bluuebunny/crossref_metadata_2025_split huggingface dataset:
Efficient Automatic Induction of Rules in Biological Systems
Authors: Whiting Mark E , Leduc Phil R , Cagan Jon 
Published: November 2023

Rule based analysis of biological phenomena has rich potential but has been limited by our lack of methods for establishing systems of rules that discretely represent arbitrary structured data. Graph grammar is a formalism affording this kind of rule based representation of arbitrary information, and many tools have been developed to use graph grammars in engineering and design domains. However, inducting new graph grammar rules directly from a dataset is computationally complex and has not been automated; today it is done almost exclusively by hand, limiting the impact of the approach and mitigating its generalized use for analyzing biological phenomena.This work introduces a method for improving the complexity bound of this problem by using chunking and probabilistic matching of new rules, and a system architecture for facilitating the quick evaluation of rules in new and unknown datasets. The new method has been evaluated with engineering, architectural and statistical datasets and offers insight into rules about the construction, function and fundamental dynamics of systems. This work provides novel insights to areas from multiscale modeling to representations of biological phenomena.
Determining the Effects of Intracellular pH on the Translational Response to Heat Shock
Authors: Triandafillou Catherine G , Dinner Aaron R. , Drummond D. Allan 
Published: November 2023

Single‐celled organisms must be able to dynamically respond to changes in their environment to ensure survival and replication. The budding yeast S. cerevisiae grows best in acidic conditions, yet maintains cytosolic pH at or just above neutrality, expending a considerable portion of cellular ATP resources to do so. When cells experience stresses such as high temperatures or energy depletion, intracellular pH drops, equilibrating with the acidic environment. Given the strong buffering capacity of the cytosol, due mainly to an abundance of ionizable groups in biological molecules, this pH drop reflects a dramatic chemical change with wide‐ranging consequences for biological reactions in the cell. It has been shown that acidification drastically alters the material state of the cytoplasm, leading to solidification and decreased diffusion. Furthermore, acidification has been shown to be important for long‐term fitness following energy depletion.In the case of heat shock, very little is known about the interplay between changes in pH and other, more well‐studied cellular changes such as the transcription and translation of the heat shock genes, reduction in cellular energy production, and the formation of mRNA‐protein granules. In order to understand how changes in intracellular pH are interpreted by the cell, and to what degree they affect the heat shock response and cellular fitness, we use a pH‐sensitive, ratiometric GFP derivative to measure intracellular pH during acute heat shock and recovery while simultaneously measuring the induction of heat shock response proteins using quantitative, multi‐color flow cytometry.We find that the degree of cytosolic acidification alters the expression dynamics of molecular chaperones, independent of heat shock temperature and duration. We also find that cells which fail to acidify their interior suffer long‐term defects in pH regulation following stress, potentially indicating a loss of fitness.Support or Funding InformationResearch reported in this publication was supported by the National Institute of Biomedical Imaging And Bioengineering of the National Institutes of Health under Award Number T32EB009412 and the National Science Foundation Graduate Research Fellowship Program under Grant No. DGE‐1144082.
Effect of thermal manipulation during Broiler chicken embryogenesis on the differential expression of Heat shock protein and Factor during heat stress on post‐hatch chicken
Authors: Alzghoul Mohammad Borhan 
Published: November 2023

The objective of this study was to determine the effect of thermal manipulation during broiler chicken embryogenesis on the differential expression of heat shock proteins (HSPs) and heat shock factors (HSFs) during thermal stress at post hatch days 14 and 28 of age. Fertile chicken eggs (n=1500) were divided into five incubation treatment groups (300 each): control group was maintained at 37.8 °C 56% relative humidity (RH) throughout the incubation period; TM1 was subjected to TM at 38.5°C for 24 h and 65% RH daily during ED12–18; TM2 was subjected to TM at 39°C for 24 h and 65% RH daily during ED12–18; TM3 was subjected to TM at 39.5°C for 24 h and 65% RH daily during ED12–18 and TM4 was subjected to TM at 40°C for 24 h and 65% RH daily during ED12–18. At post‐hatch days 14 and 28 of age, chicks in TC groups were subjected to thermal challenge (TC) at 41.0°C for 6 h while naïve chicks were kept under regular conditions. Chick's response to TC was evaluated by determination of body temperature (Tb) and differential muscle mRNA expression of Hsp108, Hsp90, Hsp70 and Hsp60. During TC at days14 and 28 of age, the Tb of TM chicks was significantly lower than those of the controls. When compared to the control, TM resulted in a rapid significant increase in mRNA levels of Hsps and HSFs in the muscle during TC at post hatch days 14 and 28 of age.Support or Funding InformationDeanship of Research, Jordan University of Science and Technology (Project ID# 66/2016).
Identification of a Novel Pathomechanism Underlying a Congenital Disorder of Glycosylation: Crosstalk between Hexosamine Biosynthetic Pathway, PI3K/AKT Signaling, and Protein Glycosylation
Authors: Wong Sunnie Yan‐Wai , Perez Stefanie , Huang Xiaoping , Stiers Kyle , Beamer Lesa , Foulquier Francois , Berry Gerard , Kozicz Tamas , Morava Eva 
Published: November 2023

Phosphoglucomutase 1 (PGM1) deficiency is a recently identified subtype of congenital disorder of glycosylation that can be treated by dietary modification. PGM1 is required for the interconversion of glucose 1‐phosphate and glucose 6‐phosphate, and is a key enzyme in glycogen metabolism. Although the exact mechanism remains unclear, PGM1 deficiency has been associated with abnormal intracellular glucose and galactose metabolites, as well as reduced N‐linked glycosylation in the endoplasmic reticulum and Golgi. These metabolic disturbances are thought to be responsible for both missing and truncated glycans that have been detected in patient serum transferrin. A recent landmark study demonstrated that oral D‐galactose supplementation improved cellular glycosylation in six patients and resolved hypogonadotropic hypogonadism in two patients. While the clinical benefits of galactose supplementation in PGM1 deficiency are clear, its biological effect on the biochemical and cellular level has not been characterized in detail. It was assumed that dietary galactose supplementation improves galactosylation by increasing intracellular UDP‐galactose relative to UDP‐glucose; however, this has not been confirmed experimentally, nor has an alternative mechanism of action been explored. Here, we report no difference in the ratio of intracellular UDP‐glucose to UDP‐galactose between patient and control cells, despite significant improvement in N‐linked and O‐linked glycosylation in patient cells following galactose supplementation. We found no evidence to support galactose acting as a pharmacological chaperone for PGM1 missense variants. Surprisingly, we discovered disruptions in the hexosamine biosynthetic pathway (HBP) at the metabolic and transcriptional level, as well as downregulation of PI3K/AKT signaling in PGM1 deficient patient cells. Interestingly, galactose supplementation appears to rescue HBP and PI3K/AKT signaling. Collectively, our preliminary studies suggest a hitherto unexplored crosstalk between HBP, PI3K/AKT signaling, and protein glycosylation.Support or Funding InformationThis study is supported in part by the Hayward Foundation and by 1 U54 GM104940 from the National Institute of General Medical Sciences of the National Institutes of Health, which funds the Louisiana Clinical and Translational Science Center.
From Bookworm to Team Player: Problem Based Learning
Authors: Rao Sandy 
Published: November 2023

Medical education faces a daunting task: ensure medical students are equipped with a comprehensive knowledge base while simultaneously developing future clinical physicians. Often this is achieved through an educational dichotomy: academic learning during the first two years and clinical learning during the final two years of medical school. But wouldn't it be more effective to introduce medical students to clinical skills like critical thinking and working with groups before they start seeing patients? Wouldn't they be more prepared to translate their knowledge base into practice if they were taught to do just that from the start of their education? This is where Problem Based Learning (PBL) offers a means of transitioning medical students from bookworms to team players.Problem based learning is a method of teaching where students work through a clinical case in small groups. It requires students to problem solve, guide their own learning, and work together with other students. Students must formulate questions, research solutions, and present their findings to the group (Gijselaears, 1996). These tasks require critical thinking and strong communication skills, both of which are vital for a career as a physician. A facilitator is present to help students strengthen these skills by offering guidance in formulating appropriate questions, conveying vital information, and potentially offering real‐life experiences (Gallagher, 1997).Several studies have found improved anatomy test scores in students participating in PBL learning over didactic learning, suggesting that PBL is a more effective teaching style (Williams, 2014). However, some studies showed no difference between these scores and that PBL students rated themselves as possessing less medical knowledge (Koh, 2008). Further aspects of PBL learning were addressed through a questionnaire focused on student's experiences with an anatomy PBL. Some responses discussed the practicality of a PBL session; how each group has different experiences based on the effectiveness of their facilitator and how learning is difficult since learning objectives are not answered as clearly as in a didactic model. This lecture will focus on the advantages and disadvantages of PBL in anatomy education, as well as the personal experiences of medical students with this style of learning.
The (AAA+) ATPases PSMC5 and VCP/p97 control ERK1/2 signals transmitted through the Shoc2 scaffolding complex
Authors: Galperin Emilia , Jang Eun Ryoung , Anderson Daniel , Jang HyeIn 
Published: November 2023

Signaling scaffolds guide the flow of information and the spatial organization of the enzymes within the ERK1/2 signaling pathway. However, mechanisms that control assembly and dynamics within scaffolding complexes as well as mechanisms regulating the cellular distribution of these complexes remain largely unknown. Our studies unravel a novel, multi‐level paradigm in which allosteric modifications alter the ability of the scaffold protein Shoc2 to actively accelerate transmission of ERK1/2 signals.Shoc2 accelerates ERK1/2 signaling by means of integrating Ras and RAF‐1 into a multi‐protein complex. Germ‐line mutations in Shoc2, affecting spatial distribution of Shoc2 or its ability to assemble signaling complex, result in Noonan‐like RASopathy, a developmental disorder with a wide spectrum of symptoms. Recently we determined that the amplitude of the ERK1/2 signals transduced through the complex is fine‐tuned by the HUWE1‐mediated ubiquitination of Shoc2 and its signaling partner RAF‐1. This ubiquitination is a part of the negative feedback mechanism that actively controls ERK signals.To provide the mechanistic basis of how ubiquitination of the Shoc2 scaffold and RAF‐1 is controlled, we identified previously unknown binding partners of Shoc2, the proteins of the ubiquitin machinery (AAA+) ATPases, PSMC5 and VCP/p97. We demonstrated that both ATPases modulate ubiquitination of Shoc2 and RAF‐1 through remodeling of the complex and sequestration of the E3 ligase HUWe1 from the complex. Fluorescence microscopy and biochemical analysis were utilized to demonstrate that PSMC5 and VCP/p97 are also involved in recruitment of the Shoc2 scaffolding complexes to endosomes. Importantly, the Noonan‐like RASopathy mutation that causes aberrant distribution of Shoc2 to the plasma membrane also affects mechanisms controlling Shoc2 ubiquitination as it becomes inaccessible to PSMC5 and VCP/p97.In summary, our studies are the first to demonstrate that mechano‐enzymes PSMC5 and VCP/p97 are the novel players regulating Shoc2‐ERK1/2 signal transmission and to show that mislocalization of the Shoc2 complexes affects remodeling of the scaffolding module and may lead to the developmental pathology. Furthermore, this study makes a significant advance in our understanding of the mechanisms by which scaffolds regulate specificity and dynamics of the ERK1/2 signaling networks.Support or Funding InformationR00CA126161 (NIH); R01GM113087 (NIH); RSG‐14‐172‐01‐CSM (ACS); 15PRE25090207 (AHA)
Galectin‐1 Modulates Focal Adhesion Turnover and Migration of Vascular Smooth Muscle Cells
Authors: Chau Lee‐Young , Chiang Ming‐Tsai , Tsai Dong‐Lin , Tsai Min‐Shao 
Published: November 2023

BackgroundVascular smooth muscle cell (VSMC) migration play a key role in the development of atherosclerosis and restenosis. Galectin‐1 (Gal‐1) is a galactose‐binding lectin highly expressed in VSMCs. Previous studies have shown that Gal‐1 binds to extracellular matrix and β1integrin. Whether Gal‐1 influences VSMC motility via regulating focal adhesion dynamics remains to be characterized.Methods and ResultsThe motilities of primary VSMCs isolated from wild type (WT) and Gal‐1 null mice were assessed by wound healing and Boyden chamber assays. Gal‐1 null VSMCs were shown to exhibit greater motility than WT cells. Moreover, recombinant Gal‐1 (0.5~2 μg/ml) inhibited the migration of Gal‐1 null VSMCs in a dose‐dependent manner. On the other hand, adhesion assay revealed that WT VSMCs adhered better than Gal‐1 null cells on surfaces coated with matrix proteins, including fibronectin, laminin and collagen. Cell spreading and focal adhesion formation examined by phalloidin and vinculin staining following plating on fibronectin were significantly greater in WT SMCs. Concomitantly, FAK phosphorylation examined by Western blot analysis was induced to greater extent in WT cells. Nocodazole washout assay demonstrated that focal adhesion disassembly was facilitated in Gal‐1 null VSMCs, which was correlated with faster decrease in FAK phosphorylation in these cells. In line with the in vitro findings, the neointimal hyperplasia induced by carotid artery ligation was much greater in Gal‐1 null mice comparing to WT control.ConclusionThese data demonstrate that Gal‐1 restricts neointimal formation post vascular injury at least in part through attenuating focal adhesion turnover in VSMCs.Support or Funding InformationThis work was supported by a grant from the Ministry of Science and Technology of Taiwan (MOST‐103‐2321‐B‐001‐071)
Serglycin Regulates Cytoskeletal‐related Proteins Associated with Cell Motility in Breast Cancer In Vitro
Authors: Bay Boon Huat , Chua Pei Jou , Yip George Wai‐Cheong , Gunaratne Jayantha 
Published: November 2023

Despite advances in cancer treatment, triple‐negative (ER−/PR−/HER2−) breast cancer represents a complicated subtype with no specific treatment regime. Serglycin (SRGN) is an intracellular proteoglycan which has been shown to be highly expressed in the triple‐negative MDA‐MB‐231 breast cancer cell line. In this study, we aim to decipher the molecular networks and pathways regulated by SRGN in breast cancer cells using a global gene expression analysis approach. We first analyzed the expression of SRGN in a dataset containing 1,881 breast cancer tissues from the GOBO database (http://co.bmc.lu.se/gobo/gobo.pl). For the in vitro experiments, siRNA‐mediated down‐regulation of the SRGN gene in MDA‐MB‐231 cells was performed. Transcriptomic analysis of si‐SRGN breast cancer cells was then carried out. Subsequently real time PCR for specific gene targets and expression of selected proteins by Western Blot were performed. Cell motility was determined using commercially available cell migration chambers. The Gene Set analysis from the GOBO database verified that the SRGN gene is highly expressed in basal (triple negative) breast tumors. Knockdown of the SRGN gene in MDA‐MB‐231 cells induced differential expression of 225 genes. Gene ontology analysis revealed the presence of a cluster of genes that were highly enriched in cellular processes, including cell movement. Reduced expression of SRGN was accompanied by down‐regulation of several cytoskeletal‐related genes, namely ABLIM1, LIMA1, CFL1, RAC1, RAC2 and RHOA, concomitant with decreased cell motility. Decreased expression of RAC1 and RHOA proteins were also demonstrated. The results suggest that SRGN is important in regulating actin cytoskeletal organization associated with cell migration, a crucial event during cancer metastasis.Support or Funding InformationThis work is supported by the National Medical Research Council Singapore Grant NMRC/CIRG/1370/2013.
The ULK3 Kinase Regulates the ESCRT pathway in the Abscission Checkpoint
Authors: Wenzel Dawn Marie , McCullough John , Caballe Anna , Marin‐Serrano Juan , Sundquist Wesley I 
Published: November 2023

The endosomal sorting complex required for transport (ESCRT) pathway mediates important membrane fission events, including the physical separation of daughter cells during the abscission step of cytokinesis. Late acting proteins in this pathway, called ESCRT‐III subunits, are recruited to the intercellular bridge that connects two daughter cells where they appear to polymerize into spiraling membrane‐bound filaments that draw membranes together and promote fission. Abscission is highly regulated; if a dividing cell cuts its membrane prematurely (e.g., in the presence of unsegregated DNA) or fails to divide entirely, the daughters may become aneuploid. Progression through abscission is regulated by the abscission checkpoint; a genome protection mechanism that functions through the Aurora B kinase and the ESCRT‐III subunit CHMP4C to delay abscission until upstream mitotic events have been resolved. Checkpoint inputs include lagging chromosomes within the intercellular bridge, aberrant nuclear pore assembly, and mechanical tension at the intercellular bridge. Our goal is to understand how ESCRT‐mediated abscission is coordinated with these other steps in the mitotic program.We recently identified a second kinase, ULK3, that functions downstream of Aurora B in the abscission checkpoint. ULK3 contains tandem C‐terminal Microtubule Interacting and Trafficking (MIT) domains, which serve as docking sites for ESCRT‐III proteins. Notably, ULK3 binds and phosphorylates a subset of ESCRT‐III proteins, including CHMP4C and IST1. We have determined the crystal structure of the second ULK3 MIT domain in complex with its IST1 binding site, and characterized the unusually tight binding interaction. We further find that ULK3 phosphorylation provides a reversible inhibitory signal that stalls abscission until mitotic errors can be resolved; phospho‐mimetic IST1 fails to support cytokinesis, and non‐phosphorylateable IST1 cannot support a functional abscission checkpoint. We are now mapping ULK3 phosphorylation sites on other ESCRT‐III subunits, with the goal of identifying a consensus site for ULK3 substrates. We are also testing the mechanistic consequences of ULK3 phosphorylation on ESCRT‐III function using in vitro ESCRT‐III assembly assays and cytokinesis assays in cells. Preliminary studies suggest that ULK3 phosphorylation inhibits the ability of ESCRT‐III proteins to form the filaments that constrict the midbody. Thus, we are learning how ULK3 phosphorylation of ESCRT‐III proteins inhibits the abscission checkpoint and laying the groundwork for identifying additional ULK3 substrates.Support or Funding InformationThis work was supported in part by an American Cancer Society Postdoctoral Fellowship to DMW (“ULK3 regulation of the ESCRT pathway in abscission”, PF‐14‐102‐01‐CSM) and NIH GM112080 to WIS
3,4′,7‐O‐Trimethylquercetin as a Novel Agent to Inhibit in Vitro Ovarian Cancer Cell Migration and Invasion
Authors: Yamauchi Kosei , Afroze Syeda Humayra , Dean DeShaundra M , Mitsunaga Tohru , Zawieja David C , Uddin Mohammad Nasir 
Published: November 2023

ObjectiveQuercetin is a representative flavonoid that presents widely in variety of foods and medicinal plants. So far quercetin has been reported to inhibit migration and invasion of cancer via decreasing the matrix metalloproteinase (MMP)‐2. 3,4′,7‐O‐trimethylquercetin (34′7TMQ) was synthesized from rutin as a starting material in order to evaluate the anti‐migration and anti‐invasion activity of ovarian cancer cells.Study DesignWe evaluated the effect of 34′7TMQ on three ovarian cancer cells SK‐OV‐3, CRL‐1978, and CRL‐11731 function in vitro. Each Cell lines were treated with different concentrations of 34′7TMQ (0.0, 3.125, 6.25 and 12.5 μM). For each cell line cell proliferation, migration and invasion were measured by using a CellTiter Assay (Promega), Cytoselect Assay (Cell Biolabs) and by using a FluoroBlock Assay (BD) respectively. Proliferating Cell Nuclear Antigen (PCNA) was also evaluated in cell lysates of 34′7TMQ‐treated these 3 ovarian cancer cells by western blot analysis. Expressions of urokinase plasminogen activator (uPA) and plasminogen activator inhibitor 1 (PAI‐1) and matrix metalloproteinase‐2 (MMP‐2) were also evaluated in 34′7TMQ‐treated ovarian cancer cells by western blot analysis. Statistical comparisons were performed using analysis of variance with Duncan's post hoc test.Results34′7TMQ significantly inhibited migration and invasion of three ovarian cancer cells. 34′7TMQ had no effect on proliferation and PCNA expression in ovarian cancer cells. Moreover, 34′7TMQ significantly inhibited the expressions of uPA and MMP‐2 for all ovarian cancer cells.ConclusionThese data indicate that 34′7TMQ inhibited migration and invasion of ovarian cancer cell without inhibiting the proliferation. 34′7TMQ may inhibit the metastasis activity of ovarian cancer cell by decreasing uPA and MMP‐2 expression. 34′7TMQ might be further investigated as a novel anti‐ovarian cancer agent.Support or Funding InformationThe Discovery Foundation (MNU), Grimes Foundation Endowment Award (MNU), Japan Society for Promotion of Science (JSPS) (KY)