bluuebunny/crossref_metadata_2025_split huggingface dataset:
Sequence Elements in Yeast Introns Regulate Translation to Make Functional Proteins
Authors: Hossain Munshi Azad , Codallos Nicholas , Johnson Tracy L. 
Published: April 2020

RNA splicing is an important mode of eukaryotic gene regulation. By the process of splicing, introns are excised from the pre‐mRNA and exons are ligated to make a mature message, which is then translated to make protein. In eukaryotes, introns play a key role in alternative splicing whereby alternative exons are ligated to make different mRNAs from the same pre‐RNA transcript. These mRNAs can, in turn, be translated to make different protein isoforms and increase protein diversity.Here, we explore a unique role for inefficiently‐spliced introns. Previously, we showed that an intron‐retained isoform of GCR1 encodes a protein which is initiated from an in‐frame intronic AUG. We have identified regulatory sequences upstream of the AUG that control translation from the intronic translation start site. Furthermore, we show that Rps25, a small ribosomal protein subunit, regulates utilization of the intronic AUG to facilitate the expression of the protein and control the relative levels of the two Gcr1p isoforms—one from the spliced RNA and one from the unspliced RNA. In light of this result, we next analyzed the introns of all known intron‐containing genes to assess whether other introns contain an AUG that is in‐frame with the same stop codon as the spliced isoform. We have identified and tested several such genes to determine whether the intronic AUGs direct protein expression and find that, indeed, they do. Moreover, when cells deleted of these genes express only the intron‐retained isoform, this restores viability to sick cells, suggesting that the proteins produced by intron retention are functional. These studies demonstrate a unique role for introns in regulating alternative isoform production to generate functionally important protein diversity.Support or Funding InformationThis work was supported by the National Science Foundation (BIO/MCB 1518316 to T.L.J) and National Institute of General Medical Sciences (GM‐085474 to T.L.J)
Developing a molecular age model for oocyte assessment
Authors: Lee Tin Lap , Ng Judy Kin Wing , Qao Qin , Chan David Yiu Leung , Yip Kelvin , Chow King , Chan Wai Yee , Lee Tin Chiu 
Published: April 2020

The issue of advanced maternal age (AMA) has become a global issue, the average maternal age increased dramatically through the past decades. In vitro fertilization (IVF) is generally presented as a viable option but the success rate is limited by maternal age. The low success rate is also compound by subjective visual quality assessment, which creates a huge challenge for AMA women.A novel genetic‐based oocyte assessment platform for age prediction using mouse oocytes had been developed in this study. Based on the transcription profile of both immature (GV) and mature (MII) oocytes in young (6 weeks old) and aged group (12 months old) obtained by single cell RNA sequencing, we were able to identify the differential expression genes (DEGs) that govern the aging process. A total of 1377 DEGs in GV oocyte aging were identified. Of which 745 genes were up‐regulated and 631 genes were down‐regulated. On the other hand, we compared the transcriptome of MII oocytes and identified 1432 DEGs, 706 of them were upregulated and 726 were downregulated DEGs in aging process.The candidate genes for the age prediction model was selected by logistic regression model classifier with L1 norm penalty from the above sample, the power of prediction was ROC=0.81. Furthermore, we are developing a scoring system of 1–10 to give a clear grading regarding the oocyte quality. Based on the result obtained in mouse oocyte, a similar approach can be applied in human oocyte. Hence, the patients can have better idea about the oocyte quality and may proceed to oocyte treatments before IVF.Support or Funding InformationHong Kong Research Grant Council Collaborative Research Fund (C4054‐16G),
Effect of bisphenol Z and its analogs on reproductive health of C. elegans
Authors: Roberts Andrew H. , Bowen John , Zhou Xinrui , Timmons Shannon C. , Kuzmanov Aleksandra 
Published: April 2020

Bisphenol A (BPA) is an organic synthetic molecule used in thousands of different plastic‐based products throughout the world. Over the years BPA has been repeatedly linked to neurobehavioral, cardiovascular and reproductive disorders. Because of growing human health concerns, BPA has been increasingly replaced by structurally similar chemicals such as bisphenol S (BPS) and bisphenol Z (BPZ). In recent years, some of these analogs have been under scrutiny by scientists whose research uncovered adverse health effects in model organisms. Whereas numerous studies suggest that BPS may be as toxic as BPA, the impact of BPZ is less understood. To assess its toxicity, we exposed the nematode C. elegans to BPZ at a final concentration of 1 mM throughout their development (from eggs to adulthood). Following exposure, we observed a marked reduction in the brood size compared to the wild type. Moreover, the BPZ‐exposed gonads showed a significant increase in the number of apoptotic nuclei. In the search for potentially safer alternatives, we synthesized three novel analogs of BPZ. Interestingly, these compounds exhibited even stronger effect on the reproductive ability of C. elegans. Our findings suggest that, similar to BPA and BPS, exposure to BPZ and its analogs results in reproductive toxicity.Support or Funding InformationDepartment of Natural Sciences, Lawrence Technological University.
CDC20 and TRIB3 Upregulated by TFAP2C Facilitate Cell Proliferation in Non‐small Cell Lung Cancer Cells
Authors: Kim Dain , Seo Danbi , Kim Wanyeon 
Published: April 2020

In recent years, non‐small cell lung cancer (NSCLC) is the most serious cause of global cancer‐related mortality. To resolve this circumstance, many studies for identification of novel molecular targets have been conducted. In our previous investigation, a microarray analysis that associated with transcription factor activating enhancer‐binding protein 2C (TFAP2C) was carried out and we found out TFAP2C's oncogenic roles in NSCLC development. In the current study, we intended to reveal novel biomarkers for NSCLC, especially focused on several oncogenes transcriptionally regulated by TFAP2C. With the result of microarray analysis, cell division cycle 20 (CDC20) and tribbles pseudokinase 3 (TRIB3) were selected as promising oncogenes by transcriptionally upregulated by TFAP2C. In the treatment of TFAP2C‐specific siRNA in two NSCLC cell lines (NCI‐H292 and NCI‐H838 cells), we observed that mRNA and protein levels of CDC20 and TRIB3 were down‐regulated. In addition, when CDC20 or TRIB3 was overexpressed, cell viability was increased and reversely apoptosis of these cells was suppressed. Consequently, these results indicated that NSCLC tumorigenesis affected by two promising oncogenes, CDC20 and TRIB3, and they could act as potent markers to prognosis of NSCLC.Support or Funding InformationThis work was supported by the National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT (2019R1C1C1009423).
Downregulation of GADD45B and PMAIP1 Mediated by TFAP2C Promotes Cell Proliferation in Non‐small Cell Lung Cancer Cells
Authors: Seo Danbi , Kim Dain , Kim Wanyeon 
Published: April 2020

Non‐small cell lung cancer (NSCLC) is one of the main causes of death worldwide. At early stage, NSCLC can be treated with positive prognosis, but the limitation of biomarkers makes early diagnosis of lung cancer difficult. To identify lung cancer‐related biomarkers, we focused on the role of transcription factor TFAP2C as oncogene in lung cancer. In this study, microarray data were analyzed to identify tumor suppressor genes and 9 genes were screened for downregulation by TFAP2C. Of the 9 genes, growth arrest and DNA‐damage‐inducible beta (GADD45B) and phorbol‐12‐myristate‐13‐acetate‐induced protein 1 (PMAIP1) were selected as promising candidates for tumor suppressor genes downregulated by TFAP2C. When TFAP2C was overexpressed in NSCLC cells, the expressions of GADD45B and PMAIP1 at mRNA and protein levels were inhibited. In addition, GADD45B and PMAIP1 with downregulated by TFAP2C contributed to induction of cell proliferation and cell motility in NSCLC cells. Altogether, this study showed that GADD45B and PMAIP1 can act as tumor suppressors in NSCLC and can be used as useful markers in NSCLC therapy.Support or Funding InformationThis work was supported by the National Research Foundation of Korea (NRF) funded by the Ministry of Science and ICT (2019R1C1C1009423).
Tyrosine‐based Signals Converge on Daple&[bull]PARD3 Complex to Fine‐tune Polarized Planar Cell Migration
Authors: Ear Jason , Saklecha Anokhi , Rajapakse Navin , Choi Julie , Ghassemian Majid , Kufareva Irina , Ghosh Pradipta 
Published: April 2020

Polarized distribution of organelles and molecules inside a cell is vital for a range of cellular processes and its loss is frequently encountered in disease. Polarization during planar cell migration is a special condition in which cellular orientation is triggered by cell‐cell contact. Here, we demonstrate that the multi‐modular signaling scaffold Daple (CCDC88C) is a component of cell junctions in epithelial cells which serves like a cellular ‘compass’ for establishing and maintaining contact‐triggered planar polarity via its interaction with the polarity regulator PARD3. This interaction, mediated by Daple’s PDZ‐binding motif (PBM) and the third PDZ domain of PARD3, is fine‐tuned by two tyrosine phosphoevents on Daple’s PBM that are triggered by a multitude of growth factors. Hypophosphorylation strengthens the interaction, whereas hyperphosphorylation disrupts it. These findings reveal an unexpected role of Daple within the planar cell polarity pathway as a platform for signal integration and gradient sensing for tyrosine‐based signals.Support or Funding InformationThis paper was supported by NIH CA238042,CA100768 and CA160911 (to P.G). J.E was supported by an NCI/NIH‐funded Cancer Biology, Informatics & Omics (CBIO) Training Program (T32 CA067754) and a Postdoctoral Fellowship from the American Cancer Society (PF‐18‐101‐01‐CSM). I.K. was supported by NIH grants GM071872, AI118985, and GM117424.
The ageing PVN: cardiovascular implications for reduced TRPV4 expression?
Authors: O'Brien Fiona , Haidar Omar , Tanigawa Hitoshi , Kumagai Kosuke , Barrett-Jolley Richard 
Published: April 2020

Several changes in cardiovascular, metabolic and autonomic function associate with ageing and given the increase in the average human lifespan, a greater understanding of age‐related changes in the physiological control of homeostasis is needed. For example, cardiovascular control by the autonomic nervous system is one of the most vulnerable functions in the aging process, however, the underlying mechanisms are not fully understood.The paraventricular nucleus (PVN) of the hypothalamus is an important autonomic control centre in the brain with many homeostatic roles. PVN neurones project directly to the spinal cord and can modulate cardiovascular function via the sympathetic system. Age‐related changes to the PVN remain largely unknown: PVN cell numbers remain unaltered but little is known about changes in the expression profile of the ion channels. It is hypothesised that any changes in PVN ion channels is likely to result in perturbed physiological processes and/or declined cardiovascular function.In this study, we compared the cardiovascular function of younger (3 months) and older (26 months) adult male Wistar rats. We measured the heart rate, blood pressure (BP) and tail blood volume using non‐invasive tail plethysmography. In addition, we determined the gene expression profiles in the PVN with RNA deep sequencing (RNA‐seq). Results are given as mean ± SEM; significances were assessed by one‐way ANOVA or Student’s t‐tests where appropriate.We found no differences in baseline measurements of blood pressure, heart rate or tail blood volume between adult and aged rats (n=6, p>0.05). We found that slightly higher‐than‐thermoneutral temperatures of 34 °C were required to achieve stable readings from the aged animals. In adult rats, intraperitoneal (i.p) administration of the TRPV4 agonist GSK 1016790A (50 μg/kg) resulted in increased blood pressure and tail blood volume (n=6, p<0.05), whereas this response was absent in aged rats.Our RNA‐seq data showed profound differences in the gene profile of the adult PVN compared to the aged PVN. Bioinformatic analysis showed 3.5‐fold decreased expression of TRPV4 (p<0.05) and the most greatly enriched KEGG pathway was the “Neuroactive Ligand Receptor Interaction” pathway (p<0.5×106) including several important homeostatic control receptors and peptides such as tachykinin 3.Our data illustrates that activation of TRPV4 results in increased blood pressure and tail blood volume in adult rodents, and in aged rodents where there is widespread change of receptor expression, this effect is ameliorated. These experiments were conducted in higher than‐thermoneutral temperatures and TRPV4 has known thermoregulatory roles, therefore further experiments are required to understand the relationship between reduced expression of TRPV4 in ageing and the decline in both cardiovascular and thermoregulatory function via the PVN.Support or Funding InformationThis work was funded by the BBSRC and King Abdulaziz University
Biased allosteric modulation of G protein‐coupled chemoattractant receptor FPR2
Authors: Ye Richard D. , Zhang Shuo , Gong Hao 
Published: April 2020

Formyl peptide receptor 2 (FPR2), a G protein‐coupled receptor (GPCR), transduces both proinflammatory and anti‐inflammatory signals in an agonist‐dependent manner. To determine how a GPCR transduces opposing signals, fluorescent biosensors of FPR2 were constructed using single‐molecule Frost resonance energy transfer (FRET). Incubated with Ac2‐26, an annexin AI‐derived peptide ligand with anti‐inflammatory activity, induced decreases in FRET intensity at 10 pM that is far below its Ca2+ flux‐inducing concentrations. WKYMVm (W‐pep) and Aβ42, both proinflammatory agonists of FPR2, stimulated increases in FRET intensity, suggesting that different FPR2 conformational states were induced for pro‐ and anti‐inflammatory signaling. Ac2‐26 and Aβ42 produced biphasic dose curves, but in opposite directions. Neither ligands could compete for W‐pep binding at this concentration, suggesting that they use allosteric sites on FPR2. Preincubation with Ac2‐26 at 10 pM diminished subsequent response to W‐pep in Ca2+ and cAMP inhibition assays, reduced FPR2 binding of W‐pep and ERK phosphorylation, but potentiated W‐pep‐stimulated membrane translocation of β‐arrestin2 and phosphorylation of p38 MAPK. The opposite effects were observed when the FPR2‐expressing cells were first incubated with 10 pM of Aβ42 and then stimulated with W‐pep. These results identified Ac2‐26 and Aβ42 as biased allosteric modulators at the subnanomolar concentrations used, that dose‐dependently alter signaling of the orthosteric agonist WKYMVm. Exploration of this feature may help direct FPR2 to pro‐ or anti‐inflammatory signaling pathways.Support or Funding InformationThis work was supported in part by the National Natural Science Foundation of China grant 31470865.
Inguinal White Adipocytes Differentiate to Alveolar Epithelial Cells that Constitute Mammary Cells in Pregnant Rats
Authors: Albustanji Layla , Dellschaft Neele , Budge Helen , Symonds Michael 
Published: April 2020

IntroductionInguinal adipose tissue has been shown to exhibit high plasticity that exceeds its capacity to differentiate to beige or brown adipocytes (
,
). This has led to the concept of pinking whereby adipocytes differentiate to develop an alveolar structure that forms part of the mammary gland.MethodsVirgin and pregnant Sprague Dawley rats were used in this study. Food intake for virgin animals (aged 4 weeks) and body weight for virgin and pregnant animals were measured three times a week. Virgin rats were tissue sampled at 10 weeks of age while pregnant rats, mated at 10 weeks of age, were tissue sampled at either 50% and 90% of pregnancy (10 and 19 days of pregnancy, respectively). Gene expression was studied in the interscapular BAT, omental and inguinal adipose tissue using qPCR. Omental and inguinal sections were stained with H&E for examination of histological appearance.ResultsThe histological sections showed differentiation of inguinal adipocytes to show an alveoli appearance composed of epithelial cells in pregnant but not virgin rats. Gene expression analysis revealed a higher expression of whey acidic protein (WAP) and E74‐Like ETS Transcription Factor 5 (ELF5) genes during pregnancy in inguinal adipocytes of pregnant rats compared to virgin rats. These two genes were absent in the interscapular and omental fat depots of virgin rats. Continuous loss of PPARG with pregnancy appeared in the inguinal adipose tissue. At the gross level, the inguinal fat appeared more compact in pregnant compared to virgin rats.ConclusionsInguinal adipocytes appear to exhibit a pronounced ability to form alveoli which comprises part of the mammary cell structure through gestation. Previous studies have confirmed this from measures of histology and molecular analysis. Further studies designed to examine the mechanism will help to determine factors that may accelerate the formation of neoplastic cells in the mammary glands and possibly breast cancer. Inguinal adipose tissue may no longer be considered a true fat depot in pregnancy.Support or Funding InformationThis work was funded by the EU‐CASCADE fellowship scheme funded by the EU’s 7th FP PCOFUND‐GA‐2012‐600181 (ND), LA was the recipient of a doctoral scholarship from Mutah University.
Role of B vitamins on Oxidative Stress and Apoptotic Proteins Expression in Experimental Colon Cancer Model
Authors: Taranikanti Varna , Padmanabhan Smitha , Waly Mostafa 
Published: April 2020

BackgroundAzoxymethane is a potent carcinogenic agent commonly used to induce colon cancer and oxidative stress in rats. The endoplasmic reticulum (ER) stress response, represents an adaptive mechanism to support cellular survival in response to adverse microenvironment conditions by accumulating misfolded proteins and leading to apoptosis of cells. GRP78 has the potency of (potential to) inhibiting apoptosis by blocking BAX activity and thereby switching off intrinsic apoptotic pathway. Clinical studies continue to stress that oxidative stress (GRP78) is mediated B‐vitamins (folate and B12) deficiencies, oxidative and hyper homocysteinemia. However, it is relatively unknown how B vitamins affect oxidative stress on colon cancer tissue.ObjectiveTo study the expression of GRP78 and apoptotic proteins on azoxymethane(AOM) induced colon cancer using B vitamins and also to see any ultrastructure changes using Electron Microscopy.MethodsAzoxymethane (AOM)‐induced colon cancer model was used in Sprague‐Dawley rats were randomly divided into groups. The control group fed a basal diet with no AOM injection; the AOM‐treated group fed a basal diet with AOM intraperitoneal injections, whereas the other experimental groups received daily doses of folate or vitamin B12 supplementation in the presence or absence of AOM injection. Another 6 groups of rats were tested for the potential synergistic effects of both folate and vitamin B12 supplementation. All animals continuously fed ad‐libitumuntil 16 weeks, then all rats were sacrificed and the colon tissues were examined for the immunohistochemical and ultrastructural changes. Briefly, 2–3mm of colon tissue sections were stored in glutaraldehyde and from these semithin and ultrathin sections were cut and viewed to delineate the cellular organelles architecture in a transmission electron microscope (TEM). Paraffin blocks were cut and the expression of GRP78, Bcl2 and Bax was observed under a light microscope using Immunohistochemistry (IHC) technique.ResultsThere was over expression of GRP78 , Bcl2 and Bax proteins on IHC in colon cancer tissues treated with B vitamins however their expression was dose dependent. There were also ultrastructure changes in the cell organelles with dilation of endoplasmic reticulum and increase in the number of mitochondria. This is consistent with our earlier finding that early exposure to AOM causes morphological changes in the colonic mucosa of the assayed groups.ConclusionVitamin B12 and folate play a protective role against oxidative stress at both the cellular and protein levels and might ameliorate the metabolic stress on colon cells caused by cancer. Overexpression of GRP78 and the role of B vitamins will help in future to study the UPR components for understanding the cellular mechanisms involved in cancer progression.Support or Funding InformationSQU Institutional Fund
Endothelins contribute to early renal insufficiency engendered by acute urinary tract obstruction in neonatal pigs
Authors: Afolabi Jeremiah , Soni Hitesh , Adebiyi Adebowale 
Published: April 2020

Urinary tract obstruction reduces kidney functions, which, if left uncorrected, may lead to irreversible renal loss, especially in infants. Despite the removal of obstruction, a decline in steady‐state renal blood flow (RBF) persists, vascular mechanisms of which are poorly understood. Urinary tract obstruction‐induced increase in the levels of vasoactive endothelin (ET)‐1 has been reported in humans and rodents. However, whether obstructive renal vasculopathy is associated with increased renal production of all ET isoforms (ET1‐3) remains unresolved. Also, the mechanisms that underlie ET‐induced renal vasoregulation in neonates are unclear. Here, we show that ET receptor (ETR)‐operated calcium entry via TRPC3 channels increases renal vascular resistance and reduces RBF in neonatal pigs. Acute unilateral urinary tract obstruction (UUO) in neonatal pigs increased peptidase endothelin converting enzyme 1 (ECE1)‐dependent renal production of ET1‐3 and diacylglycerol (DAG). Despite the removal of obstruction, acute UUO reduced kidney perfusion and caused an increase in renal vascular resistance (RVR) and the urinary levels of NGAL, the early predictive biomarker of acute kidney injury. The protein expression levels of ETRs (ETA and ETB) and TRPC3 channels in renal microvessels were unaltered in neonatal pigs subjected to acute UUO. However, pharmacological inhibition of ECE1, ETR, and TRPC3 mitigated acute UUO‐induced increase in RVR and urine NGAL in the pigs. These data suggest that increased ECE1 production and proteolytic processing of all big ETs to their vasoactive isoforms contribute to early neonatal renal insufficiency engendered by UUO. ET‐derived DAG activates renal vascular smooth muscle cell TRPC3 channels, leading to extracellular calcium entry, vasoconstriction, increased RVR and sustained hypoperfusionSupport or Funding InformationNIH/NIDDK: R01DK101668 and R56DK120595