bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reconstructing regulatory circuits: lessons from immune cells (92.1)
Authors: Regev Aviv 
Published: June 2021

Molecular circuits are the information processing devices of cells and organisms, transforming extra‐ and intra‐cellular signals into coherent cellular responses. While there has been hope that genomic approaches would make it possible to systematically reconstruct circuitry, genomic studies have largely been observational and rarely involve large‐scale testing and refinement of models.We develop a systematic computational and experimental approach to reconstruct circuitry by profiling the circuit’s output or internal state along a relevant time course, learning a computational model that explains the observed data, perturbing every key component proposed by our model, and repeating the process, until data and model converge.All circuits are dynamic, and rewire in response to perturbation, at time scales from minutes to eons, as cells respond to new environmental conditions, differentiate, or evolve. We focus on a carefully selected model system at each time scale, from minutes to eons. In this talk, I will focus on describing our studies in immune cells, especially DCs and T cells, showing how we can dissect transcriptional and signaling circuits and their functionality in key physiological responses.
Three‐dimensional analysis of basic multicellular units using micro‐computed tomography: Does morphology indicate behavior? (920.2)
Authors: Harrison Kimberly , Tsukamoto Suyoko , Cooper David 
Published: June 2021

Basic Multicellular Units (BMUs) are groups of cells responsible for the coordination of resorption and formation in cortical bone remodeling. Due to a lack of three‐dimensional (3D) methods, relatively little is known regarding BMU spatio‐temporal ‘behavior’. It has, for example, been hypothesized that all remodeling events are targeted towards microdamage and thus BMU ‘steering’ is an essential aspect of this process. A previous 2D study involving Ursus americanus (black bear) bone revealed extensive active remodeling spaces; thus providing a unique platform for the current study. We sought to characterize the 3D morphology of BMUs to assess the extent of steering as indicated by sudden changes in trajectory. Micro‐CT of metacarpal and metatarsal diaphyses (n=4) provided an unprecedented number of BMUs (3,144) for analysis. Results indicated that majority of BMUs were oriented along the longitudinal axes of the diaphysis. Overwhelmingly, BMUs had a roughly linear course with little evidence of sudden changes in course or branching. This suggests that the BMUs observed were largely untargeted or targeting is tightly associated with the initiation rather than progression of BMUs.Grant Funding Source: Supported by the CIHR Training grant in Health Research Using Synchrotron Techniques
Investigation of the role of calcaneal dimensions in pes cavus and pes planus (920.4)
Authors: Van Osch Kylen , Johnson Marjorie , Balsdon Megan , Dombroski Colin , Jenkyn Thomas 
Published: June 2021

Background: Disruption in the medial longitudinal arch (MLA) of the foot can lead to pes cavus (high arched foot) or pes planus (low arched foot). The importance of the calcaneus in MLA structure can be inferred in the treatment of severe pes planus, where alteration of calcaneal length is performed if conservative treatments have failed.Purpose: To our knowledge, no previous study has investigated whether variations in calcaneal size can be correlated to MLA height. The purpose of this study was to compare calcaneal dimensions between pes cavus, normal MLA, and pes planus groups.Methods: Utilizing OsiriX software, several dimensions of 3D calcanei were compared between pes cavus, normal MLA, and pes planus subjects.Results: The pes cavus, normal MLA, and pes planus groups did not show any significant differences between group means for all calculated dimensions. Although not statistically significant, calcaneal length (p=0.140), talar articular surface width (p=0.228), and calcaneal tuberosity height (p=0.087) exhibited increasing size with increasing MLA height. This study should be repeated with a larger population to further verify this trend.Conclusion: There is no significant difference in these specific calcaneal dimensions between pes cavus, normal MLA, and pes planus groups. This study provides evidence that calcaneal lengthening procedures may be altering a normally sized calcaneus.
Extracellular matrix protection factor treatment in a rat model of osteoarthritis slows the progress of cartilage and bone destruction associated with the disease (922.10)
Authors: Chmielewski Sarah , Cho Ellen , Lukashova Lyudmila , Friedrich Sarah , Althauser Samuel , Selim Abdulhafez , D'Angelo Marina 
Published: June 2021

Osteoarthritis (OA) is a disease of the joints caused by an imbalance between extracellular matrix destruction and production. We have developed an innovative disease modifying therapeutic technology to treat OA. Extracellular matrix protection factor (ECPF‐1) is a novel, safe and effective intra‐articular injection effective in alleviating tissue pathology associated with OA. Knees of rats in an OA model were treated with ECPF‐1 peptide or BMP‐7 protein as a control because BMP‐7 has been shown to be chondroprotective in a rabbit model of OA. Micro computed tomography (uCT) indicates the amount of bone volume present in the samples and the areas of mineralization. Since healthy cartilage is not normally mineralized, one would expect a low bone volume in these samples and a higher bone volume in cartilage of OA. ECPF‐1 treated OA joints contained the lowest bone volume after four weekly injections of peptide. Trabecular thickness indicates the strength of the bone, and the ECPF‐1 treated animals had the best trabecular thickness numbers following 4 weekly injections of peptide. This data provides critical proof of concept that ECPF‐1 acts as a disease modifying therapeutic in a rat model of OA.Grant Funding Source: Supported by intramural funds
Interaction between rhBMP‐2 and different types of bone grafts (922.18)
Authors: Issa Joao Paulo , Dias Fernando , Fazan Valeria , Ervolino Edilson , Iyomasa Mamie , Gerlach Raquel , Kotake Bruna Gabriela , Gonzaga Miliane 
Published: June 2021

This study evaluated the bone healing process in surgical defects on rat skulls using different bone grafts, associated or not with rhBMP ‐2 (5 µg).It was used 112 rats (♂, 250g) euthanized at 4 or 6 weeks, divided into 8 groups: G1. autologous bone graft; G2. homologous bone graft; G3. heterologous bone graft (lyophilized bovine bone); G4. autologous bone graft + rhBMP‐2; G5. homologous bone graft + rhBMP‐2 and G6. heterologous bone graft + rhBMP‐2; G7. rhBMP‐2; G8. surgical bone defect. The following methodologies were used for evaluation of the new bone formation: histological, radiographic, immunohistochemical, zymographic, and mineral quantity (Ca).After 4 weeks, the zymographic analyses revealed increased production of MMP‐2, the MMP‐9 levels remained consistently in both surgical times. The G1 group shows better results, followed by G2 and G3 respectively, however the addition of rhBMP‐2 on the graft (G4, G5, G6) does not appear to influence the MMP‐2 and MMP‐9 levels. The Ca dose revealed that G1 and G2 were the most mineralized, the other groups had lower Ca levels that decreasing after 6 weeks. The histological and radiographic analyses demonstrated that the bone grafts improve the bone repair specially when associated with rhBMP‐2, increasing the new bone formation after 4 and 6 weeks, without significant statistical differences between G4, G5 and G6. Immunohistochemistry for osteogenic and angiogenic growth factors showed positive identification for all groups, particularly for G4 , G5 and G6.
Susceptibility of the aging thorax to motor vehicle crash injuries (922.2)
Authors: Sochor Mark , Heltzel Sara , Kent Richard 
Published: June 2021

Susceptibility of the Aging Thorax to Motor Vehicle Crash Injuries Objective: Evaluate the appearance of the phenomenon that the aging thorax ribs become more horizontally oriented. It is hypothesized that the more horizontal orientation of the rib cage appears to cause more rib fractures in the elderly population when exposed to crash forces through a seat belt. It is well documented that thoracic injury tolerance decreases with age. Cadaver and field data (National Automotive Sampling System) have shown that older subjects generally sustain more rib fractures for a similar impact severity.Methods: Full thorax computed tomography (CT) scans of 60 patients age 18 to 89 years were analyzed to quantify the angle of the ribs in the sagittal plane. A standardized method of measuring the angle of the rib in relation to the thoracic spine was developed. Additionally, height, weight and Body Mass Index (BMI) were combined in a dataset to look for the relationship between these different factors.Results: Slope of the regression line with age was significantly different than zero with rib angle increasing with increasing age. Average increase in rib angle was about 4 degrees from young adult 18 years to elderly adult 88 years. Surprisingly, Weight and BMI were found to be significantly related to rib angle (p<.001). The rib angles increased from 45 degrees at 40kg to 68 degrees at 160kg.Conclusions: Rib angles become more horizontal with increasing age but this increase appears to be minimal (<5 degrees). What appears to actually drive rib angle more horizontally is weight. Limitations of the study is obviously geometric change of the thorax is not the only change in the elderly thorax as kyphosis and osteoporosis also occur simultaneously and will also have large effects.
Consequence of various wrist angulations at impact on the severity of Colles’ fractures (922.4)
Authors: Baral Sumit , Chatterjee Depaul , Caceres Noel , Feuer Gavriel , Hayes Westley , Jones Colton , Saha Subrata , Marquez Samuel 
Published: June 2021

A Colles’ fracture, eponymously named after Irish surgeon Abraham Colles, is a transverse break of the distal radius (2.5 cm from the radio‐carpal joint) with dorsal displacement of the carpus and hand. It is most commonly a consequence of falling onto outstretched hands. As the exact angle of the wrist changes with each fall, this study tested for correlation between wrist angulation at impact and the severity of the resulting Colles’ fracture. A sample of 15 cadaveric upper limbs exhibiting no evidence of traumatic injuries on gross observation was used to study this relationship. Specimens were cut transversely at mid‐forearm and randomly assigned to either the 90 degree wrist extension group (n=7) or the 45 degree wrist extension group (n=8). Specimens were secured and a drop‐weight impactor was used to apply force to the extended palms, recreating a scenario of falling. After impact, each specimen was radiographed and assessed for evidence and severity of fracture graded via Frykman’s classification system. Results showed that falling with the wrist extended 90 degrees was more likely to produce a Colles’ fracture while falling onto a wrist extended 45 degrees produced extensive damage to the ulna and carpus. Better understanding of the relationship between carpal angulation and likelihood/severity of fractures may aid preventative approaches for populations at high‐risk for falls such as the elderly and athletes.Grant Funding Source: Supported by SUNY Downstate Alumni Association
Embryology of extraocular muscles: a new vision (923.7)
Authors: Tréchot Fanny , Tonnelet Romain , Micard Emilien , Labrousse Marc , Angioi Karine , Braun Marc 
Published: June 2021

Purpose : To describe the embryology of extraocular muscles through 3D viewing algorithm from Carnegie stage XVII to Carnegie stage XXIII (41st‐57th day of development).Materials and Method : The work consisted of a scanning and a data processing reconstruction of embryonic histological material. Material came from anatomical universities collections. 12 embryos were selected, and 7 were dedicated to muscle study (from 14.5mm to 54.5mm). This data processing has allowed a study in three spatial planes.Results : From stage XVII, all extraocular muscles are in place, including levator palpebrae. The study in 3 planes makes their individualization easier. Gilbert (Carnegie Institution) described the origin of inferior rectus and inferior oblique by a common primordium, however from the stage XVII the two muscles are clearly separated. The decussation of the superior oblique is seen from the stage XIX, the trochlea appears at stage XXII. Our work also demonstrates the nerves : optic, oculomotor, trochlear, trigeminal and abducens. The junctions between nerve and muscle are found, especially for the lower branch of the oculomotor nerve.Conclusion : This new study tool has resulted in explicit images of the development of extraocular muscles in the embryonic period. It helped to provide details with respect to the work already established by the Carnegie Institution.
Novel ubiquitin binding sites of S. cerevisiae polymerase η identified by a genetically encoded photoactive probe (927.4)
Authors: Urban Matthew , Yang Kun , Zhuang Zhihao 
Published: June 2021

DNA translesion synthesis is carried out by specialized DNA polymerases such as Polη. Polη contains a ubiquitin‐binding zinc finger (UBZ) domain required for its effective recruitment to the stalled replication fork in response to DNA damages. Our previous study reported a novel ubiquitin‐binding mode of S. cerevisiae Polη in which the C‐terminal portion of Polη binds ubiquitin with 30‐fold higher affinity than the UBZ domain alone. However, the mechanism of such higher binding affinity is not clear. In this study, a genetically encoded photoactive probe, p‐benzoyl‐L‐phenylalanine (pBpa), was incorporated at various positions on ubiquitin to map the interaction sites between Polη and ubiquitin. Data suggests that besides the Ile44 hydrophobic patch which was known to bind UBZ domain of Polη, several other residues at the ubiquitin C‐terminus and a surface opposite from the hydrophobic patch on ubiquitin also bind to Polη. These new binding sites increase the binding affinity between ubiquitin and Polη. Our finding is important for understanding the role of ubiquitin in the recruitment of Polη during DNA translesion synthesis.Grant Funding Source: Supported by U.S National Science Foundation Grant MCB‐0953764 to Z. Zhuang
Screening nicastrin antibodies for specificity for immunofluorescence (934.2)
Authors: Deshaies Derek , Yu Gang , Dries Daniel 
Published: June 2021

Alzheimer’s disease is a type of dementia that can cause problems with memory, learning and behavior. Nicastrin is a component of the protein complex involved in the development of Alzheimer’s disease. In our lab, tissue‐specific nicastrin conditional knockout mice were developed and displayed a striking neurological phenotype. The aim of this research project, then, is to confirm the tissue‐specific knockout by using immunofluorescence. In order to ask this question, we must first identify an immunofluorescence‐compatible antibody that is specific for the nicastrin protein. This is important due to the cross reactivity of many antibodies that are thought to be anti‐nicastrin. In an effort to test for antibody specificity, researchers use pre‐blocking techniques to pre‐absorb (block) their antibodies with antigen before doing their experiment. However, this only proves that the antibody produced is specific for the antigen against which it was raised. Using wild‐type and nicastrin knockout cells, our approach will use a series of anti‐nicastrin antibodies for immunofluorescence to test their specificity towards their intended antigen, rather than staining antigens other than the one against which the antibodies were raised.Grant Funding Source: Supported by National Institute of Neurological Disorders and Stroke grant 1R01NS079796
Proteasome inhibition increases expression of angiogenic chemokines in ovarian cancer cells through IKKβ, S536P‐p65 and EGR‐1 dependent pathways (935.1)
Authors: Singha Bipradeb , Gatla Himavanth , Chang Tzu‐Pei , Manna Subrata , Sanacora Shannon , Vancurova Ivana 
Published: June 2021

Pro‐inflammatory and pro‐angiogenic chemokines interleukin‐8 (IL‐8), CCL2 (MCP‐1) and CXCL5 (ENA‐78) contribute to ovarian cancer progression through their induction of tumor cell proliferation, survival, angiogenesis and metastasis. Though proteasome inhibition by bortezomib (BZ) has been considered for the treatment of ovarian cancer, it has not been used because of its limited effectiveness; however, the responsible mechanisms remain elusive. Here, we show that proteasome inhibition dramatically increases the expression of IL‐8, CCL2 and CXCL5. The responsible mechanism involves an increased nuclear accumulation of IKKβ, and an increased recruitment of the nuclear IKKβ, p65 phosphorylated at S536, and transcription factor early growth response‐1 (EGR‐1) to the endogenous IL‐8, CCL2 and CXCL5 promoters. Co‐immunoprecipitation studies identified nuclear EGR‐1 associated with IKKβ and with p65, with preferential binding to S536P‐p65. Both IKKβ activity and EGR‐1 expression were required for the increased expression of IL‐8, CCL2 and CXCL5 induced by proteasome inhibition in ovarian cancer cells. These data indicate that the increased expression of IL‐8, CCL2 and CXCL5 may represent one of the underlying mechanisms responsible for the decreased effectiveness of proteasome inhibition in ovarian cancer treatment, and identify IKKβ and EGR‐1 as potential new targets in ovarian cancer therapies.Grant Funding Source: Supported by NIH grants AI085497 and CA173452 to I.V.
Uncovering transcription factor binding pockets in the tail subdomain of the human mediator complex (943.2)
Authors: Polinkovsky Mark , Sierecki Emma , Giles Nichole , Alexandrov Kirill , Gambin Yann 
Published: June 2021

The Mediator Complex plays a major role in regulating gene transcription in eukaryotes. One of its fundamental roles is to integrate inputs from a variety of transcription factors to control the gene’s transcriptional state. The majority of these transcription factors are thought to bind to the Mediator’s Tail subdomain. In humans, the Tail is composed of eight subunit proteins, whose structure and arrangement remain unknown, largely due to difficulties in expressing and purifying them. Moreover, only a few interactions between transcription factors and some of the Tail subunits have been found.To overcome difficulties in protein expression and interaction analysis, we used the Leishmania cell‐free protein expression system and pair‐wise measurements of protein interactions via the AlphaScreen assay. These methods allowed us to build a model of the interactions between protein subunits in the Mediator Tail. As validation, we pulled down all the component proteins in the Tail subdomain from a single cell‐free co‐expression. The same techniques were used to test the binding of various transcription factors to the Tail subunits. Our results show that different families of transcription factors bind to distinct groups of subunits in the Tail. Combined with our model of the Tail, this data reveals binding pockets on the Tail’s surface.Grant Funding Source: Supported by Australian Research Council
Mutant versions of histone H3 are defective for nucleosome reassembly and histone chaperone recruitment during transcription (944.3)
Authors: Hainer Sarah , Martens Joseph 
Published: June 2021

Expression of the Saccharomyces cerevisiae SER3 gene is regulated by transcription interference. In the presence of serine, transcription of SRG1 ncDNA is initiated upstream of the adjacent SER3 gene and extends across the SER3 promoter. Our previous studies provided evidence that during SRG1 transcription, Spt6 and Spt16 histone chaperones reassemble nucleosomes over the SER3 promoter after the passage of RNA Pol II, which then interfere with transcription factor binding resulting in SER3 repression. In response to serine starvation, SRG1 transcription is reduced causing nucleosome depletion over the SER3 promoter, which in turn allows transcription factors to bind the SER3 promoter and activate SER3 transcription. We recently reported the identification of mutations altering eight histone residues that strongly increase SER3 expression without reducing transcription of intergenic SRG1 ncDNA. Nucleosome occupancy across SRG1 in these mutants was reduced to degrees that correlated well with the level of SER3 derepression. Additional analyses of these mutants indicated a broader defect in transcription‐coupled nucleosome occupancy at highly transcribed genes, but not lowly transcribed genes. Taken together, these data defined a new class of histone mutants that are defective for transcription‐dependent nucleosome occupancy. Further analysis focused on a subset of these histone mutants revealed a reduced rate of nucleosome reassembly during transcription in vivo. Moreover, we provide evidence that Spt6 and Spt16 histone chaperones fail to be recruited to genes being transcribed by RNA Pol II in these mutants. These results suggest that amino acids in histone H3 and H4 promote transcription‐coupled nucleosome assembly by facilitating the recruitment or retention of Spt6 and/or Spt16 histone chaperones.Grant Funding Source: Supported by NIGMS
Acetyltransferase association and histone acetylation at the Myod1 locus during myogenic differentiation (946.13)
Authors: Hamed Munerah , Khilji Saadia , Chen Jihong , Li Qiao 
Published: June 2021

Chromatin modifications can provide a useful readout for enhancer activities. However, it is unclear whether these modification marks are a cause or consequence of enhancer activation and transcription factors occupancy. We have examined in details the acetyltransferase associations and histone acetylations at different regulatory regions of the Myod1 locus. Our studies demonstrate that the histone acetyltransferase (HAT) p300 is stepwise enriched at distinct Myod1 regulatory regions during myogenic differentiation. This enrichment of p300 is associated with increased histone acetylation in a distinct pattern. Inhibition of p300 HAT activity delays myogenic differentiation, which is coupled with decreased histone acetylation at specific Myod1 regulatory regions. We show for the first time that p300 is directly involved in the early Myod1 enhancer regulation, and provide molecular insights into how p300 HAT activity and histone acetylation are related to enhancer activation and, consequently, gene transcriptionGrant Funding Source: supported by The Ministry of higher Education of Saudi Arabia (to MH) and CIHR grant (to QL)