Miracle-dz/UniFAR-FTUs huggingface dataset:
Structure of the Absent in Melanoma 2 (AIM2) Pyrin Domain Provides Insights into the Mechanisms of AIM2 Autoinhibition and Inflammasome Assembly*

Background: AIM2 binds dsDNA and associates with ASC through their PYDs to form an inflammasome. Results: The AIM2 PYD structure illustrates distinct charge distribution and a unique hydrophobic patch. Conclusion: The AIM2 PYD may bind the ASC PYD and the AIM2 HIN domain through overlapping surface. Significance: These findings provide insights into the mechanisms of AIM2 autoinhibition and inflammasome assembly. Absent in melanoma 2 (AIM2) is a cytosolic double-stranded (dsDNA) sensor essential for innate immune responses against DNA viruses and bacteria such as Francisella and Listeria. Upon dsDNA engagement, the AIM2 amino-terminal pyrin domain (PYD) is responsible for downstream signaling to the adapter protein apoptosis-associated speck-like protein containing a caspase recruitment domain (ASC) through homotypic PYD-PYD interactions and the assembly of an inflammasome. Toward a better understanding of the AIM2 signaling mechanism, we determined the crystal structure of the human AIM2 PYD. The structure reveals a death domain fold with a short α3 helix that is buttressed by a highly conserved lysine residue at the α2 helix, which may stabilize the α3 helix for potential interaction with partner domains. The surface of the AIM2 PYD exhibits distinct charge distribution with highly acidic α1-α2 helices and highly basic α5-α6 helices. A prominent solvent-exposed hydrophobic patch formed by residues Phe-27 and Phe-28 at the α2 helix resembles a similar surface involved in the death effector domain homotypic interactions. Docking studies suggest that the AIM2 PYD may bind the AIM2 hematopoietic interferon-inducible nuclear (HIN) domain or ASC PYD using overlapping surface near the α2 helix. This may ensure that AIM2 interacts with the downstream adapter ASC only upon release of the autoinhibition by the dsDNA ligand. Our work thus unveils novel structural features of the AIM2 PYD and provides insights into the potential mechanisms of the PYD-HIN and PYD-PYD interactions important for AIM2 autoinhibition and inflammasome assembly.
Tip II Diabetes Mellituslu hastalarda Helicobacter pylori prevalansı

Background/aim: Helicobacter pylori is the most common seen infectious agent in the world and causes life-long chronic gastritis, predominantly antral, in all carriers without exception. Diabetes mellitus is a disease characterized by a high risk for infections. Therefore, in this study we aimed to evaluate the prevalence of Helicobacter pylori in patients with diabetes mellitus, the metabolic status of these patients and the relation to the complications of diabetes. Materials and methods: Forty type 2 diabetes mellitus patients followed between August 2001- February 2002 by the Endocrinology Outpatient Clinic in Ataturk Training and Research Hospital, Izmir were included into the study. Twenty-eight non-diabetic patients with dyspeptic complaints served as the control group. Patients were evaluated with regard to diabetes mellitus complications and metabolic control. Upper gastrointestinal tract endoscopy was performed in both groups. For the histopathologic diagnosis and pathologic investigation of Helicobacter pylori, biopsies were taken from corpus and antrum. Results: There were no significant differences between the two groups concerning age and gender. No significant relation was found between Helicobacter pylori and type 2 diabetes mellitus, metabolic parameters, glycemic control duration and complications. Antral gastritis and chronic active gastritis were found to be significantly more frequent in the diabetes mellitus group, both endoscopically and histopathologically, and erosive duodenitis was found to be significantly more frequent in the control group. Conclusion: Our results do not support a relation between Helicobacter pylori and type 2 diabetes mellitus. However, the significant difference between the types of gastritis seen in the two groups suggests the need for further researches on gastritis in diabetic patients and Helicobacter pylori prevalence.
Influence of CYP2C9 and CYP2C19 genetic polymorphisms on pharmacokinetics and pharmacodynamics of gliclazide in healthy Chinese Han volunteers

Background and objective: CYP2C9 is the major contributor to gliclazide metabolic clearance in vitro, while the pharmacokinetics of gliclazide modified release are affected mainly by CYP2C19 genetic polymorphisms in vivo. This study aims to investigate the influence of CYP2C9 and CYP2C19 genetic polymorphisms on the pharmacokinetics and pharmacodynamics of gliclazide in healthy Chinese Han volunteers.
A cost‐effectiveness analysis of sunitinib in patients with metastatic renal cell carcinoma intolerant to or experiencing disease progression on immunotherapy: perspective of the Spanish National Health System

Aim: To investigate the cost‐effectiveness of sunitinib (50 mg/day, schedule 4/2) vs. best supportive care (BSC) in patients with cytokine‐refractory metastatic renal cell carcinoma (mRCC), from the perspective of the Spanish National Health Service.
Inactivation of the Bacterial RNA Polymerase Due to Acquisition of Secondary Structure by the ω Subunit*

Background: Although universally conserved, ω is the only nonessential subunit of RNA polymerase, and its function is mostly undetermined. Results: Dominant lethal mutants of ω were isolated and analyzed genetically and biochemically. Conclusion: Mutations in ω that alter its structure interfere with RNA polymerase catalytic properties. Significance: Results suggest a critical role for ω during transcription, bypassing the effects of compensatory proteins. The widely conserved ω subunit encoded by rpoZ is the smallest subunit of Escherichia coli RNA polymerase (RNAP) but is dispensable for bacterial growth. Function of ω is known to be substituted by GroEL in ω-null strain, which thus does not exhibit a discernable phenotype. In this work, we report isolation of ω variants whose expression in vivo leads to a dominant lethal phenotype. Studies show that in contrast to ω, which is largely unstructured, ω mutants display substantial acquisition of secondary structure. By detailed study with one of the mutants, ω6 bearing N60D substitution, the mechanism of lethality has been deciphered. Biochemical analysis reveals that ω6 binds to β′ subunit in vitro with greater affinity than that of ω. The reconstituted RNAP holoenzyme in the presence of ω6 in vitro is defective in transcription initiation. Formation of a faulty RNAP in the presence of mutant ω results in death of the cell. Furthermore, lethality of ω6 is relieved in cells expressing the rpoC2112 allele encoding β′2112, a variant β′ bearing Y457S substitution, immediately adjacent to the β′ catalytic center. Our results suggest that the enhanced ω6-β′ interaction may perturb the plasticity of the RNAP active center, implicating a role for ω and its flexible state.
Interleukin-2 Inhibits HIV-1 Replication in Some Human T Cell Lymphotrophic Virus-1-infected Cell Lines via the Induction and Incorporation of APOBEC3G into the Virion*

Background: Some cytokines exhibit dichotomous effects on HIV replication in different cell types. Results: IL-2 inhibits HIV-1 replication in MT-2 cells via intracellular induction and virion incorporation of the host restriction factor, APOBEC3G. Conclusion: Stimulation of MT-2 cell with IL-2 produces viruses with impaired replication competency. Significance: This new insight could open the door to additional host-based strategies to suppress HIV-1 replication. IL-2 has been used in culture of primary T cells to maintain cell proliferation. We have previously reported that IL-27 inhibits HIV-1 replication in primary T cells in the presence of IL-2. To gain a better understanding of the mechanisms involved in this inhibitory effect, we attempted to investigate in detail the effects of IL-27 and IL-2 using several cell lines. Unexpectedly, IL-27 did not inhibit HIV-1 in T cell lines, whereas IL-2 inhibited HIV-1 replication in the human T cell lymphotrophic virus (HTLV)-1-transformed T cell lines, MT-2, MT-4, SLB-1, and ATL-2. No effects were seen in HTLV-1-negative cell lines. Utilizing MT-2 cells, we demonstrated that IL-2 treatment inhibited HIV-1 syncytia-inducing ability and dose-dependently decreased supernatant p24 antigen levels by >90%. Using real time PCR and Western blot analysis, we observed that IL-2 treatment induced the host restriction factor, APOBEC3G with accumulation into the lower molecular mass active form as characterized by FPLC. Further analysis revealed that the virus recovered from IL-2-treated MT-2 cells had impaired replication competency. This was found to be due to incorporation of APOBEC3G into the virion despite the presence of Vif. These findings demonstrate a novel role for IL-2 in regulating production of infectious HIV-1 virions in HTLV-1-infected cells through the induction of APOBEC3G.
Effect of CYP3A4*1G on the fentanyl consumption for intravenous patient‐controlled analgesia after total abdominal hysterectomy in Chinese Han population

What is known and Objective: Clinical investigations into postoperative intravenous patient‐controlled analgesia (PCA) have indicated interindividual differences in fentanyl consumption. Cytochrome P450 3A4 (CYP3A4) is the main metabolism enzyme of fentanyl, and single nucleotide polymorphisms within the CYP3A4 gene may contribute to the variability of fentanyl analgesic efficacy. The aim of this study was to investigate whether the most common genetic variation in Chinese, CYP3A4*1G, has an impact on the fentanyl consumption for intravenous PCA in Chinese Han women undergone abdominal total hysterectomy.
Molecular Impact of Electronic Cigarette Aerosol Exposure in Human Bronchial Epithelium

Little evidence is available regarding the physiological effects of exposure to electronic cigarette (ECIG) aerosol. We sought to determine the molecular impact of ECIG aerosol exposure in human bronchial epithelial cells (HBECs). Gene-expression profiling was conducted in primary grown at air liquid interface and exposed to 1 of 4 different ECIG aerosols, traditional tobacco cigarette (TCIG) smoke, or clean air. Findings were validated experimentally with quantitative polymerase chain reaction and a reactive oxygen species immunoassay. Using gene set enrichment analysis, signatures of in vitro ECIG exposure were compared with those generated from bronchial epithelial brushings of current TCIG smokers and former TCIG smokers currently using ECIGs. We found 546 genes differentially expressed across the ECIG, TCIG, and air-exposed groups of HBECs (ANOVA; FDR q < .05; fold change > 1.5). A subset of these changes were shared between TCIG- and ECIG-exposed HBECs. ECIG exposure induced genes involved in oxidative and xenobiotic stress pathways and increased a marker of reactive oxygen species production in a dose-dependent manner. ECIG exposure decreased expression of genes involved in cilia assembly and movement. Furthermore, gene-expression differences observed in vitro were concordant with differences observed in airway epithelium collected from ECIG users (q < .01). In summary, our data suggest that ECIG aerosol can induce gene-expression changes in bronchial airway epithelium in vitro, some of which are shared with TCIG smoke. These changes were generally less pronounced than the effects of TCIG exposure and were more pronounced in ECIG products containing nicotine than those without nicotine. Our data further suggest that the gene-expression alterations seen with the in vitro exposure system reflects the physiological effects experienced in vivo by ECIG users.
FOXO1 Competes with Carbohydrate Response Element-binding Protein (ChREBP) and Inhibits Thioredoxin-interacting Protein (TXNIP) Transcription in Pancreatic Beta Cells*

Background: Control of thioredoxin-interacting protein (TXNIP) expression is critical for pancreatic beta cell survival. Results: FOXO1 binds to the TXNIP promoter; blocks ChREBP occupancy, and inhibits glucose-induced beta cell TXNIP transcription. Conclusion: FOXO1 controls glucose-induced gene expression by competing with ChREBP at target promoters, e.g. TXNIP and L-PK. Significance: This represents a novel gene regulatory mechanism and is the first demonstration of FOXO1-ChREBP cross-talk. Thioredoxin-interacting protein (TXNIP) has emerged as an important factor in pancreatic beta cell biology, and tight regulation of TXNIP levels is necessary for beta cell survival. However, the mechanisms regulating TXNIP expression have only started to be elucidated. The forkhead boxO1 transcription factor (FOXO1) has been reported to up-regulate TXNIP expression in neurons and endothelial cells but to down-regulate TXNIP in liver, and the effects on beta cells have remained unknown. We now have found that FOXO1 binds to the TXNIP promoter in vivo in human islets and INS-1 beta cells and significantly decreases TXNIP expression. TXNIP promoter deletion analyses revealed that an E-box motif conferring carbohydrate response element-binding protein (ChREBP)-mediated, glucose-induced TXNIP expression is necessary and sufficient for this effect, and electromobility shift assays confirmed FOXO1 binding to this site. Moreover, FOXO1 blocked glucose-induced TXNIP expression and reduced glucose-induced ChREBP binding at the TXNIP promoter without affecting ChREBP expression or nuclear localization, suggesting that FOXO1 may compete with ChREBP for binding to the TXNIP promoter. In fact, a FOXO1 DNA-binding mutant (FOXO1-H215R) failed to inhibit TXNIP transcription, and the effects were not restricted to TXNIP as FOXO1 also inhibited transcription of other ChREBP target genes such as liver pyruvate kinase. Together, these results demonstrate that FOXO1 inhibits beta cell TXNIP transcription and suggest that FOXO1 confers this inhibition by interfering with ChREBP DNA binding at target gene promoters. Our findings thereby reveal a novel gene regulatory mechanism and a previously unappreciated cross-talk between FOXO1 and ChREBP, two major metabolic signaling pathways.
Secondhand Smoke‐Prevalent Polycyclic Aromatic Hydrocarbon Binary Mixture‐Induced Specific Mitogenic and Pro‐inflammatory Cell Signaling Events in Lung Epithelial Cells

&NA; Low molecular weight polycyclic aromatic hydrocarbons (LMW PAHs; < 206.3 g/mol) are prevalent and ubiquitous environmental contaminants, presenting a human health concern, and have not been as thoroughly studied as the high MW PAHs. LMW PAHs exert their pulmonary effects, in part, through P38‐dependent and ‐independent mechanisms involving cell‐cell communication and the production of pro‐inflammatory mediators known to contribute to lung disease. Specifically, we determined the effects of two representative LMW PAHs, 1‐methylanthracene (1‐MeA) and fluoranthene (Flthn), individually and as a binary PAH mixture on the dysregulation of gap junctional intercellular communication (GJIC) and connexin 43 (Cx43), activation of mitogen activated protein kinases (MAPK), and induction of inflammatory mediators in a mouse non‐tumorigenic alveolar type II cell line (C10). Both 1‐MeA, Flthn, and the binary PAH mixture of 1‐MeA and Flthn dysregulated GJIC in a dose and time‐dependent manner, reduced Cx43 protein, and activated the following MAPKs: P38, ERK1/2, and JNK. Inhibition of P38 MAPK prevented PAH‐induced dysregulation of GJIC, whereas inhibiting ERK and JNK did not prevent these PAHs from dysregulating GJIC indicating a P38‐dependent mechanism. A toxicogenomic approach revealed significant P38‐dependent and ‐independent pathways involved in inflammation, steroid synthesis, metabolism, and oxidative responses. Genes in these pathways were significantly altered by the binary PAH mixture when compared with 1‐MeA and Flthn alone suggesting interactive effects. Exposure to the binary PAH mixture induced the production and release of cytokines and metalloproteinases from the C10 cells. Our findings with a binary mixture of PAHs suggest that combinations of LMW PAHs may elicit synergistic or additive inflammatory responses which warrant further investigation and confirmation.
Hsp70 Targets a Cytoplasmic Quality Control Substrate to the San1p Ubiquitin Ligase*

Background: San1p is a nuclear ubiquitin ligase that helps degrade misfolded cytoplasmic proteins in yeast. Results: The Hsp70, Ssa1p, facilitates an interaction between a novel misfolded substrate and San1p. Conclusion: Chaperones play a direct role in bridging aberrant cytoplasmic proteins to ubiquitin ligases. Significance: Understanding how chaperones select and target cytoplasmic proteins will help define how diseases associated with proteotoxic stress might be treated. Accumulation of misfolded proteins in cellular compartments can result in stress-induced cell death. In the endoplasmic reticulum (ER), ER-associated degradation clears aberrant proteins from the secretory pathway. In the cytoplasm and nucleus, this job is left to the cytoplasmic quality control (CytoQC) machinery. Both processes utilize chaperones and the ubiquitin-proteasome system to aid in protein elimination. Previous studies in yeast have drawn comparisons between these processes using data from structurally and topologically different substrates. We sought to draw a direct comparison between ERAD and CytoQC by studying the elimination of a single misfolded domain that, depending on its residence, is disposed by either of these pathways. The truncated, second nucleotide binding domain (NBD2*) from a yeast ERAD substrate, Ste6p*, resides at the cytoplasmic face of the ER. We show that a soluble form of NBD2* is cytoplasmic and unlike wild-type NBD2 is targeted for proteasome-mediated degradation. In contrast to Ste6p*, which employs the ER-localized Doa10p ubiquitin ligase, NBD2* is ubiquitinated by a nuclear E3 ligase San1p, a factor that is also required for its degradation. Although the yeast cytoplasmic Hsp70 chaperone, Ssa1p, has been thought to facilitate the nuclear import or to maintain the solubility of most CytoQC substrates, we discovered that Ssa1p facilitates the interaction between San1p and NBD2*, demonstrating that chaperones can aid in substrate recognition and San1p-dependent protein degradation. These results emphasize the diverse action of molecular chaperones during CytoQC.
Long-term psychosocial outcomes of children after invasive treatment for congenital heart disease and psychological adjustment of their parents

textabstractThe objective of the study described in this thesis was to examine a range of long-term psychosocial outcomes of children and adolescents who underwent invasive treatment for congenital heart disease at a young age. In addition, the psychological adjustment of their parents was assessed. In chapter 1, the background and the aims of this study were presented. Over the past decades, advances in diagnostic and surgical techniques and medical treatment of ConHD have gradually evolved and have significantly improved long-term survival of patients with ConHD. Despite improved survival, many patients with ConHD have more or less cardiac sequelae after surgical or interventional treatment. Next to survival, long-term morbidity is of great interest. Morbidity may impair the psychosocial functioning and quality of life of patients with ConHD. Hence, both clinicians and researchers have become more interested in the long-term psychosocial outcomes of patients treated for ConHD. In the present study, various indicators of psychosocial functioning of children and adolescents with ConHD were measured. A follow-up examination was performed (from 2003-2004) among consecutive surviving patients of 4 diagnostic groups, who underwent their first invasive treatment for ConHD at least 7 years and 6 months ago (between 1 January 1990 and 1 January 1996) in the Erasmus University Medical Centre Rotterdam, and who were younger than 15 years at the time of the treatment. At follow-up 206 patients were aged 7-28 years. Of this group 35 patients were aged 18-28 years. Results of the 18-28-year-old patients were not included in this thesis. The present patient sample consisted of 171 patients, aged 7-17 years, and their parents.
Crystal Structures of Copper-depleted and Copper-bound Fungal Pro-tyrosinase

Background: Fungal tyrosinase maturation involves multiple processes of the dinuclear copper assembly and proteolytic activation. Results: Structural examinations and mutational studies of the pro-tyrosinases revealed that three endogenous cysteines contribute to the copper incorporation. Conclusion: The three highly flexible cysteines are essential for assembly of the active site across the protein shell. Significance: Elucidation of such a copper incorporation process provides useful insights into metal homeostasis. Tyrosinase, a dinuclear copper monooxygenase/oxidase, plays a crucial role in the melanin pigment biosynthesis. The structure and functions of tyrosinase have so far been studied extensively, but the post-translational maturation process from the pro-form to the active form has been less explored. In this study, we provide the crystal structures of Aspergillus oryzae full-length pro-tyrosinase in the holo- and the apo-forms at 1.39 and 2.05 Å resolution, respectively, revealing that Phe513 on the C-terminal domain is accommodated in the substrate-binding site as a substrate analog to protect the dicopper active site from substrate access (proteolytic cleavage of the C-terminal domain or deformation of the C-terminal domain by acid treatment transforms the pro-tyrosinase to the active enzyme (Fujieda, N., Murata, M., Yabuta, S., Ikeda, T., Shimokawa, C., Nakamura, Y., Hata, Y., and Itoh, S. (2012) ChemBioChem. 13, 193–201 and Fujieda, N. , Murata, M. , Yabuta, S. , Ikeda, T. , Shimokawa, C. , Nakamura, Y. , Hata, Yl, and Itoh, S. (2013) J. Biol. Inorg. Chem. 18, 19–26). Detailed crystallographic analysis and structure-based mutational studies have shown that the copper incorporation into the active site is governed by three cysteines as follows: Cys92, which is covalently bound to His94 via an unusual thioether linkage in the holo-form, and Cys522 and Cys525 of the CXXC motif located on the C-terminal domain. Molecular mechanisms of the maturation processes of fungal tyrosinase involving the accommodation of the dinuclear copper unit, the post-translational His-Cys thioether cross-linkage formation, and the proteolytic C-terminal cleavage to produce the active tyrosinase have been discussed on the basis of the detailed structural information.
New Human Retroviruses Discovered

trastuzumab in this trial were similar to those seen in the NSABP and NCCTG trials. All patients in the HERA trial will continue to be followed up for longterm safety and patients in the observation-only arm will be offered trastuzumab. Results regarding optimal trastuzumab duration (2 years vs 1 year) should be available in 2008. Sledge reiterated the importance of investigating trastuzumab’s cardiotoxicity, including whether the adverse effects are completely or partially reversible. “We know virtually nothing about the long-term effects of [trastuzumab] on the heart,” he stressed. Nonetheless, he added, with NSABP/NCCTG and HERA results clearly indicating that adjuvant trastuzumab improves diseasefree survival for women with HER2positive breast cancer, the drug’s benefits far outweigh its risks. “There’s no question in my mind about this— biology has spoken, and we should listen,” he said. “But the price [of potential cardiotoxicity] is real and has to be discussed with patients. ” MORE TO BE DONE The promising data from these monoclonal antibody trials have created a buzz among oncologists and cancer researchers, but they also caution that for most of the women participating in the studies, the new drugs provide a prolongation of survival, not a cure. Combining targeted therapies—a strategy similar to that used for treating patients with HIV—may someday prove to be the way to go, but life-saving drug cocktails for cancer have not yet been discovered.