bluuebunny/crossref_metadata_2025_split huggingface dataset:
Signals, forces, and cells: Decoding tissue morphogenesis
Authors: Zallen Jennifer 
Published: June 2021

A major challenge in developmental biology is to understand how changes in tissue structure are generated by processes that occur on a cellular and molecular scale. In Drosophila, the characteristic elongated shape of the body axis is achieved through the coordinated movements of hundreds of cells. We discovered that these movements are oriented by subcellular asymmetries in the localization and activity of proteins that generate contractile and adhesive forces within cells. In addition, we identified a positional code that systematically orients cell movements throughout the embryo and demonstrate that this spatial information is provided by an ancient family of Toll‐related receptors that are widely used for pathogen recognition by the innate immune system. Using quantitative live imaging and automated cell tracking, we showed that these molecular asymmetries result in dynamic, collective cell behaviors in which multicellular rosette structures form and resolve directionally, driving tissue elongation. Planar polarized actomyosin contractility and rosette behaviors have now been shown to promote tissue elongation in chicks, frogs, and mice, and represent a general mechanism linking cellular asymmetry to global tissue reorganization. We are currently using genetic, cell biological, biophysical, and live imaging approaches to understand how genes encode the forces that shape tissues, and to elucidate the mechanotransduction mechanisms that allow cells to modulate their behavior in response to changes in their mechanical environment.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Integration and the genetics of variation in facial shape
Authors: Hallgrimsson Benedikt , Aponte Jose David , Katz David C , Bannister Jordan J , Green Rebecca M , Young Nathan M , Cheverud James M , Forkert Nils Daniel , Marcucio Ralph S 
Published: June 2021

Human facial form is both highly variable and heritable. Despite considerable effort, however, the genetic basis for the strong and often very particular patterns of resemblance among relatives are largely unknown. The apparently highly polygenic basis for facial shape variation appears to be at odds with the strong and often highly specific patterns of heritability for facial features. Facial shape variation tends to be structured around developmentally determined patterns of correlated variation. This tendency for covariation or integration results in morphological variation that occupies only a fraction of it possible dimensions. Synthesizing results from experimental and quantitative genetics of the face and applying multivariate genotype‐phenotype mapping, we argue that the integrated nature of variation in facial form can simplify qualitative explanations of the genetics of face but greatly complicate the ability to quantitatively relate genetic to phenotypic variation. Acting on variation in development, many genetic variants push or pull variation along the same limited number of dimensions that correspond to patterns of covariation among aspects of craniofacial variation, producing complex and overlapping patterns of pleiotropic effects. Developmental nonlinearities and interactions among processes at multiple levels result in gene interaction effects that can result in specific genetic variants having genetic background specific effects whilst having small and difficult to detect effects on variation at the population level. These findings have important general implications for the genetics of complex traits.Support or Funding InformationCIHR Foundation Grant, NSERC #238992‐17, NIH R01DE019638; U01DE024440This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
FAM20C is Essential for Maintaining Brain Homeostasis
Authors: Zhang Hua , Lu Yongbo , Qin Chunlin 
Published: June 2021

OBJECTIVESFAM20C (Family with sequence similarity 20, member C) mutations cause Raine syndrome in humans, characterized by generalized osteosclerosis, distinctive craniofacial dysmorphism, along with extensive intracranial calcification. While much progress has been made in understanding the role of FAM20C in osteogenesis and odontogenesis, the function of FAM20C in brain is still unclear. The goal of this study was to determine whether FAM20C is required for normal brain homeostasis in vivo.METHODS1) Reverse transcription polymerase chain reaction (RT‐PCR), Western‐blotting and in situ hybridization analyses were used to examine expression patterns of FAM20C in the mouse brain. 2) Global and conditional FAM20C‐knockout mice were generated by crossing FAM20C loxP mice with sox2‐cre (global) mice, Nestin‐cre (active in neuronal and glial cell precursors in brain) mice and 2.3 Col I‐Cre (active in osteoblasts/osteocytes in bone) mice, respectively. 3) A combination of histology, μ‐CT, and x‐ray methods were used to characterize the brain and bone phenotypes of the global and conditional FAM20C‐knockout mice.RESULTS1) FAM20C was broadly expressed in the neuronal cells in the brain. 2) The global deletion (mediated by Sox‐2 cre) and brain‐specific (mediated by Nestin‐cre) deletion of Fam20C resulted in cerebral calcification in mice after postnatal 3 months and 6 months, respectively. Interestingly, although the bone‐specific (mediated by 2.3 Col I‐Cre) deletion, like the global deletion, of Fam20C caused similar hypophosphatemic rickets/osteomalacia in mice, it did not lead to intracranial calcification after postnatal 6 months. 3) X‐ray and histological analyses showed that the calcifications were bilaterally distributed within the brain. These calcifications were not associated with dystrophic changes. There were mild perifocal microgliosis as well as astrogliosis around calcospherites.CONCLUSIONSThe local loss of FAM20C function in the brain may directly account for intracranial calcification. FAM20C may play an essential role in maintaining normal brain homeostasis and preventing ectopic brain calcification.Support or Funding InformationNIH/NIDCR DE022549 to CQThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
The 4th Dimension of Transcriptional Networks: TIME
Authors: Coruzzi Gloria , Varala Kranthi , Marshall‐Colon Amy , Brooks Matthew , Ruffel Sandrine , Alvarez Jose , Pasquino Angelo , Cirrone Jacopo , Shasha Dennis 
Published: June 2021

Our study exploits time ‐ the relatively unexplored dimension of gene regulatory networks (GRNs) ‐ to learn the temporal transcriptional logic that underlies dynamic nitrogen (N) signaling in plants [1, 2]. Because causality moves forward in time, fine‐scale time‐series experiments are a valuable resource to infer GRN models that can predict TF‐target relationships in out‐of‐sample data ‐ the ultimate goal in systems biology [3]. First, using fine‐scale time‐series transcriptome datasets from N‐treated plants we developed a in a “just‐in‐time” analysis approach that uncovered a temporal cascade of cis‐regulatory elements underlying dynamic N‐signaling [2]. Next, to learn the associated transcription factor (TF) cascade, we inferred a GRN using a time‐based machine learning method ‐ Dynamic Factor Graph ‐ capable of predicting future gene responses under untested conditions [1]. We performed network validation studies using TF perturbations in plant cells using the TARGET system [4], and also in planta [2]. Our TF‐target validations of seven TF hubs in this predicted network were used in a precision/recall AUPR analysis to identify high‐confidence TF‐target edges in the time‐inferred GRN [1]. This high‐confidence GRN recovered TFs previously validated in the N‐response, as well as novel ones that were validated to regulate 15NO3−‐uptake and assimilation in planta [1]. This validated time‐based GRN now provides the temporal transcriptional logic and high‐confidence target predictions for >150 TFs in the dynamic N‐signaling response in Arabidopsis [1, 2]. More broadly, this time‐based approach ‐ can be applied to uncover the temporal transcriptional logic for any signaling response system in biology, agriculture or medicine.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Genomic and Proteomic Signatures of Replication Fork Collapse
Authors: Shastri Nishita , Rivard Rebecca S. , Yeng Ya‐Chu , Anastassiadis Theonie , Kulej Katarzyna , Jagannathan Veena , Mandal Rahul , Borole Piyush , Garcia Benjamin , Belinsky Anja‐Katrin , Brown Eric 
Published: June 2021

Transient obstruction of DNA polymerase progression activates the ATR checkpoint kinase, which in turn suppresses fork breakage and DNA repair‐factor recruitment. To characterize the causes of and responses to replication fork collapse driven by inhibition of ATR, two unbiased, information‐rich approaches were applied: genome‐wide identification of replication fork collapse sites and quantification of protein recruitment to such sites. Over 500 murine and human sites in the genome were identified as dependent on ATR for stability. The vast majority of these sites were characterized by repetitive DNA, including quasipalindromic AT‐rich repeats, inverted retrotransposable elements and purine‐rich ministatelites. While the prevalence of these types of break‐associated repeats in human and mouse cell lines differed, the formation of stable intrastrand structures was a common feature. These data indicate that intrastrand structure formation is a primary driver of fork collapse upon ATR inhibition. Using a novel two‐step replication fork retrieval approach (iPOND2), we have gone on to show that the response to replication fork collapse involves both the rapid recruitment of various repair factors and subsequent large‐scale ubiquitin‐driven turnover of these same factors. We speculate that the establishment of this dynamic equilibrium of repair factors may allow the best repair mechanism for the specific type of damage and intermediate generated to gain access and be favored. These findings and how distinct types of DNA repeats could drive differing repair responses will be discussed.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Antibody Recognition of a Polysaccharide Common to many Microbes and Biofilms
Authors: Soliman Caroline , Walduck Anna K. , Yuriev Elizabeth , Richards Jack S. , Cywes‐Bentley Colette , Pier Gerald B. , Ramsland Paul A. 
Published: June 2021

Hospital‐acquired infections and multidrug resistant microbes represent a healthcare crisis where alternative treatments such as therapeutic antibodies and vaccines are needed. Poly‐N‐acetyl‐D‐glucosamine (PNAG) is a polysaccharide that is produced by many microbes, including bacteria, fungi, and protozoan parasites. Antibodies that interact with PNAG have demonstrated efficacy against a wide range of microbes. A human monoclonal antibody (mAb) F598 that binds PNAG has shown opsonic and protective activity against multiple microbial pathogens and is undergoing clinical assessment as a broad‐spectrum antimicrobial therapy. We recently determined high resolution crystal structures of the unliganded F598 antigen binding fragment (Fab) and its complexes with N‐acetyl‐D‐glucosamine (GlcNAc) and a PNAG oligosaccharide [Soliman et al (2018) J Biol Chem 293:5079]. Recognition of PNAG occurs in a large groove‐shaped binding site that traverses the entire light and heavy chain interface and accommodates at least 5 GlcNAc residues. The Fab‐GlcNAc complex revealed a deep binding pocket with near identical positioning of the monosaccharide and a core GlcNAc of the oligosaccharide suggesting an anchored binding mechanism of PNAG by the F598 mAb. Although intact F598 IgG is required for effector functions, the Fab used here retained binding to PNAG on the surface of an antibiotic‐resistant biofilm‐forming strain of Staphylococcus aureus. A model of intact F598 IgG binding to two pentasaccharide epitopes shows the antibody can span across an extended PNAG chain. This study reveals the structural basis for antibody recognition of PNAG on surfaces of microbial pathogens and in biofilms.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
ITGB1‐DT and ITGB1 enhance lung cancer cell metastatic abilities and are associated with poor prognoses in NSCLC patients
Authors: Lai Tsung‐Ching , Hsiao Michael 
Published: June 2021

Non‐small cell lung cancer (NSCLC) is one of the major leaders in lethal cancer for decades. It has two major types: lung adenocarcinoma (LUAD) and lung squamous cell carcinoma (LUSC). In the molecular analysis, the genomic backgrounds were different among two sub‐types. But most deaths from these two types of NSCLC were due to the metastatic cells which present different molecular characteristics compared to the primary cells. The differences may provide a key for novel diagnosis and/or therapeutic strategy to treat NSCLC. Here in this study, we have found a long non‐coding RNA, ITGB1‐DT (RP11‐462L8.1) and its neighboring gene, ITGB1 were found associated with poor prognosis of overall survival and recurrence‐free survival analysis from TCGA lung cancer cohort in both LUAD and LUSC. We determined the expression levels with our own clinical cohort and confirmed the findings. We also found that the ITGB1‐DT RNA expression levels were correlated to the higher invasion and migration abilities in CL1‐5 lung cancer cells compared to lower invasion and migration ability parental CL1‐0 cells. It is also involved in epithelial‐mesenchymal‐transition in A549 after TGF‐beta treatment. ShRNA induced inhibition of the ITGB1‐DT gene expression was found to reduce the invasion and migration ability of the highly aggressive NSCLC cells with endogenous ITGB1‐DT overexpression. Knockdown of IGTB1‐D1 in lung cancer cells also significantly suppressed cancer cell invasions and metastases in in‐situ human lung cancer established NSG mouse model. The putative molecular mechanisms of ITGB1_DT and ITGB1 in promoting lung cancer cell metastasis were elucidated. Together, our results identified a new long non‐coding RNA ITGB1‐DT who may interact with its neighbor coding gene ITGB1 to promote lung cancer cell metastasis. Inhibition of ITGB1‐DT and ITGB1 expressions and interactions may provide a novel treatment strategy to combat lung cancer patients with metastasis.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
O‐GlcNAcylation: The Switch between Termination of Regeneration and Initiation of Hepatic Dysplasia
Authors: Huck Ian , McGreal Steven R , Dalal Khyati , Menta Blaise , Gunewardena Sumedha , O'Neil Maura , Zachara Natasha , Slawson Chad 
Published: June 2021

BackgroundO‐GlcNAcylation is a posttranslational modification where a single N‐acetyl glucosamine (O‐GlcNAc) sugar is added to Ser/Thr residue of a protein catalyzed by an enzyme called GlcNAc transferase (OGT). O‐GlcNAcylation plays a significant role in cell proliferation, signaling and cancer pathogenesis. We investigated the role of O‐GlcNAcylation in liver regeneration after partial hepatectomy (PH) using hepatocyte specific OGT knockout (OGTKO) mice.MethodsTwo‐three month old male WT and OGTKO mice were subjected to PH and samples were collected over a time course of 0 to 28 days after surgery. Liver regeneration was determined using liver to body weight ratio, H&E staining; PCNA immunohistochemistry, and Western blot for proteins critical to cell cycle progression. RNAseq studies were performed to identify global gene expression changes.ResultsWT mice had a normal regenerative response with peak proliferation at 48 hr after PH and the lost liver mass was regained within 14 days. OGT KO mice showed significantly faster regeneration as demonstrated by a rapid return to pre‐PHX liver to body weight ratio as compared to WT mice. OGT KO mice also showed significantly higher cell proliferation than WT mice at 5, 7, and 14 days, which continued till 28 days after PH. At 28 days after PH, the OGT KO liver showed significant histopathological abnormalities including giant cells, abnormal mitoses, significant intracellular globule accumulation and extensive ductular reaction. Morphometric analysis revealed that OGTKO hepatocytes and hepatocyte nuclei were significantly larger than WT cells. Most strikingly, the OGTKO mice showed several small dysplastic nodules at 28 day after PH. The increased proliferation was accompanied by significant induction of cell cycle regulators such as Cyclin D1 and pRb. RNAseq data revealed that OGTKO livers had a promitogenic and dedifferentiated gene expression profile consistent with histopathological changes. Finally, OGTKO mice has significant downregulation of HNF4aexpression and Co‐IP studies revealed that HNF4ais O‐GlcNAcylated in WT mice.ConclusionsThese data show that loss of O‐GlcNAcylation secondary to deletion of OGT results in uncontrolled hepatocyte proliferation and failed redifferentiation leading to dysplasia following PH. O‐GlcNAcylation is a major regulator of cell proliferation during termination of liver regeneration and disruption in cellular O‐GlcNac status may promote hepatocarcinogenesis.Support or Funding InformationNIH R01 DK098414This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Identification of Two Novel Mutations from Congenital Heart Defects and Related Cellular Function
Authors: Chen Huan‐Xin , Yang Zi‐Yue , Hou Hai‐Tao , Yang Qin , Liu Lin , He Guo‐Wei 
Published: June 2021

ObjectiveCongenital heart defects (CHD) represent the most common congenital anomaly in newborns. The causes of CHD are complex, and are not fully understood. A number of genetic studies have linked gene mutations to cardiac abnormalities. In this study, we found a child who was diagnosed as having a complex including complete endocardial cushion defect, patent ductus arteriosus, secondary atrial septal defect, severe pulmonary hypertension, and polydactyly, we aimed to identify potential pathogenic mutations from this complex.MethodsThe whole blood was collected and genomic DNA was extracted to identify mutations by whole exome sequencing (WES). The CRISPR/Cas9 system was used to generate human pluripotent stem cell with mutations (hPSC‐Mut) separately. As pluripotency markers, Oct4, Nanog, Klf4, SSEA4 were tested in hPSC‐Mut cell, by the methods of Immunofluorescence, Real‐Time PCR, Western Blot. The hPSC‐Mut cell was then inducted and differentiated into cardiomyocytes (CM‐Mut), The differentiation efficiency and contraction of CM‐Mut was detected in 0d, 2d, 4d, 8d, 13d.ResultTwo heterozygous mutations, LTBP2 (c.2206G>A), TCTN3 (c.1268G>A) were identified via WES and analysed by bioinformatics. The hPSC‐LT/TC stable cell line was constructed, inducted and differentiated into CM‐LT/TC. Compare to the wild type, there were no significant differences in cell pluripotency and differentiation efficiency. The cell contraction was observed in the 8th day and lasted to the 13rd day, the contraction of CM‐LT was faster and CM‐LT was slower than wild type cell line.ConclusionTwo heterozygous mutations LTBP2 (c.2206G>A) and CTN3 (c.1268G>A) with alteration of the contraction of CM‐LT/LT cell were found to be pathogenic in complex CHD.Support or Funding InformationNational Natural Science Foundation of China (81870288, 81641017), National Central Grants for Research Institute (2017NL31001), Binhai New Area Health Bureau ( 2016BWKZ 003).This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.
Endothelial Calmodulin and CaMKII Play a Role in Leukocyte Transmigration
Authors: Dalal Prarthana J , Sullivan David P , Muller William A 
Published: June 2021

Inflammation results in the dilation of blood vessels and recruitment of circulating leukocytes into damaged tissues for repair. A transient increase in endothelial cytosolic free calcium (↑[Ca2+]i) is required for leukocyte transendothelial migration (TEM). We have also found that IQ‐domain GTPase‐activating protein 1 (IQGAP1) is essential for TEM. Specifically, the calmodulin‐binding isoleucine‐glutamine (IQ) motif domain is critical for its function during TEM. Calmodulin (CaM) is an intracellular calcium‐binding protein, however, its role in TEM is undescribed. Therefore, we hypothesized that it is involved in the endothelial calcium signaling cascade essential for supporting leukocyte transmigration.In endothelial cells IQGAP1 knockdown reduced TEM substantially. Re‐expressing IQGAP1 truncation mutants containing both the actin‐binding and IQ‐motif domains rescued TEM but truncation mutants lacking the IQ motif domain but did not support TEM.Human endothelial cells treated with the calmodulin inhibitor trifluoperazine (TFP) demonstrated a marked reduction in leukocyte TEM. Only 13% of leukocytes transmigrated through endothelial monolayers pretreated with 100 mM TFP compared to 84% TEM in control, untreated monolayers (p<0.05). We also looked at the role of calmodulin kinase II (CaMKII). Treating endothelial monolayers with 10 mM KN‐93, a CaMKII inhibitor, substantially reduced leukocyte TEM. Here 22% of leukocytes transmigrated which was significantly reduced compared to control TEM rates (p<0.05). Calmodulin pulldowns also showed that without the IQ‐motif domain IQGAP1 cannot substantially interact with calmodulin further suggesting a link between endothelial calcium, IQGAP1 and CaM.Current experiments focus on inhibiting CaM and CaMKII in endothelial cells using genetically encoded selective inhibitory peptides and inducible endothelial‐specific CaMKII‐deficient mice. Identifying the mechanism by which endothelial Ca2+ influx mediates TEM will provide novel insight into the signaling and also provide potential targets for anti‐inflammatory therapy.Support or Funding InformationR01 HL046849, R01 HL064774, F30 HL134202This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.