological conditions. In cell culture, the ND-ProGlo construct delivered increased concentrations of ProGlo to target cells compared to ProGlo alone. Importantly, these results were accomplished without the use of solvents such as DMSO, providing a significant advance toward formulating ProGlo for translational applications. Biodistribution studies confirm the delivery of ProGlo to PR(+) tissues with enhanced efficacy over untargeted controls. These results demonstrate the potential for a noncovalent ND-CA construct as a general strategy for solubilizing and delivering hydrophobic targeted MR CAs.

Giant taxon-character matrices II: a response to Laing et al. (2017).

The trend towards big data analyses in evolutionary biology has been observed in phylogenetics via the assembly of giant datasets composed of genomic and phenotypic data. We recently (Simões et al., 2017. Giant taxon-character matrices: Quality of character constructions remains critical regardless of size. Cladistics 33, 198-219) presented a critique of the phylogenetic character concepts used in current morphological datasets, with the caution that giant datasets did not obviate the empirical requirement of rigor in character construction. Laing et al. (2017. Giant taxon-character matrices: The future of morphological systematics. Cladistics, https://doi.org/10.1111/cla.12197) have since argued that we had 'suggested' that large datasets inherently contain flawed characters, and that we had presented a substandard methodology of phylogenetic analysis. Laing et al. concluded by discussing their approach to phylogenetic signal, total evidence and the inevitability of large datasets. We here reply to Laing et al. by reviewing what we actually wrote regarding dataset size, characters and methodology. We show that Laing et al.'s. central premise is unsupported, thus characterizing a Straw Man argument, and deeply misrepresents our original study. In part two, we discuss total evidence and phylogenetic signal issues raised by Laing et al. that are of major consequence to the appropriate construction of large morphological datasets.

Mosasaurs and snakes have a periodontal ligament: timing and extent of calcification, not tissue complexity, determines tooth attachment mode in reptiles.

Squamates present a unique challenge to our understanding of dental evolution in amniotes because they are the only extant tooth-bearing group for which a ligamentous tooth attachment is considered to be absent. This has led to the assumption that mammals and crocodilians have convergently evolved a ligamentous tooth attachment, composed of root cementum, periodontal ligament, and alveolar bone, whereas squamates are thought to possess a single bone of attachment tissue that fuses teeth to the jaws. The identity and homology of tooth attachment tissues between squamates, crocodilians, and mammals have thus been a focal point of debate for decades. We provide a novel interpretation of the mineralized attachment tissues in two focal taxa in this debate, mosasaurids and snakes, and compare dental tissue histology with that of the extant crocodilian Caiman sclerops. We identify a periodontal ligament in these squamates that usually exists temporarily as a soft connective tissue anchoring each tooth to the alveolar bone. We also identify two instances where complete calcification of the periodontal ligament does not occur: in a durophagous mosasaur, and in the hinged teeth of fossil and modern snakes. We propose that the periodontal ligament rapidly calcifies in the majority of mosasaurids and snakes, ankylosing the tooth to the jaw. This gives the appearance of a single, bone-like tissue fusing the tooth to the jaw in ankylosed teeth, but is simply the end stage of dental tissue ontogeny in most snakes and mosasaurids.

Giant taxon-character matrices: quality of character constructions remains critical regardless of size.

Giant morphological data matrices are increasingly common in cladistic analyses of vertebrate phylogeny, reporting numbers of characters never seen or expected before. However, the concern for size is usually not followed by an equivalent, if any, concern for character construction/selection criteria. Therefore, the question of whether quantity parallels quality for such influential works remains open. Here, we provide the largest compilation known to us of character construction methods and criteria, as derived from previous studies, and from our own de novo conceptualizations. Problematic character constructions inhibit the capacity of phylogenetic analyses to recover meaningful homology hypotheses and thus accurate clade structures. Upon a revision of two of the currently largest morphological datasets used to test squamate phylogeny, more than one-third of the almost 1000 characters analysed were classified within at least one of our categories of "types" of characters that should be avoided in cladistic investigations. These characters were removed or recoded, and the data matrices re-analysed, resulting in substantial changes in the sister group relationships for squamates, as compared to the original studies. Our results urge caution against certain types of character choices and constructions, also providing a methodological basis upon which problematic characters might be avoided.

Markov Logic Networks for Adverse Drug Event Extraction from Text.

Adverse drug events (ADEs) are a major concern and point of emphasis for the medical profession, government, and society. A diverse set of techniques from epidemiology, statistics, and computer science are being proposed and studied for ADE discovery from observational health data (e.g., EHR and claims data), social network data (e.g., Google and Twitter posts), and other information sources. Methodologies are needed for evaluating, quantitatively measuring, and comparing the ability of these various approaches to accurately discover ADEs. This work is motivated by the observation that text sources such as the Medline/Medinfo library provide a wealth of information on human health. Unfortunately, ADEs often result from unexpected interactions, and the connection between conditions and drugs is not explicit in these sources. Thus, in this work we address the question of whether we can quantitatively estimate relationships between drugs and conditions from the medical literature. This paper proposes and studies a state-of-the-art NLP-based extraction of ADEs from text.