bluuebunny/crossref_metadata_2025_split huggingface dataset:
Physiological Examination of Ratite Orthopedic Disorders and Soft‐Tissue Visualization via Micro‐CT
Authors: Green Todd , De Miranda Michael , Larson Ashley , Bonitz Shayla , Gignac Paul , Kley Nathan , Kanatous Shane 
Published: November 2023

Many hard‐tissue (e.g., bone, dentine, enamel) pathologies directly impact the development and function of soft‐tissue structures. Such pathologies can be unique to captive individuals and tend to be more common among large‐bodied captives such as crocodilians, elephants, and flightless birds. Emus (Dromaius novaehollandiae) are large‐bodied flightless birds that are uniquely efficient at both anaerobic sprinting and aerobic, sustained running. Native to Australia, they are commonly farmed in North America for oil and meat, but growth of the emu industry has been hampered by poorly understood orthopedic disease states (i.e., splayed‐leg disorder). Few studies have examined captive emu skeletal muscle, and none have documented the enzymatic profile of ratite cardiac tissue. We sought to bridge this gap by providing a quantified understanding of physical degradation in this large farm‐raised species. Surprisingly, we found the metabolic profile of captive emu cardiac tissue to be most similar to that of active, flying birds. Additionally, metabolic baselines for primary locomotor muscles between splayed and non‐splayed limbs indicate enhanced metabolic enzyme activities and myoglobin levels, resulting in a distinctly more “athletic” phenotype than control limbs. This compensatory increase in aerobic capacity demonstrates how soft tissues can mitigate functional issues caused by pathologies and suggests that muscle atrophy does not contribute to splayed‐leg disorder. Likely, other factors are to blame (e.g., nutrition). With the advent of more detailed imaging techniques, such as contrast‐enhanced micro‐CT imaging, we hope to test for signal of these factors and better understand the anatomy and physiology of health and disease states in ratite birds. Through documentation of the interplay between hard and soft structures, including their physiologies, we are now beginning to apply new tools to an ancient clade of poorly‐understood birds.Support or Funding InformationFunding was provided to Dr. Shane Kanatous from the Colorado State University Department of Biology (muscle physiology study), and to Dr. Paul Gignac and Nathan Kley through National Science Foundation grants no. 1450850, 1457180, 0749750 and 1450842 (micro‐CT studies).
Iroquois 1 (Irx1) Marks the Stratum Intermedium and Periodontal Complex Cells
Authors: Romero‐Bustillos Miguel , Yu Wenjie , Eliason Steve , Amendt Brad A. 
Published: November 2023

Iroquois 1 (Irx1) is a homobox transcription factor that was identified in craniofacial tissues through RNA‐sequencing and bioinformatics analyses. Irx1 is expressed in specific dental tissues during development and adult stages. Irx1 is present in the outer enamel epithelium and the stratum intermedium at prenatal stages. The expression of Irx1 is maintained until tooth eruption and at this stage it appears to play a role in root formation. Heterozygous Irx1 knockout mice show Irx1 expression in the Hertwig Epithelial Root Sheath and in the outer enamel epithelium at post‐natal stage p12 in molars. Epithelial rests of Malassez and isolated cells in the inter‐radicular cementum are positive for Irx1 expression. The presence of Irx1 is nonexistent in late stages on the root surface. Differences in Irx1 levels can be found in cultured cementoblast and periodontal ligament cells. Cementoblasts have a higher level of Irx1 than periodontal ligament cells. These findings were confirmed by real‐time PCR and protein levels. Under mineralization conditions cementoblasts show a reduction in the level of Irx1 expression. The presence of Irx1 during tooth development is indicative of the implication of this novel transcription factor in tooth formation. Moreover, the positive expression of Irx1 in cementoblasts under non‐mineralization conditions and its reduction of expression under‐mineralization conditions may suggest it regulates genes involved in root formation and possibly the origin progenitor cells of the cementum.Support or Funding InformationMiguel Romero‐Bustillos would like to acknowledge the support received from the NIH under the R90 DE024296‐03 grant.
The Depth of Commonly Grafted Costal Cartilages at Different Locations along the Cartilages: Considerations for Autografts
Authors: Lynch Hannah L , Ganoe Maria R , Bender‐Heine Adam N , Holmes J Scott , Rickards Allen A , Armeni Mark A , Lambert H Wayne , Zdilla Matthew J 
Published: November 2023

Costal cartilage grafting is a commonly used procedure in reconstructive surgery. The decision regarding which cartilage to select is often a question of the volume of material necessary to shape the graft. However, there is little information regarding the depth (superficial‐to‐deep) of commonly grafted costal cartilages. Therefore, this cadaveric study sought to determine the average depth of the 5th, 6th, 7th, and 8th costal cartilages at the medial, lateral, and intermediate locations along the cartilages. Results revealed the thickest cartilage is found at the medial portion of the 6th cartilage while the thinnest cartilage is found at the medial aspect of the 8th cartilage. The average thickness of each cartilage near its respective rib did not differ much between cartilage levels; however, the thickness of cartilage closest to the sternum differed widely. Moreover, any location along the 6th costal cartilage is, on average, thicker than any part of the 5th, 7th, and 8th cartilages.Support or Funding InformationWV Research Challenge Fund [HEPC.dsr.14.13] andWVU Initiation to Research Opportunities (INTRO) Summer Research Program
The Anterior Contour of the Seventh Costal Cartilage: Considerations for Grafting to the Nasal Dorsum and Columella
Authors: Russell Michelle L , Bender‐Heine Adam N , Holmes J Scott , Rickards Allen A , Armeni Mark A , Lambert H Wayne , Zdilla Matthew J 
Published: November 2023

When viewed from the anterior, the seventh costal cartilage tends to have an “L” shape that lends itself to a single‐block graft to reconstruct the dorsum and columella of the nose. However, it has been observed that the 7th costal cartilage can be bowed anteriorly. Because the anterior contour of the 7th costal cartilage has never been examined, this cadaveric study analyzed the anterior contour of the 7th costal cartilage as viewed from the superior via geometric morphometric techniques to determine the average contour and most likely contour variance. On average, the anterior contour of the seventh cartilage had moderate anterior bowing; however, the contour ranged from severely bowed to nearly flat. When present, the anterior bowing was most pronounced a distance two‐thirds the length of the cartilage away from the sternum. Although a single‐block “L” shaped cartilage graft may be possible in individuals with relatively flat anterior contours, in patients with significant bowing of the 7th costal cartilage one could cut the cartilage into two straight segments, one segment from the medial 2/3 and the other segment from the lateral 1/3 of the cartilage for separate dorsal and columellar grafts.Support or Funding InformationWV Research Challenge Fund [HEPC.dsr.14.13] andWVU Initiation to Research Opportunities (INTRO) Summer Research Program
Low Intensity Vibration to Improve Postural Stability, Reduce Chronic Low Back Pain and Improve Function
Authors: McCrae Shaun A , Einstein George P , Tulp Orien L 
Published: November 2023

Low back and extremity pain has risen to one of the leading causes for physician visits and will impact approximately 80% of Americans during their lifetime. The cost of this epidemic will be approximately $8 Billion per year. The impact of this health issue is without prejudice and will not only impact the lives of approximately 31 million Americans but it will also impact the lives of countless family and friends as well as taking time and energy away from other patients who may have more pressing health issues. The idea of putting forth effort, at a level that could allow the individual the ability to significantly strengthen their core in such a way that it could provide the benefit needed to reduce axial and radicular pain is a difficult one at best. The thought that the individuals range of motion (ROM) would be pain free enough so as to allow the individual to put forth maximum effort and increase their muscle endurance is an unlikely idea, especially to the degree needed to effectively compress the core organs and displace them up towards the floor of the diaphragm and down toward the ceiling of the pelvis, thereby creating a larger distance between the diaphragm and the pelvis which could result in an unloading of the discs of the lumbar spine. This treatment may create an environment that will draw the discs out of the spinal canal and create a larger foraminal opening, thereby enabling the nerve roots at that level to exit the spinal canal with less potential stressors both of which would likely reduce the excitation of the nerve tissue at each specific level within the lumbar spine both bilaterally and within the spinal canal, resulting in a reduction in the expression of axial and radicular pain in the patient suffering from chronic low back and extremity pain.Support or Funding InformationSupported by Institutional Resources of USAT College of Medicine and Einstein Medical Institute
Modulation of Chondrocyte Differentiation by the Hyaline Extracellular Matrix.
Authors: Domowicz Miriam S , Henry Judith G. , Glory Velazquez M. , Vaval Diandra S. , Schwartz Nancy B. 
Published: November 2023

The development of the skeleton involves a highly regulated, spatially organized series of events that require precise temporal control of a multitude of morphogens, growth factors, transcription factors, and mechanical‐signaling pathways. In the growth plate, the size of the limb element is regulated by the rate of chondrocyte proliferation and maturation to hypertrophy, accompanied by substantial changes in the extracellular matrix (ECM) composition. Chondroitin sulfate proteoglycans (CSPGs), in particular aggrecan, are critical for proper limb growth‐plate development in vertebrates, since several animal models have shown that defects in aggrecan composition and/or content lead to accelerated chondrocyte maturation and consequent chondrodysplasia. To explore how CSPGs in the extracellular matrix (ECM) influence chondrocyte differentiation we established a tissue‐culture system from primary chick chondrocytes, and altered their extracellular matrix by enzymatic digestion (chondroitinase or hyaluronidase treatment) or biosynthetic modification (sodium chlorate or 4‐nitrophenyl β‐D‐xylopyranoside treatment). We showed by qPCR that treatment with chondroitinase, hyaluronidase or chlorate, increased levels of collagen 10A1 (COL10A1) mRNA, a marker of chondrocyte hypertrophy, and enhanced matrix production as indicated by increases in SOX9, collagen 2A1 and aggrecan mRNA levels. Increased hypertrophy was confirmed by changes in cellular morphology and by mRNA in situ hybridization studies. In contrast, treatment with 4‐nitrophenyl β‐D‐xylopyranoside, which reduces CS chains in aggrecan but increases levels of free CS released, does not influence chondrocyte differentiation. Furthermore, levels of FGFR3 mRNA were increased in chondroitinase, hyaluronidase, and chlorate‐treated chondrocytes but that was not accompanied by changes in DNA content, i.e. cell proliferation. Thus, these results are consistent with observations in animal models, in which loss of aggrecan from the matrix induces acceleration of chondrocyte differentiation, allowing this culture system to be used to dissect matrix requirements and signaling pathways that lead to the increased rate of differentiation upon matrix aggrecan loss.Support or Funding InformationSupported by U.S. Public Health Service Grants HD107332 and GM066522.
3D Imaging using MRI of a Non‐mineralized Complex Organism: The Jawless Sea Lamprey (Petromyzon marinus) as a Model
Authors: Wood Bradley M , Jia Guang , Carmichael Owen , McKlveen Kevin , Homberger Dominique G. 
Published: November 2023

The three‐dimensional visualization of complex organisms lacking mineralized tissues has been challenging because (1) histology maintains cohesiveness of the tissues, but hinders a 3D conceptualization; (2) microdissection provides a three‐dimensional view, but is destructive; and (3) x‐ray CT imaging provides three‐dimensionality, but requires contrast staining that results in significant shrinkage due to the absence of mineralized tissue. MRI, however, is a non‐destructive method that provides soft‐tissue contrast without shrinkage. Jawless vertebrates, such as lampreys, are good models for organisms without mineralized tissues, yet are characterized by a complex connective tissue skeleton that provides a framework for their segmentally arranged musculature (myomeres). Furthermore, as the largest lamprey species, adult Sea Lampreys (ca. 75 cm long and 5 cm in diameter) are amenable to standard MRI scanning. We acquired high resolution MRI scans of a Sea Lamprey specimen by using an 8‐channel wrist coil and 3‐Tesla MRI scanner. Both 2D (horizontal and sagittal) and 3D scans were acquired as T1 and T2 weighted without moving the specimen in order to contrast tissues with high fat content (T1) and high water content (T2). For a field of view of 101 cm2, a slice thickness of 1.2 mm, and an acquisition matrix of 288 × 288, the voxel size was 0.451 mm × 0.271 mm × 1.2 mm. 3D scans take more time, but minimize gaps between slices. The MRI data were visualized by using the imaging software Avizo®. In our MRI data, certain connective tissue structures, such as myosepta, were not identifiable in their entirety in either T1 or T2 scans, but parts of them could be identified in one or the other. Therefore, segmentation (marking as a separate object) of a myoseptum was performed in T1 and the available information was augmented by toggling to T2, or vice versa. Using this approach, we were able to show how the sheet‐like myosepta curve and twist dorso‐ventrally and cranio‐caudally within the trunk. In combination with microdissection, the configuration of the visualized myosepta provides a framework for diagramming the length and orientation of the myomeric muscle fibers. The visualization‐of the connective tissue and muscle structures as separate objects is necessary for 3D animation as a step towards modeling lamprey locomotion.Support or Funding InformationLSU Foundation to D.G. Homberger
Fibrosis and Scarring of the Brachial Plexus as Displayed by MRI/MRA/MRV
Authors: Collins James D , Saxton Ernestina H , Gelabert Hugh A , Carnes Alfred E 
Published: November 2023

Bilateral rounding of the shoulders (laxity) associated with kyphosis of the thoracic spine causes costoclavicular venous compression and brachial plexopathy. This form of thoracic outlet syndrome is usually not amenable to surgical treatment in older patients, particularly in severe kyphosis of the thoracic spine. The objective of this presentation is to display the sites of landmark anatomy compressing the brachial plexus that decreases venous return to the nerves causing a shortage of oxygen and glucose needed for cellular metabolism causing fibrosis and scarring of the soft tissues marginating the brachial plexus. Magnetic resonance imaging (MRI) is the only modality that displays fibrosis and scarring of fascial plane anatomy obstructing venous and lymphatic return, not possible with Ultrasound and/or Computerized Axial Tomography (CAT).The longer venous obstruction, transient ischemia or permanent obstruction ischemia if unrelieved, progressively affect the nerve fibers in increasing numbers and to an increasing degree. Pathology develops with edematous swelling and vascular congestion. If the pressure is unrelieved and continues to increase, the nerve(s) suffer a first degree or a conduction block injury. Compression ischemia with degeneration and fibrosis develop. In absence of relief, the endoneurial tubes and funniculi atrophy and with increasing ischemia, fibrosis becomes marked.This presentation displays costoclavicular compression of the brachial plexus with fibrosis and scarring in two patients. One patient post resection of the scalene triangle complicated by laceration of the second division of right subclavian artery and the second patient with bilateral scalenectomy with incomplete first rib resection.Monitored bilateral MRI, MRA and MRV of the brachial plexus is the only modality of choice to display costoclavicular compression and fibrosis and scarring of the brachial plexus.
Impact of Histone Mutations on Mismatch Repair and Cancer
Authors: Fang Jun 
Published: November 2023

Mutations in histone 3 (H3), particularly H3K36M/I and H3G34V/R have been identified as novel drivers for several types of human cancer. Because H3K36me3 is essential for DNA mismatch repair (MMR) in vivo by recruiting mismatch recognition protein MutSa to replicating chromatin, cancers with H3K36M/I mutations are expected to have a defective MMR system, which leads to genome instability and cancer development. However, how H3G34V/R mutations confer tumorigenesis is unknown. Given that both Arg and Val contain a bigger side chain in comparison to Gly, we hypothesize that these big side chains at position 33 of H3 impairs H3K36 interactions with MutSa and/or SETD2, the major methyltransferase responsible for H3K36 trimethylation. We show here both in vitro and in vivo evidence that G34V/R mutations block H3K36 trimethylation and its interaction with MutSa. The crystal structures of the SETD2 catalytic domain bound to H3K36 peptide with SAH (S‐adenosylhomocysteine) reveal that the SETD2 catalytic domain adopts an open conformation, with the K36 peptide snuggly positioned in a newly formed substrate channel, which is essential for SETD2‐H3K36 interaction. It is obvious that substitution of G34 with V34 or R34 obstructs the catalytic domain and the SETD2‐H3K36 interaction. We therefore conclude that like H3K36M/I mutations, H3G34V/R mutations promote mutagenesis and tumorigenesis by blocking MMR in vivo
Impact of H3G34D/R/V on H3K36 methylation in vivo by Mas‐spec analysis. A. H3K36 methylation ratio in G1‐S boundary cell lines. B. H3K36 methylation ratio in unsynchronized cell lines. Unsynchronized cells have less H3K36me3 than G1‐S boundary cells.

A H3K36 methylation ratio in G1‐S boundary cell lines

H3.3‐WT

H3.1‐WT

non
45.8%
93.8%
57.6%
82.9%
50.0%

mono‐
44.0%
1.7%
11.6%
16.3%
8.7%

di‐
9.4%
3.7%
16.2%
0.8%
14.2%

tri‐
0.8%
0.9%
14.6%
0.0%
27.1%

B H3K36 methylation ratio in unsynchronized cell lines

H3.3‐WT

H3.1‐WT

non
56.2%
52.3%
37.3%
91.8%
30.8%

mono‐
27.9%
18.7%
18.9%
7.4%
18.0%

di‐
14.7%
26.2%
34.5%
0.8%
43.3%

tri‐
1.2%
2.8%
9.3%
0.0%
7.9%
Identifying the contribution of sumoylation and ubiquitination to yeast Replication Factor A function through the examination of “lysine‐less” RFA mutants
Authors: Senger Barbara L , Haring Stuart J 
Published: November 2023

Replication Protein A (RPA) is a heterotrimeric protein complex present in all eukaryotes that is essential for DNA replication, repair/recombination, and cell cycle regulation. The major biochemical function of RPA is binding to single stranded DNA (ssDNA) intermediates, especially those formed during the processes above. In response to DNA damage, the N‐terminus (NT) of the 32 kDa subunit, Rpa2, becomes hyper‐phosphorylated by protein kinases that are integral to the DNA damage response (DDR).Recently, phosphorylation of RPA has been demonstrated to be influenced by other upstream post‐translational modifications, including ubiquitination and sumoylation. In response to DNA damage, sumoylation occurs on the Rpa1 C‐terminus, which recruits in proteins that allow for ubiquitination. The covalent attachment of ubiquitin (and SUMO) has been proposed to affect RPA function through signaling for degradation via the proteasome, changes in protein interactions, and/or changes in downstream post‐translational modification of RPA. Sumoylation and ubiquitination of RPA occur on multiple lysine residues present in all three subunits. It is possible that there is a post‐translational modification cascade required to ultimately influence RPA function.To examine the importance of sumoylation and ubiquitination on yeast RPA (called Replication Factor A; RFA) function, mutant forms of Rfa1 and Rfa2 were generated in which ALL of the lysine residues in each subunit were mutated to arginines: rfa1‐K‐>R (39 residues mutated), rfa2‐K‐>R (15 residues mutated), and the rfa1‐K‐>R rfa2‐K‐>R double mutant (54 residues mutated). These mutants were examined with respect to growth, the DNA damage response, and checkpoint initiation/maintenance/exit. We have demonstrated that all “lysine‐less” mutants are viable and have varying degrees of DNA damage sensitivity. Despite mutation of the targets for sumoylation and ubiquitination, we observe phosphorylation of Rfa2, suggesting that sumoylation/ubiquitination and phosphorylation of Rfa2 may be independent of one another. Additionally, mutations in RFA that lead to DNA damage sensitivities have been demonstrated by us and others to have a major defect in checkpoint regulation. Therefore, we are in the process of determining if lack of sumoylation/ubiquitination affects checkpoint function of RFA, particularly its role in exit from a checkpoint.Support or Funding InformationThis work was supported by award NSF‐CAREER‐1253723 from the National Science Foundation to SJH.
“Purification and Characterization of Deinococcus radiodurans Polynucleotide Phosphorylase a phosphate stimulated Mn2+‐dependent nuclease”
Authors: Spence Madison N. , Uranga Lee , Lusetti Shelley 
Published: November 2023

DNA double strand breaks, if unrepaired, pose a threat to the cell because they can cause a wide variety of genetic alteration and apoptosis. Therefore, DNA double‐strand break repair pathways are critical for the survival of all organisms. Deinococcus radiodurans is one of the most radiation resistant organisms known exhibiting a D10 dose of 10,000 gy. Its survival is attributed to robust DNA repair mechanisms. Previous work with DNA repair proteins has identified a potential interacting partner, Polynucleotide Phosphorylase (PNPase). PNPase was first characterized for its polymerase and phosphorylase activities on RNA, where it is involved in regulating RNA turnover. In its synthetic mode, PNPase is a metal‐dependent template independent single stranded RNA polymerase that adds nucleotide diphosphates (NDPs) onto an existing RNA chain; as well as a Mg2+‐PO4 ‐dependent RNA phosphorylase. In vitro studies have shown that PNPase can also work on single stranded DNA substrates when manganese is used as a metal cofactor. Our lab is interested in how PNPase activity can be influenced by other DNA repair proteins and vice versa. The purified D. radiodurans PNPase displays the expected DNA degradation activity with phosphate and its NDP‐dependent polymerase activity. However, we have also observed that the enzyme can degrade DNA in the absence of added phosphate suggesting nuclease activity; and that the addition of phosphate stimulates this Mn2+ ‐dependent nuclease activity.Support or Funding InformationR01GM104375