Miracle-dz/UniFAR-FTUs huggingface dataset:
Discovery of Critical Residues for Viral Entry and Inhibition through Structural Insight of HIV-1 Fusion Inhibitor CP621–652*

Background: CP621–652 is a HIV-1 fusion inhibitor peptide containing the gp41 621QIWNNMT627 motif. Results: The crystal structure of CP621–652 in complex with T21 was determined and mutational analyses were performed. Conclusion: The residues Met626 and Thr627 in the gp41 621QIWNNMT627 motif are critical for HIV-1 entry and inhibition. Significance: Our data provide important information for designing novel HIV fusion inhibitors. The core structure of HIV-1 gp41 is a stable six-helix bundle (6-HB) folded by its trimeric N- and C-terminal heptad repeats (NHR and CHR). We previously identified that the 621QIWNNMT627 motif located at the upstream region of gp41 CHR plays critical roles for the stabilization of the 6-HB core and peptide CP621–652 containing this motif is a potent HIV-1 fusion inhibitor, however, the molecular determinants underlying the stability and anti-HIV activity remained elusive. In this study, we determined the high-resolution crystal structure of CP621–652 complexed by T21. We find that the 621QIWNNMT627 motif does not maintain the α-helical conformation. Instead, residues Met626 and Thr627 form a unique hook-like structure (denoted as M-T hook), in which Thr627 redirects the peptide chain to position Met626 above the left side of the hydrophobic pocket on the NHR trimer. The side chain of Met626 caps the hydrophobic pocket, stabilizing the interaction between the pocket and the pocket-binding domain. Our mutagenesis studies demonstrate that mutations of the M-T hook residues could completely abolish HIV-1 Env-mediated cell fusion and virus entry, and significantly destabilize the interaction of NHR and CHR peptides and reduce the anti-HIV activity of CP621–652. Our results identify an unusual structural feature that stabilizes the six-helix bundle, providing novel insights into the mechanisms of HIV-1 fusion and inhibition.
ORAL HEALTH STATUS OF 9 TO 12 YEAR OLD SCHOOL GOING CHILDREN IN URBAN MEERUT

Background: Oral health is an integral part of general health. Oral Health status has a direct impact on general health and conversely, general health influences oral health. It has also become clear that causative and risk factors in oral diseases are often the same as those implicated in the major general diseases.Hence this study was done to estimate the prevalence, type and degree of oral diseases in the study area. Materials and Method: It is a cross- sectional study design conducted among schools in , Multan Nagar which is the field practice area of department of Community Medicine, SMC (Subharti Medical College), Meerut.A total of 534 school going children aged 9 to 12 years old were examined using standard WHO Oral Health Survey methods. Results: One third of the study population (34.3%) had good oral hygiene according to oral hygiene index simplified. The overall prevalence of gingivitis among children was 53.4 percent.The prevalence of dental caries among 9 to 12 year old school going children was 60.1 %. The mean DMFT score of the study population was 0.89. The index study findings revealed a strong relationship between oral health status and socio economic status and mother’s educational status. Conclusion: The overall prevalence of dental caries was high in the study subjects.Mother’s educational status has a significant role in improving the oral health status of children.
Characterization of Conformational Changes and Protein-Protein Interactions of Rod Photoreceptor Phosphodiesterase (PDE6)*

Background: Photoreceptor PDE6 is the central enzyme in vision, but conformational changes during visual transduction are not understood. Results: Binding of cGMP or regulatory proteins to PDE6 induces conformational changes detected by analytical ultracentrifugation. Conclusion: Allosteric communication may contribute to regulating PDE6. Significance: Understanding PDE6 molecular organization will aid understanding of how defects in PDE6 can result in retinal disease. As the central effector of visual transduction, the regulation of photoreceptor phosphodiesterase (PDE6) is controlled by both allosteric mechanisms and extrinsic binding partners. However, the conformational changes and interactions of PDE6 with known interacting proteins are poorly understood. Using a fluorescence detection system for the analytical ultracentrifuge, we examined allosteric changes in PDE6 structure and protein-protein interactions with its inhibitory γ-subunit, the prenyl-binding protein (PrBP/δ), and activated transducin. In solution, the PDE6 catalytic dimer (Pαβ) exhibits a more asymmetric shape (axial ratio of 6.6) than reported previously. The inhibitory Pγ subunit behaves as an intrinsically disordered protein in solution but binds with high affinity to the catalytic dimer to reconstitute the holoenzyme without a detectable change in shape. Whereas the closely related PDE5 homodimer undergoes a significant change in its sedimentation properties upon cGMP binding to its regulatory cGMP binding site, no such change was detected upon ligand binding to the PDE6 catalytic dimer. However, when Pαβ was reconstituted with Pγ truncation mutants lacking the C-terminal inhibitory region, cGMP-dependent allosteric changes were observed. PrBP/δ bound to the PDE6 holoenzyme with high affinity (KD = 6.2 nm) and induced elongation of the protein complex. Binding of activated transducin to PDE6 holoenzyme resulted in a concentration-dependent increase in the sedimentation coefficient, reflecting a dynamic equilibrium between transducin and PDE6. We conclude that allosteric regulation of PDE6 is more complex than for PDE5 and is dependent on interactions of regions of Pγ with the catalytic dimer.
Congenital anomalies associated with trisomy 18 or trisomy 13: A registry‐based study in 16 european countries, 2000–2011

The aim of this study was to examine the prevalence of trisomies 18 and 13 in Europe and the prevalence of associated anomalies. Twenty‐five population‐based registries in 16 European countries provided data from 2000–2011. Cases included live births, fetal deaths (20+ weeks’ gestation), and terminations of pregnancy for fetal anomaly (TOPFAs). The prevalence of associated anomalies was reported in live births. The prevalence of trisomy 18 and trisomy 13 were 4.8 (95%CI: 4.7–5.0) and 1.9 (95%CI: 1.8–2.0) per 10,000 total births. Seventy three percent of cases with trisomy 18 or trisomy 13 resulted in a TOPFA. Amongst 468 live born babies with trisomy 18, 80% (76–83%) had a cardiac anomaly, 21% (17–25%) had a nervous system anomaly, 8% (6–11%) had esophageal atresia and 10% (8–13%) had an orofacial cleft. Amongst 240 Live born babies with trisomy 13, 57% (51–64%) had a cardiac anomaly, 39% (33–46%) had a nervous system anomaly, 30% (24–36%) had an eye anomaly, 44% (37–50%) had polydactyly and 45% (39–52%) had an orofacial cleft. For babies with trisomy 18 boys were less likely to have a cardiac anomaly compared with girls (OR = 0.48 (0.30–0.77) and with trisomy 13 were less likely to have a nervous system anomaly [OR = 0.46 (0.27–0.77)]. Babies with trisomy 18 or trisomy 13 do have a high proportion of associated anomalies with the distribution of anomalies being different in boys and girls. © 2015 Wiley Periodicals, Inc.
Activation of Wnt11 by Transforming Growth Factor-β Drives Mesenchymal Gene Expression through Non-canonical Wnt Protein Signaling in Renal Epithelial Cells*

Background: TGF-β drives renal fibrosis and mesenchymal gene expression in epithelial cells. Results: Targets of TGF-β include Wnt11, which enhances mesenchymal gene expression through non-canonical signaling. Conclusion: TGF-β activates signaling pathways that promote the mesenchymal phenotype in an autocrine manner. Significance: Understanding the effects of TGF-β and downstream signaling is essential for developing new anti-fibrotic therapies for chronic renal disease. Transforming growth factor β1 (TGF-β) promotes renal interstitial fibrosis in vivo and the expression of mesenchymal genes in vitro; however, most of its direct targets in epithelial cells are still elusive. In a screen for genes directly activated by TGF-β, we found that components of the Wnt signaling pathway, especially Wnt11, were targets of activation by TGF-β and Smad3 in primary renal epithelial cells. In gain and loss of function experiments, Wnt11 mediated the actions of TGF-β through enhanced activation of mesenchymal marker genes, such as Zeb1, Snail1, Pai1, and αSMA, without affecting Smad3 phosphorylation. Inhibition of Wnt11 by receptor knockdown or treatment with Wnt inhibitors limited the effects of TGF-β on gene expression. We found no evidence that Wnt11 activated the canonical Wnt signaling pathway in renal epithelial cells; rather, the function of Wnt11 was mediated by the c-Jun N-terminal kinase (JNK) pathway. Consistent with the in vitro results, all the TGF-β, Wnt11, and JNK targets were activated in a unilateral ureteral obstruction (UUO) model of renal fibrosis in vivo. Our findings demonstrated cooperativity among the TGF-β, Wnt11, and JNK signaling pathways and suggest new targets for anti-fibrotic therapy in renal tissue.
Biological control of grey mould in strawberry fruits by halophilic bacteria

Aims: Grey mould caused by Botrytis cinerea is an economically important disease of strawberries in Tunisia and worldwide. The aim of this study was to select effective halophilic bacteria from hypersaline ecosystems and evaluate the abilities of antifungal bacteria to secrete extracellular hydrolytic enzymes, anti‐Botrytis metabolites and volatiles.
Interplay between T Cell Receptor Binding Kinetics and the Level of Cognate Peptide Presented by Major Histocompatibility Complexes Governs CD8+ T Cell Responsiveness*

Background: Adaptive immunity requires T cell receptor (TCR) recognition of antigenic peptide in complex with major histocompatibility complexes (pMHC). Results: Both TCR/pMHC binding kinetics and the amount of interacting cognate pMHC contribute to CD8+ T cell activation. Conclusion: Intermediate TCR/pMHC binding parameters confer maximum biological responses. Significance: Elucidating the mechanism of T cell activation is critical for vaccine and immunotherapeutic development. Through a rational design approach, we generated a panel of HLA-A*0201/NY-ESO-1157–165-specific T cell receptors (TCR) with increasing affinities of up to 150-fold from the wild-type TCR. Using these TCR variants which extend just beyond the natural affinity range, along with an extreme supraphysiologic one having 1400-fold enhanced affinity, and a low-binding one, we sought to determine the effect of TCR binding properties along with cognate peptide concentration on CD8+ T cell responsiveness. Major histocompatibility complexes (MHC) expressed on the surface of various antigen presenting cells were peptide-pulsed and used to stimulate human CD8+ T cells expressing the different TCR via lentiviral transduction. At intermediate peptide concentration we measured maximum cytokine/chemokine secretion, cytotoxicity, and Ca2+ flux for CD8+ T cells expressing TCR within a dissociation constant (KD) range of ∼1–5 μm. Under these same conditions there was a gradual attenuation in activity for supraphysiologic affinity TCR with KD < ∼1 μm, irrespective of CD8 co-engagement and of half-life (t1/2 = ln 2/koff) values. With increased peptide concentration, however, the activity levels of CD8+ T cells expressing supraphysiologic affinity TCR were gradually restored. Together our data support the productive hit rate model of T cell activation arguing that it is not the absolute number of TCR/pMHC complexes formed at equilibrium, but rather their productive turnover, that controls levels of biological activity. Our findings have important implications for various immunotherapies under development such as adoptive cell transfer of TCR-engineered CD8+ T cells, as well as for peptide vaccination strategies.
HBx Protein of Hepatitis B Virus Promotes Reinitiation of DNA Replication by Regulating Expression and Intracellular Stability of Replication Licensing Factor CDC6*

Background: CDC6 is a replication licensing factor, which is tightly regulated to prevent reinitiation of replication. Results: Hepatitis B virus HBx protein up-regulates CDC6 both transcriptionally as well as post-transcriptionally and promotes its recruitment to β-globin origin of replication. Conclusion: Accumulation of CDC6 protein under HBx microenvironment facilitates origin licensing. Significance: Deregulation of replication factors could be a mechanism associated with viral oncogenesis. Prevention of re-replication via negative regulation of replication initiator proteins, such as CDC6, is key to maintenance of genomic integrity, whereas their up-regulation is generally associated with perturbation in cell cycle, genomic instability, and potentially, tumorigenesis. The HBx oncoprotein of hepatitis B virus is well known to deregulate cell cycle and has been intricately linked to development of hepatocellular carcinoma. Despite a clear understanding of the proliferative effects of HBx on cell cycle, a mechanistic link between HBx-mediated hepatocarcinogenesis and host cell DNA replication remains poorly perused. Here we show that HBx overexpression in both the cellular as well as the transgenic environment resulted in the accumulation of CDC6 through transcriptional and post-translational up-regulation. The HBx-mediated increase in CDK2 activity altered the E2F1-Rb (retinoblastoma) balance, which favored CDC6 gene expression by E2F1. Besides, HBx impaired the APCCdh1-dependent protein degradation pathway and conferred intracellular stability to CDC6 protein. Increase in CDC6 levels correlated with increase in CDC6 occupancy on the β-globin origin of replication, suggesting increment in origin licensing and re-replication. In conclusion, our findings strongly suggest a novel role for CDC6 in abetting the oncogenic sabotage carried out by HBx and support the paradigm that pre-replicative complex proteins have a role in oncogenic transformation.
Identification of Amino Acid Residues Required for the Substrate Specificity of Human and Mouse Chondroitin Sulfate Hydrolase (Conventional Hyaluronidase-4)*

Background: Hyaluronidase-4 is a chondroitin sulfate-specific endo-β-N-acetylgalactosaminidase. Results: The amino acid residues responsible for the substrate specificity of hyaluronidase-4 were identified. Conclusion: The combination of the amino acid residues at 261–265 and glutamine 305 was essential. Significance: These results could help to generate artificial chondroitin sulfate hydrolases, which recognize specific structures. Human hyaluronidase-4 (hHYAL4), a member of the hyaluronidase family, has no hyaluronidase activity, but is a chondroitin sulfate (CS)-specific endo-β-N-acetylgalactosaminidase. The expression of hHYAL4 is not ubiquitous but restricted to placenta, skeletal muscle, and testis, suggesting that hHYAL4 is not involved in the systemic catabolism of CS, but rather has specific functions in particular organs or tissues. To elucidate the function of hyaluronidase-4 in vivo, mouse hyaluronidase-4 (mHyal4) was characterized. mHyal4 was also demonstrated to be a CS-specific endo-β-N-acetylgalactosaminidase. However, mHyal4 and hHYAL4 differed in the sulfate groups they recognized. Although hHYAL4 strongly preferred GlcUA(2-O-sulfate)-GalNAc(6-O-sulfate)-containing sequences typical in CS-D, where GlcUA represents d-glucuronic acid, mHyal4 depolymerized various CS isoforms to a similar extent, suggesting broad substrate specificity. To identify the amino acid residues responsible for this difference, a series of human/mouse HYAL4 chimeric proteins and HYAL4 point mutants were generated, and their preference for substrates was investigated. A combination of the amino acid residues at 261–265 and glutamine at 305 was demonstrated to be essential for the enzymatic activity as well as substrate specificity of mHyal4.
Milk Inhibits the Biological Activity of Ricin

Background: Ricin is reported to be a bioterrorism agent. Results: Reconstituted fat-free milk removes ricin from a glycoprotein-ricin complex and competitively binds to ricin and inhibits its biological effect in Vero cells. Conclusion: The protective effect was at the same level as that of the anti-ricin antibody. Significance: The competitive inhibition by milk compounds reduces the amount of toxin uptake by the cells. Ricin is a highly toxic protein produced by the castor plant Ricinus communis. The toxin is relatively easy to isolate and can be used as a biological weapon. There is great interest in identifying effective inhibitors for ricin. In this study, we demonstrated by three independent assays that a component of reconstituted powdered milk has a high binding affinity to ricin. We discovered that milk can competitively bind to and reduce the amount of toxin available to asialofetuin type II, which is used as a model to study the binding of ricin to galactose cell-surface receptors. Milk also removes ricin bound to the microtiter plate. In parallel experiments, we demonstrated by activity assay and by immuno-PCR that milk can bind competitively to 1 ng/ml ricin, reducing the amount of toxin uptake by the cells, and thus inhibit the biological activity of ricin. The inhibitory effect of milk on ricin activity in Vero cells was at the same level as by anti-ricin antibodies. We also found that (a) milk did not inhibit ricin at concentrations of 10 or 100 ng/ml; (b) autoclaving 10 and 100 ng/ml ricin in DMEM at 121 °C for 30 min completely abolished activity; and (c) milk did not affect the activity of another ribosome inactivating protein, Shiga toxin type 2 (Stx2), produced by pathogenic Escherichia coli O157:H7. Unlike ricin, which is internalized into the cells via a galactose-binding site, Stx2 is internalized through the cell surface receptor glycolipid globotriasylceramides Gb3 and Gb4. These observations suggest that ricin toxicity may possibly be reduced at room temperature by a widely consumed natural liquid food.
Interstitial 6q25 microdeletion syndrome: ARID1B is the key gene

Interstitial deletions of the long arm of chromosome 6 are rare. Clinically, these deletions are considered to be part of a unique microdeletion syndrome associated with intellectual disability and speech impairment, typical dysmorphic features, structural anomalies of the brain, microcephaly, and non‐specific multiple organ anomalies. The critical region for the interstitial 6q microdeletion phenotype was mapped to 6q24–6q25, particularly the 6q25.3 region containing the genes ARID1B and ZDHHC14. It has been hypothesized that haploinsufficiency of these genes impairs normal development of the brain and is responsible for the phenotype. This case report describes a girl presenting with typical features of 6q microdeletion syndrome, including global developmental delay, speech impairment, distinct dysmorphic features, dysgenesis of the corpus callosum, common limb anomalies, and hearing loss. Chromosome analysis by array‐CGH revealed a small interstitial 6q deletion spanning approximately 1.1 Mb of DNA and containing only one coding gene, ARID1B. We suggest that ARID1B is the key gene behind 6q microdeletion syndrome, and we discuss its possible role in the phenotypic manifestations. © 2016 Wiley Periodicals, Inc.
The role of biofilms and protozoa in Legionella pathogenesis: implications for drinking water

Current models to study Legionella pathogenesis include the use of primary macrophages and monocyte cell lines, various free‐living protozoan species and murine models of pneumonia. However, there are very few studies of Legionella spp. pathogenesis aimed at associating the role of biofilm colonization and parasitization of biofilm microbiota and release of virulent bacterial cell/vacuoles in drinking water distribution systems. Moreover, the implications of these environmental niches for drinking water exposure to pathogenic legionellae are poorly understood. This review summarizes the known mechanisms of Legionella spp. proliferation within Acanthamoeba and mammalian cells and advocates the use of the amoeba model to study Legionella pathogenicity because of their close association with Legionella spp. in the aquatic environment. The putative role of biofilms and amoebae in the proliferation, development and dissemination of potentially pathogenic Legionella spp. is also discussed. Elucidating the mechanisms of Legionella pathogenicity development in our drinking water systems will aid in elimination strategies and procedural designs for drinking water systems and in controlling exposure to Legionella spp. and similar pathogens.
Prevalence and Distributions of Feline Immunodeficiency Virus and Feline Leukemia Virus Infections in Bangkok and Its Vicinity, Thailand During 2013-2014

Feline immunodeficiency virus (FIV) and Feline leukemia virus (FeLV) are known as pathogens associated with chronic diseases in cat. This present study determined the prevalence of FIV and FeLV infections in Bangkok and its vicinity, including Nonthaburi and Pathumthani, during April 2013-March 2014 in owned cats. A total of 777 serum or plasma samples were submitted to a private veterinary laboratory in Bangkok. The prevalence of FIV infection, FeLV infection and co-infection was 5.4% (42/777), 16.5% (128/777) and 3.5% (27/777), respectively. The infections were detected all year round, with higher prevalence of FeLV infection. In addition, geographical analyses revealed that FIV and FeLV infections were widely spread in Bangkok and its surrounding areas with similar patterns of geographical distribution. The information provided updated the epidemiological information and will be useful for the development and monitoring of disease management and control.
Understanding Motivations for Sex Among Detained Youth

Abstract This investigation examined reasons for having sex among a sample of 369 African-American and White adolescent detainees, aged 14–18. Using A-CASI technology, sociodemographic variables and motivations for having sex were assessed among this population. Findings indicated that adolescents hold underlying motivations for having sex and that these differ to some degree by gender, SES, but less by race. For programs to be optimally effective, program goals should address gender and SES differentials for having sex.
The society for craniofacial genetics and developmental biology 38th annual meeting

The mission of the Society for Craniofacial Genetics and Developmental Biology (SCGDB) is to promote education, research, and communication about normal and abnormal development of the tissues and organs of the head. The SCGDB welcomes as members undergraduate students, graduate students, post doctoral researchers, clinicians, orthodontists, scientists, and academicians who share an interest in craniofacial biology. Each year our members come together to share their novel findings, build upon, and challenge current knowledge of craniofacial biology. © 2016 Wiley Periodicals, Inc.