Miracle-dz/UniFAR-FTUs huggingface dataset:
Site-Specific Recombination by SSV2 Integrase: Substrate Requirement and Domain Functions

ABSTRACT SSV-type integrases, encoded by fuselloviruses which infect the hyperthermophilic archaea of the Sulfolobales, are archaeal members of the tyrosine recombinase family. These integrases catalyze viral integration into and excision from a specific site on the host genome. In the present study, we have established an in vitro integration/excision assay for SSV2 integrase (IntSSV2). IntSSV2 alone was able to catalyze both integration and excision reactions in vitro. A 27-bp specific DNA sequence is minimally required for the activity of the enzyme, and its flanking sequences influence the efficiency of integration by the enzyme in a sequence-nonspecific manner. The enzyme forms a tetramer through interactions in the N-terminal part (residues 1 to 80), interacts nonspecifically with DNA and performs chemical catalysis in the C-terminal part (residues 165 to 328), and appears to recognize and bind the specific site of recombination in the middle portion (residues 81 to 164). It is worth noting that an N-terminally truncated mutant of IntSSV2 (residues 81 to 328), which corresponded to the putative product of the 3′-end sequence of the IntSSV2 gene of the integrated SSV2 genome, was unable to form tetramers but possessed all the catalytic properties of full-length IntSSV2 except for the slightly reduced recombination activity. Our results suggest that, unlike λ integrase, SSV-type integrases alone are capable of catalyzing viral DNA recombination with the host genome in a simple and reversible fashion. IMPORTANCE Archaea are host to a variety of viruses. A number of archaeal viruses are able to integrate their genome into the host genome. Many known archaeal viral integrases belong to a unique type, or the SSV type, of tyrosine recombinases. SSV-type integrases catalyze viral integration into and excision from a specific site on the host genome. However, the molecular details of the recombination process have yet to be fully understood because of the lack of an established in vitro recombination assay system. Here we report an in vitro assay for integration and excision by SSV2 integrase, a member of the SSV-type integrases. We show that SSV2 integrase alone is able to catalyze both integration and excision and reveal how different parts of the target DNA and the enzyme serve their roles in these processes. Therefore, our results provide mechanistic insights into a simple recombination process catalyzed by an archaeal integrase.
Pregnancy Outcome and Placental Findings in Pregnancies Complicated by Fetal Growth Restriction With and Without Preeclampsia

Objective: To compare pregnancy outcome and placental pathology in pregnancies complicated by fetal growth restriction (FGR) with and without preeclampsia. Methods: Labor, fetal/neonatal outcome, and placental pathology parameters from neonates with a birth weight below the10th percentile (FGR), born between 24 and 42 weeks of gestation, were reviewed. Results were compared between pregnancies complicated with preeclampsia (hypertensive FGR [H-FGR]) to those without preeclampsia (normotensive FGR [N-FGR]). Composite neonatal outcome, defined as 1 or more of early complication (respiratory distress, necrotizing enterocolitis, sepsis, transfusion, ventilation, seizure, hypoxic–ischemic encephalopathy, phototherapy, or death), Apgar score ≤7 at 5 minutes, and days of hospitalization, were compared between the groups. Placental lesions, classified as lesions related to maternal vascular supply, lesions consistent with fetal thrombo-occlusive disease and inflammatory lesions, maternal inflammatory response, and fetal inflammatory response, were also compared. Results: Women in the H-FGR group (n = 72) were older, with higher body mass index (BMI) and higher rate of preterm labor (<34 weeks) than in the N-FGR group (n = 270), P < . 001 for all. Composite neonatal outcome was worse in the H-FGR than in the N-FGR group, 50% versus 15.5%, P < . 001. Higher rate of maternal placental vascular lesions was detected in H-FGR compared with N-FGR, 82% versus 57.7%, P < . 001. Using a stepwise logistic regression model, maternal BMI (1.13 odds ratio [OR], confidence interval [CI] 1.035-1.227, P = .006) and neonatal birth weight (0.996 OR, CI 0.995-0.998, P < .001) were independently associated with worse neonatal outcome. Conclusion: Worse neonatal outcome and more maternal placental vascular lesions in pregnancy complicated by FGR with preeclampsia versus FGR without preeclampsia suggest different pathophysiology in these entities.
MAVS Dimer Is a Crucial Signaling Component of Innate Immunity and the Target of Hepatitis C Virus NS3/4A Protease

ABSTRACT The mitochondrial antiviral signaling (MAVS) protein plays a central role in innate antiviral immunity. Upon recognition of a virus, intracellular receptors of the RIG-I-like helicase family interact with MAVS to trigger a signaling cascade. In this study, we investigate the requirement of the MAVS structure for enabling its signaling by structure-function analyses and resonance energy transfer approaches in live cells. We now report the essential role of the MAVS oligomer in signal transduction and map the transmembrane domain as the main determinant of dimerization. A combination of mutagenesis and computational methods identified a cluster of residues making favorable van der Waals interactions at the MAVS dimer interface. We also correlated the activation of IRF3 and NF-κB with MAVS oligomerization rather than its mitochondrial localization. Finally, we demonstrated that MAVS oligomerization is disrupted upon expression of HCV NS3/4A protease, suggesting a mechanism for the loss of antiviral signaling. Altogether, our data suggest that the MAVS oligomer is essential in the formation of a multiprotein membrane-associated signaling complex and enables downstream activation of IRF3 and NF-κB in antiviral innate immunity.
Effects of Maternal Dexamethasone Treatment Early in Pregnancy on Glucocorticoid Receptors in the Ovine Placenta

The effects of endogenous cortisol on binucleate cells (BNCs), which promote fetal growth, may be mediated by glucocorticoid receptors (GRs), and exposure to dexamethasone (DEX) in early pregnancy stages of placental development might modify this response. In this article, we have investigated the expression of GR as a determinant of these responses. Pregnant ewes carrying singleton fetuses (n = 119) were randomized to control (2 mL saline/ewe) or DEX-treated groups (intramuscular injections of 0.14 mg/kg ewe weight per 12 hours) at 40 to 41 days of gestation (dG). Placental tissue was collected at 50, 100, 125, and 140 dG. Total glucocorticoid receptor protein (GRt) was increased significantly by DEX at 50 and 125 dG in females only, but decreased in males at 125 dG as compared to controls. Glucocorticoid receptor α (GRα) protein was not changed after DEX treatment. Three BNC phenotypes were detected regarding GRα expression (++, +−, −−), DEX increased the proportion of (++) and decreased (−−) BNC at 140 dG. Effects were sex- and cell type dependent, modifying the responsiveness of the placenta to endogenous cortisol. We speculate that 3 maturational stages of BNCs exist and that the overall activity of BNCs is determined by the distribution of these 3 cell types, which may become altered through early pregnancy exposure to elevated glucocorticoids.
Radiation protection protocol observed amongst dentist population in the union territory of Puducherry

The risk involved with dental radiography is certainly small in comparison with many other risks that are a common part of everyday life. However, there is no basis to assume that it is zero. Though the radiation dose levels in dental practice are relatively low, one should consider the cumulative effect of repeated exposures. There should be a striving for implementation of radiation protection measures and selection criteria for radiography in private dental offices. This article presents the results of the survey conducted in the private dental offices in the Union territory of Puducherry to gain insight into the knowledge and attitude of the Puducherry dentists towards radiation protection.
Response to: De Novo Kidney Transplantation Without Use of Calcineurin Inhibitors Preserves Renal Structure and Function at 2 Years

We appreciate the comments by Dr. Abbott regarding our randomized prospective comparison of cyclosporine-based (CNI treated) and sirolimus-based (CNI free) immunosuppression in kidney transplantation. We refer him to the initial report of the clinical results to answer several of his questions (1; reference 19). This study was not powered to detect differences in patient and graft survival, but was intentionally powered to detect, using a power of 0.90 and an alpha of 0.05, a difference in mean creatinine of 0.25 ± 0.15 mg/dL and calculated creatinine clearance of 15 ± 10 cc/min. We agree that blood pressure (BP) among kidney transplant recipients is important, and as previously reported at 6 and 12 months, respectively, there were no significant differences in mean systolic and diastolic BP nor the number of anti-hypertensive agents (including diuretics) between the sirolimus-treated and the CNI-treated patients (1). Analysis at the time of the 2year biopsies demonstrated mean ± SD BP for CNI-treated versus sirolimus, respectively, Systolic 147.2 ± 18.5 versus 134.6 ± 16 and Diastolic 80.7 ± 9.4 versus 75.5 ± 9.9 mmHg. The difference in the means for systolic BP was significant (p = 0.0074), using a 2-tailed t-test assuming equal variances. The difference in the means for diastolic BP was marginally significant (p = 0.051). There was no significant difference in ACE inhibitor use, as 39% (11) of sirolimus-treated and 36% (10) CNI-treated patients were receiving a converting enzyme inhibitor. The mean number of BP drugs per patient (including diuretics) was greater for the CNI treated 2.46 than the sirolimus treated 2.04, but the difference was not significant, row mean score (CMH test, p = 0.332). These findings may reflect small sample sizes.
A Virus-Like Particle That Elicits Cross-Reactive Antibodies to the Conserved Stem of Influenza Virus Hemagglutinin

ABSTRACT The discovery of broadly neutralizing antibodies that recognize highly conserved epitopes in the membrane-proximal region of influenza virus hemagglutinin (HA) has revitalized efforts to develop a universal influenza virus vaccine. This effort will likely require novel immunogens that contain these epitopes but lack the variable and immunodominant epitopes located in the globular head of HA. As a first step toward developing such an immunogen, we investigated whether the 20-residue A-helix of the HA2 chain that forms the major component of the epitope of broadly neutralizing antibodies CR6261, F10, and others is sufficient by itself to elicit antibodies with similarly broad antiviral activity. Here, we report the multivalent display of the A-helix on icosahedral virus-like particles (VLPs) derived from the capsid of Flock House virus. Mice immunized with VLPs displaying 180 copies/particle of the A-helix produced antibodies that recognized trimeric HA and the elicited antibodies had binding characteristics similar to those of CR6261 and F10: they recognized multiple HA subtypes from group 1 but not from group 2. However, the anti-A-helix antibodies did not neutralize influenza virus. These results indicate that further engineering of the transplanted peptide is required and that display of additional regions of the epitope may be necessary to achieve protection.
Statins as Targeted “Magical Pills” for the Conservative Treatment of Endometriosis

The aim of the study was to analyze all the available evidence from both in vitro and in vivo studies regarding the efficacy of statin therapy in the treatment of endometriosis, evaluating the potential efficacy, side effects, and contraindications of their administration in humans. We focused on defining the potential benefits that the administration of statins may have on patients affected by endometriosis and the possible adverse effects of such a therapy on ovarian function and fertility profile. According to our article selection criteria, we included in the review in vitro and in vivo studies performed on human or animal models. The systematic review of literature identified 24 eligible articles, 12 of which reported evidence regarding the effects of statins on endometrial/endometriotic cells and 12 regarding their effects on ovarian function and fertility. All articles seem to emphasize the utility of statin administration in the treatment of endometriosis due to their anti-proliferative/proapoptotic effects, their ability to reduce cell viability and migration, and the inhibition of angiogenesis and anti-inflammatory activities. Regarding the potential adverse effects on gonadal activities, steroidogenesis and fertility function, no conclusive data were collected in human models (excluding women affected by polycystic ovary syndrome in which significant decline of androgen levels was reported after statin treatment), while contrasting results were reported by studies conducted in in vitro and in vivo in animal models. Despite evidence supporting statins as the potential therapeutic agent for a targeted conservative treatment of endometriosis, the uncertainties regarding their impact on gonadal function may not define them as an appropriate therapy for all young fertile women.
Vaccine-Derived Neutralizing Antibodies to the Human Cytomegalovirus gH/gL Pentamer Potently Block Primary Cytotrophoblast Infection

ABSTRACT Human cytomegalovirus (HCMV) elicits neutralizing antibodies (NAb) of various potencies and cell type specificities to prevent HCMV entry into fibroblasts (FB) and epithelial/endothelial cells (EpC/EnC). NAb targeting the major essential envelope glycoprotein complexes gB and gH/gL inhibit both FB and EpC/EnC entry. In contrast to FB infection, HCMV entry into EpC/EnC is additionally blocked by extremely potent NAb to conformational epitopes of the gH/gL/UL128/130/131A pentamer complex (PC). We recently developed a vaccine concept based on coexpression of all five PC subunits by a single modified vaccinia virus Ankara (MVA) vector, termed MVA-PC. Vaccination of mice and rhesus macaques with MVA-PC resulted in a high titer and sustained NAb that blocked EpC/EnC infection and lower-titer NAb that inhibited FB entry. However, antibody function responsible for the neutralizing activity induced by the MVA-PC vaccine is uncharacterized. Here, we demonstrate that MVA-PC elicits NAb with cell type-specific neutralization potency and antigen recognition pattern similar to human NAb targeting conformational and linear epitopes of the UL128/130/131A subunits or gH. In addition, we show that the vaccine-derived PC-specific NAb are significantly more potent than the anti-gH NAb to prevent HCMV spread in EpC and infection of human placental cytotrophoblasts, cell types thought to be of critical importance for HCMV transmission to the fetus. These findings further validate MVA-PC as a clinical vaccine candidate to elicit NAb that resembles those induced during HCMV infection and provide valuable insights into the potency of PC-specific NAb to interfere with HCMV cell-associated spread and infection of key placental cells. IMPORTANCE As a consequence of the leading role of human cytomegalovirus (HCMV) in causing permanent birth defects, developing a vaccine against HCMV has been assigned a major public health priority. We have recently introduced a vaccine strategy based on a widely used, safe, and well-characterized poxvirus vector platform to elicit potent and durable neutralizing antibody (NAb) responses targeting the HCMV envelope pentamer complex (PC), which has been suggested as a critical component for a vaccine to prevent congenital HCMV infection. With this work, we confirm that the NAb elicited by the vaccine vector have properties that are similar to those of human NAb isolated from individuals chronically infected with HCMV. In addition, we show that PC-specific NAb have potent ability to prevent infection of key placental cells that HCMV utilizes to cross the fetal-maternal interface, suggesting that NAb targeting the PC may be essential to prevent HCMV vertical transmission.
Kaposi's Sarcoma-Associated Herpesvirus ORF57 Interacts with Cellular RNA Export Cofactors RBM15 and OTT3 To Promote Expression of Viral ORF59

ABSTRACT Kaposi's sarcoma-associated herpesvirus (KSHV) encodes ORF57, which promotes the accumulation of specific KSHV mRNA targets, including ORF59 mRNA. We report that the cellular export NXF1 cofactors RBM15 and OTT3 participate in ORF57-enhanced expression of KSHV ORF59. We also found that ectopic expression of RBM15 or OTT3 augments ORF59 production in the absence of ORF57. While RBM15 promotes the accumulation of ORF59 RNA predominantly in the nucleus compared to the levels in the cytoplasm, we found that ORF57 shifted the nucleocytoplasmic balance by increasing ORF59 RNA accumulation in the cytoplasm more than in the nucleus. By promoting the accumulation of cytoplasmic ORF59 RNA, ORF57 offsets the nuclear RNA accumulation mediated by RBM15 by preventing nuclear ORF59 RNA from hyperpolyadenylation. ORF57 interacts directly with the RBM15 C-terminal portion containing the SPOC domain to reduce RBM15 binding to ORF59 RNA. Although ORF57 homologs Epstein-Barr virus (EBV) EB2, herpes simplex virus (HSV) ICP27, varicella-zoster virus (VZV) IE4/ORF4, and cytomegalovirus (CMV) UL69 also interact with RBM15 and OTT3, EBV EB2, which also promotes ORF59 expression, does not function like KSHV ORF57 to efficiently prevent RBM15-mediated nuclear accumulation of ORF59 RNA and RBM15's association with polyadenylated RNAs. Collectively, our data provide novel insight elucidating a molecular mechanism by which ORF57 promotes the expression of viral intronless genes.
Four years prospective study of the maxillofacial trauma at a tertiary center in Western Nepal

Purpose: This study was conducted to find the epidemiological characteristics of maxillofacial trauma in the Western region of Nepal. Materials and Methods: All the trauma patients attending the Department of Oral and Maxillofacial surgery in 4 years period at a tertiary center in Western Nepal were included in the study. The incidence, prevalence, age and sex distribution, etiologies and types as well as seasonal and daily variation of maxillofacial trauma were studied. Results: Maxillofacial trauma with male (71.55%) predominance was seen. Road traffic accidents (RTA, 46.5%) were the most common cause, and 41.65% of fracture cases due to RTA were under the influence of alcohol. Accidents were more common on the rural roads (38.9%), and majorities (43.3%) were due to motorcycle accidents. They were more common on Friday (36.7%) and in winter seasons (51.2%). The mandible fractures (65.85%) were more common than midface fractures (53.58%) and 19.44% of the fractures were combined fractures. Parasymphysis in mandible (32.16%) and zygoma (39.09%) in midface were the most common type of fracture. Conclusion: The increased incidence of maxillofacial trauma following RTA under the influence of alcohol noted in this study reveals the need for formulating preventive measures in the Western region of Nepal. Need to aware people to avoid drink and drive proper traffic management, prevention of carrying excessive passengers, especially on the rooftop of vehicles on the highway and disposal of out of date vehicles and timely maintenance of faulty roads is a must.
Evaluation of surface roughness of glazed and polished ceramic surface on exposure to fluoride gel, bleaching agent and aerated drink: An in vitro study

STATEMENT OF PROBLEM: The effect of acidic solutions on the surface roughness of ceramic material is not well documented. PURPOSE: Evaluate the surface roughness of three acidic solutions on exposure to two ceramic materials. MATERIALS AND METHODS: About 40 discs (10 mm diameter, 2 mm thick) were made from the following ceramic: low-fusing ceramic (Ivoclar classic) Group A and all ceramic (Ivoclar IPS empress 2) Group B. Each disc abraded with medium-grit diamond on one half of disc and polished with diamond paste while other half retains the glaze. The discs (10 specimens/group) immersed in 1.23% APF Gel, 16% carbamide peroxide, Coca-cola and distilled water (control). The surface roughness evaluated with surface profiler, before and after exposure to acidic solutions followed by SEM analysis. The data analyzed using Student's t -test and Student's independent t -test. Increase in surface roughness was calculated in percentage change. RESULTS: For Group A, Ra values for glazed surface were significantly higher than Ra values before exposure to acidic solutions (1.07 ± 0.17 mm, 1.090.33 mm, 1.29 ± 0.33 mm and P CONCLUSION: Polishing ceramic with diamond paste provides smoother surface than glazed surface. Roughening of porcelain may occur following application of fluoride gel, bleaching agent and on exposure to Coca-cola.
Different Expression of Hypoxic and Angiogenic Factors in Human Endometriotic Lesions

Endometriosis is associated with local angiogenic and hypoxic mechanisms. Indeed, peritoneal fluid of women with endometriosis generates a specific microenvironment to support the growth and development of ectopic endometrial tissues. The association between proangiogenic markers and hypoxic processes in different endometriosis phenotypes was investigated in the present study, analyzing the expression of several genes, related to hypoxic signaling pathway and involved in angiogenic processes, in nonpregnant women with different forms of endometriosis. Samples of ovarian endometrioma (OMA; n = 16) or deep infiltrating endometriosis (DIE; n = 11) were collected, and in addition, control endometrium was collected from healthy women by hysteroscopy. The gene expression of the hypoxia-inducible factors (HIF) 1/2α, protease-activated receptors (PARs) ¼, and vascular endothelial growth factor (VEGF) A was evaluated by quantitative reverse-transcription polymerase chain reaction. Ovarian endometrioma expresses high levels of HIF-1/2α, PAR-1/4, and VEGF-A, while DIE did not show significantly different gene expression compared to endometrium from unaffected women. A positive correlation between the expression of HIF-1/2α and VEGF-A mRNA was observed in OMA. The overall data point out that the heterogeneity of the disease reflects differences in expression levels of genes associated with hypoxia and angiogenesis, suggesting that such conditions may have an active role in the development of the disease.