bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary Genetics of Human Enterovirus 71: Origin, Population Dynamics, Natural Selection, and Seasonal Periodicity of the VP1 Gene
Authors: Tee Kok Keng , Lam Tommy Tsan-Yuk , Chan Yoke Fun , Bible Jon M. , Kamarulzaman Adeeba , Tong C. Y. William , Takebe Yutaka , Pybus Oliver G. 
Published: January 2010

ABSTRACT

Human enterovirus 71 (EV-71) is one of the major etiologic causes of hand, foot, and mouth disease (HFMD) among young children worldwide, with fatal instances of neurological complications becoming increasingly common. Global VP1 capsid sequences (
n
= 628) sampled over 4 decades were collected and subjected to comprehensive evolutionary analysis using a suite of phylogenetic and population genetic methods. We estimated that the common ancestor of human EV-71 likely emerged around 1941 (95% confidence interval [CI], 1929 to 1952), subsequently diverging into three genogroups: B, C, and the now extinct genogroup A. Genealogical analysis revealed that diverse lineages of genogroup B and C (subgenogroups B1 to B5 and C1 to C5) have each circulated cryptically in the human population for up to 5 years before causing large HFMD outbreaks, indicating the quiescent persistence of EV-71 in human populations. Estimated phylogenies showed a complex pattern of spatial structure within well-sampled subgenogroups, suggesting endemicity with occasional lineage migration among locations, such that past HFMD epidemics are unlikely to be linked to continuous transmission of a single strain of virus. In addition, rises in genetic diversity are correlated with the onset of epidemics, driven in part by the emergence of novel EV-71 subgenogroups. Using subgenogroup C1 as a model, we observe temporal strain replacement through time, and we investigate the evidence for positive selection at VP1 immunogenic sites. We discuss the consequences of the evolutionary dynamics of EV-71 for vaccine design and compare its phylodynamic behavior with that of influenza virus.
Internalization of Coxsackievirus A9 Is Mediated by β2-Microglobulin, Dynamin, and Arf6 but Not by Caveolin-1 or Clathrin
Authors: Heikkilä Outi , Susi Petri , Tevaluoto Tuire , Härmä Heidi , Marjomäki Varpu , Hyypiä Timo , Kiljunen Saija 
Published: January 2010

ABSTRACT

Coxsackievirus A9 (CAV9) is a member of the human enterovirus B species within the
Enterovirus
genus of the family
Picornaviridae
. It has been shown to utilize αV integrins, particularly αVβ6, as its receptors. The endocytic pathway by which CAV9 enters human cells after the initial attachment to the cell surface has so far been unknown. Here, we present a systematic study concerning the internalization mechanism of CAV9 to A549 human lung carcinoma cells. The small interfering RNA (siRNA) silencing of integrin β6 subunit inhibited virus proliferation, confirming that αVβ6 mediates the CAV9 infection. However, siRNAs against integrin-linked signaling molecules, such as Src, Fyn, RhoA, phosphatidylinositol 3-kinase, and Akt1, did not reduce CAV9 proliferation, suggesting that the internalization of the virus does not involve integrin-linked signaling events. CAV9 endocytosis was independent of clathrin or caveolin-1 but was restrained by dynasore, an inhibitor of dynamin. The RNA interference silencing of β2-microglobulin efficiently inhibited virus infection and caused CAV9 to accumulate on the cell surface. Furthermore, CAV9 infection was found to depend on Arf6 as both silencing of this molecule by siRNA and the expression of a dominant negative construct resulted in decreased virus infection. In conclusion, the internalization of CAV9 to A549 cells follows an endocytic pathway that is dependent on integrin αVβ6, β2-microglobulin, dynamin, and Arf6 but independent of clathrin and caveolin-1.
Dendritic Cell Migration Limits the Duration of CD8+T-Cell Priming to Peripheral Viral Antigen
Authors: Schell Amanda M. , Granger Erica L. , Koczot Frank , Fischer Matthew A. , Norbury Christopher C. 
Published: January 2010

ABSTRACTCD8+T cells (TCD8+) play a crucial role in immunity to viruses. Antiviral TCD8+are initially activated by recognition of major histocompatibility complex (MHC) class I-peptide complexes on the surface of professional antigen-presenting cells (pAPC). Migration of pAPC from the site of infection to secondary lymphoid organs is likely required during a natural infection. Migrating pAPC can be directly infected with virus or may internalize antigen derived from virus-infected cells. The use of experimental virus infections to assess the requirement for pAPC migration in initiation of TCD8+responses has proven difficult to interpret because injected virus can readily drain to secondary lymphoid organs without the need for cell-mediated transport. To overcome this ambiguity, we examined the generation of antigen-specific TCD8+after immunization with recombinant adenoviruses that express antigen driven by skin-specific or ubiquitous promoters. We show that the induction of TCD8+in response to tissue-targeted antigen is less efficient than the response to ubiquitously expressed antigen and that the resulting TCD8+fail to clear all target cells pulsed with the antigenic peptide. This failure to prime a fully functional TCD8+response results from a reduced period of priming to peripherally expressed antigen versus ubiquitously expressed antigen and correlated with a brief burst of pAPC migration from the skin, a requirement for induction of the response to peripheral antigen. These results indicate that a reduced duration of pAPC migration after virus infection likely reduces the amplitude of the TCD8+response, allowing persistence of the peripheral virus.
Influence of Disulfide-Stabilized Structure on the Specificity of Helper T-Cell and Antibody Responses to HIV Envelope Glycoprotein gp120
Authors: Mirano-Bascos Denise , Steede N. Kalaya , Robinson James E. , Landry Samuel J. 
Published: January 2010

ABSTRACTCD4+helper T cells specific for human immunodeficiency virus type 1 (HIV-1) are associated with control of viremia. Nevertheless, vaccines have had limited effectiveness thus far, in part because sequence variability and other structural features of the HIV envelope glycoprotein deflect the immune response. Previous studies indicated that CD4+T-cell epitope dominance is controlled by antigen three-dimensional structure through its influence on antigen processing and presentation. In this work, three disulfide bonds in the outer domain of gp120 were individually deleted in order to destabilize the local three-dimensional structure and enhance the presentation of nearby weakly immunogenic epitopes. However, upon immunization of groups of BALB/c mice, the CD4+T-cell response was broadly reduced for all three variants, and distinct epitope profiles emerged. For one variant, antibody titers were sharply increased, and the antibody exhibited significant CD4-blocking activity.
Structure Function Studies of Vaccinia Virus Host Range Protein K1 Reveal a Novel Functional Surface for Ankyrin Repeat Proteins
Authors: Li Yongchao , Meng Xiangzhi , Xiang Yan , Deng Junpeng 
Published: January 2010

ABSTRACT
Poxvirus host tropism at the cellular level is regulated by virus-encoded host range proteins acting downstream of virus entry. The functioning mechanisms of most host range proteins are unclear, but many contain multiple ankyrin (ANK) repeats, a motif that is known for ligand interaction through a concave surface. We report here the crystal structure of one of the ANK repeat-containing host range proteins, the vaccinia virus K1 protein. The structure, at a resolution of 2.3 Å, showed that K1 consists entirely of ANK repeats, including seven complete ones and two incomplete ones, one each at the N and C terminus. Interestingly, Phe82 and Ser83, which were previously shown to be critical for K1's function, are solvent exposed and located on a convex surface, opposite the consensus ANK interaction surface. The importance of this convex surface was further supported by our additional mutagenesis studies. We found that K1's host range function was negatively affected by substitution of either Asn51 or Cys47 and completely abolished by substitution of both residues. Cys47 and Asn51 are also exposed on the convex surface, spatially adjacent to Phe82 and Ser83. Altogether, our data showed that K1 residues on a continuous convex ANK repeat surface are critical for the host range function, suggesting that K1 functions through ligand interaction and does so with a novel ANK interaction surface.
In-Solution Virus Capture Assay Helps Deconstruct Heterogeneous Antibody Recognition of Human Immunodeficiency Virus Type 1
Authors: Leaman Daniel P. , Kinkead Heather , Zwick Michael B. 
Published: January 2010

ABSTRACT

Human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein (Env) on whole virions is heterogeneous, so molecular analysis of Env with monoclonal antibodies (MAbs) is challenging. Virus capture assays (VCAs) involving immobilized MAbs are typically used, but these assays suffer from immobilization artifacts and do not provide binding constants. Furthermore, we show here that certain HIV-1 neutralizing MAbs, including 2G12, 4E10, 2F5, Z13e1, and D5, will capture virion particles completely devoid of Env. We modified the VCA such that MAbs and virions are incubated in solution, and unbound MAbs are removed prior to the capture step. This modification nearly eliminated evidence of Env-independent binding by MAbs to virions and allowed determination of apparent affinity constants in solution. Three important qualitative observations were further revealed. First, neutralizing MAbs 2F5, 4E10, and Z13e1 against the membrane-proximal external region (MPER) of HIV-1 gp41 were found to capture virions efficiently only if a significant amount of uncleaved gp160 or synthetic MPER peptide was present. Second, we show how non-native forms of Env vary by Env genotype and that Env from HIV-1
JR-FL
is more homogeneously trimeric than that from HIV-1
JR-CSF
. Third, we determined that Env containing all or parts of gp41, including uncleaved gp160, binds spontaneously to free virions. This exogenous Env is an indiscriminate molecular “bridge” between Env-specific Ab and virions and can affect VCA analyses, particularly using pseudotyped virions. Heterogeneity in Env from endogenous and exogenous sources might also subvert humoral immunity to HIV-1, so in-solution VCAs may help to dissect this heterogeneity for vaccine design purposes.
Thumb Injuries in Intercollegiate Men's Lacrosse
Authors: Bowers Andrea L. , Horneff John G. , Baldwin Keith D. , Huffman G. Russell , Sennett Brian J. 
Published: January 2010

Background Men's intercollegiate lacrosse is played at a fast pace and with significant force. Glove protection is required. However, the thumb is at risk because of contact with opponents’ sticks, the ball, other players, and the ground or artificial surface. Purpose To characterize patterns of hand injuries in men's intercollegiate lacrosse and to compare them with those in similar intercollegiate stick-handling sports that require gloves. Study Design Descriptive epidemiology study. Methods The National Collegiate Athletic Association (NCAA) Injury Surveillance System was utilized to evaluate thumb injuries in intercollegiate stick-handling sports (men's lacrosse, women's lacrosse, and men's ice hockey) during 16 intercollegiate seasons. Injuries were defined as events requiring an athlete to seek medical treatment and miss competition. Data were collected for injuries to the thumb, phalanges, and hand. Descriptive statistics were performed to calculate rates of injury per 1000 athlete-exposures and the relative exposure of the thumb with respect to total hand injuries. χ2 testing with the Yates correction for continuity was performed to determine differences in proportions of injury among the 3 sports studied. Results During 16 intercollegiate seasons, there were 692 thumb, finger, and hand injuries in 3 038 255 athlete-exposures. Total thumb injuries were significantly higher in men's lacrosse, accounting for 59.4% of total hand injuries, when compared with women's lacrosse (42%) and men's ice hockey (35.8%) (P < .001). Thumb fractures and contusions were each also found to be significantly more prevalent (P < .001) when compared with women's lacrosse and men's ice hockey. Conclusion Men's intercollegiate lacrosse requires the use of gloves; nonetheless, injury rates of the thumb are significantly elevated in this sport compared with other gloved, stick-handling sports. Recommendations include the development of gloves with improved thumb protection.
In Vivo Evaluation of 3-Dimensional Polycaprolactone Scaffolds for Cartilage Repair in Rabbits
Authors: Martinez-Diaz Santos , Garcia-Giralt Natalia , Lebourg Myriam , Gómez-Tejedor Jose-Antonio , Vila Gemma , Caceres Enric , Benito Pere , Monleón Pradas Manuel , Nogues Xavier , Gómez Ribelles Jose Luis , Monllau Joan Carles 
Published: January 2010

Background Cartilage tissue engineering using synthetic scaffolds allows maintaining mechanical integrity and withstanding stress loads in the body, as well as providing a temporary substrate to which transplanted cells can adhere. Purpose This study evaluates the use of polycaprolactone (PCL) scaffolds for the regeneration of articular cartilage in a rabbit model. Study Design Controlled laboratory study. Methods Five conditions were tested to attempt cartilage repair. To compare spontaneous healing (from subchondral plate bleeding) and healing due to tissue engineering, the experiment considered the use of osteochondral defects (to allow blood flow into the defect site) alone or filled with bare PCL scaffold and the use of PCL-chondrocytes constructs in chondral defects. For the latter condition, 1 series of PCL scaffolds was seeded in vitro with rabbit chondrocytes for 7 days and the cell/scaffold constructs were transplanted into rabbits’ articular defects, avoiding compromising the subchondral bone. Cell pellets and bare scaffolds were implanted as controls in a chondral defect. Results After 3 months with PCL scaffolds or cells/PCL constructs, defects were filled with white cartilaginous tissue; integration into the surrounding native cartilage was much better than control (cell pellet). The engineered constructs showed histologically good integration to the subchondral bone and surrounding cartilage with accumulation of extracellular matrix including type II collagen and glycosaminoglycan. The elastic modulus measured in the zone of the defect with the PCL/cells constructs was very similar to that of native cartilage, while that of the pellet-repaired cartilage was much smaller than native cartilage. Conclusion The results are quite promising with respect to the use of PCL scaffolds as aids for the regeneration of articular cartilage using tissue engineering techniques.
Endothelin-1 receptor blockade induces upregulation of renin-angiotensin-aldosterone system expression in terms of blood pressure regulation
Authors: Bo Yang  , Chen Yun-Dai , Li Tian-De , Feng Quan-Zhou 
Published: January 2010

Objective. To compare the level of expression of the renin-angiotensin-aldosterone system (RAAS) in mice with or without the endothelin-1 receptor antagonist bosentan and to examine the potential value in blood pressure regulation. Materials and methods. Bosentan (10 mg/kg/d) and placebo were given to two groups of male C57BL/6 mice (n=5) from ages 6 to 12 weeks. The mRNAs of liver, kidney and lung were isolated for Northern blot analysis. A further 15 male C57BL/6 mice were divided into three groups (n=5): mice in group A were given the angiotensin II type 1 receptor blocker valsartan (10 mg/kg/d); mice in group B were given bosentan (10 mg/kg/d); and mice in group C were given both valsartan and bosentan (10 mg/ kg/d for each drug). All mice were administered the drugs from 6 to 12 weeks of age and had their systolic blood pressure (SBP) measured at the end of the drug treatments. Results. Northern blot analysis demonstrated that the expression levels of angiotensinogen in liver (p=0.0126), renin in kidney (p=0.002), and angiotensin-converting enzyme in lung (p=0.0041) were upregulated in mice treated with bosentan. No difference in SBP was found among the groups before drug administration. Six weeks after monotherapy with valsartan, SBP was slightly lowered (126±2 vs. 122±3 mmHg, p=0.0381). Monotherapy with bosentan also had a small effect on SBP (126±2 vs. 122±3 mmHg, p=0.0381), whereas dual blockade with valsartan and bosentan significantly lowered SBP (127±3 vs. 103±3 mmHg, p<0.001). Conclusions. We conclude that RAAS components are upregulated under endothelin blockade. Dual blockade of the RAAS and endothelin system is beneficial for blood pressure control.
B cell–specific lentiviral gene therapy leads to sustained B-cell functional recovery in a murine model of X-linked agammaglobulinemia
Authors: Kerns Hannah M. , Ryu Byoung Y. , Stirling Brigid V. , Sather Blythe D. , Astrakhan Alexander , Humblet-Baron Stephanie , Liggitt Denny , Rawlings David J. 
Published: January 2010

AbstractThe immunodeficiency disorder, X-linked agammaglobulinemia (XLA), results from mutations in the gene encoding Bruton tyrosine kinase (Btk). Btk is required for pre-B cell clonal expansion and B-cell antigen receptor signaling. XLA patients lack mature B cells and immunoglobulin and experience recurrent bacterial infections only partially mitigated by life-long antibody replacement therapy. In pursuit of definitive therapy for XLA, we tested ex vivo gene therapy using a lentiviral vector (LV) containing the immunoglobulin enhancer (Eμ) and Igβ (B29) minimal promoter to drive B lineage–specific human Btk expression in Btk/Tec−/− mice, a strain that reproduces the features of human XLA. After transplantation of EμB29-Btk-LV–transduced stem cells, treated mice showed significant, albeit incomplete, rescue of mature B cells in the bone marrow, peripheral blood, spleen, and peritoneal cavity, and improved responses to T-independent and T-dependent antigens. LV-treated B cells exhibited enhanced B-cell antigen receptor signaling and an in vivo selective advantage in the peripheral versus central B-cell compartment. Secondary transplantation showed sustained Btk expression, viral integration, and partial functional responses, consistent with long-term stem cell marking; and serial transplantation revealed no evidence for cellular or systemic toxicity. These findings strongly support pursuit of B lineage–targeted LV gene therapy in human XLA.
Knockdown of Fanconi anemia genes in human embryonic stem cells reveals early developmental defects in the hematopoietic lineage
Authors: Tulpule Asmin , Lensch M. William , Miller Justine D. , Austin Karyn , D'Andrea Alan , Schlaeger Thorsten M. , Shimamura Akiko , Daley George Q. 
Published: January 2010

AbstractFanconi anemia (FA) is a genetically heterogeneous, autosomal recessive disorder characterized by pediatric bone marrow failure and congenital anomalies. The effect of FA gene deficiency on hematopoietic development in utero remains poorly described as mouse models of FA do not develop hematopoietic failure and such studies cannot be performed on patients. We have created a human-specific in vitro system to study early hematopoietic development in FA using a lentiviral RNA interference (RNAi) strategy in human embryonic stem cells (hESCs). We show that knockdown of FANCA and FANCD2 in hESCs leads to a reduction in hematopoietic fates and progenitor numbers that can be rescued by FA gene complementation. Our data indicate that hematopoiesis is impaired in FA from the earliest stages of development, suggesting that deficiencies in embryonic hematopoiesis may underlie the progression to bone marrow failure in FA. This work illustrates how hESCs can provide unique insights into human development and further our understanding of genetic disease.
A comparative study of prenatal development in Miniopterus schreibersii fuliginosus, Hipposideros armiger and H. pratti
Authors: Wang Zhe , Han Naijian , Racey Paul A , Ru Binghua , He Guimei 
Published: January 2010

Abstract
Background
Bats comprise the second largest order of mammals. However, there are far fewer morphological studies of post-implantation embryonic development than early embryonic development in bats.

Results
We studied three species of bats (Miniopterus schreibersii fuliginosus, Hipposideros armiger and H. pratti), representing the two suborders Yangochiroptera and Yinpterochiroptera. Using an established embryonic staging system, we identified the embryonic stages for M. schreibersii fuliginosus, H. armiger and H. pratti and described the morphological changes in each species, including the development of the complex and distinctive nose-leaves in H. armiger and H. pratti. Finally, we compared embryonic and fetal morphology of the three species in the present study with five other species for which information is available.

Conclusion
As a whole, the organogenetic sequence of bat embryos is uniform and the embryos appear homoplastic before Stage 16. Morphological differentiation between species occurs mainly after embryonic Stage 16. Our study provides three new bat species for interspecific comparison of post-implantation embryonic development within the order Chiroptera and detailed data on the development of nose-leaves for bats in the superfamily Rhinolophoidea.
Gene expression profiling to identify eggshell proteins involved in physical defense of the chicken egg
Authors: Jonchère Vincent , Réhault-Godbert Sophie , Hennequet-Antier Christelle , Cabau Cédric , Sibut Vonick , Cogburn Larry A , Nys Yves , Gautron Joel 
Published: January 2010

AbstractBackgroundAs uricoletic animals, chickens produce cleidoic eggs, which are self-contained bacteria-resistant biological packages for extra-uterine development of the chick embryo. The eggshell constitutes a natural physical barrier against bacterial penetration if it forms correctly and remains intact. The eggshell's remarkable mechanical properties are due to interactions among mineral components and the organic matrix proteins. The purpose of our study was to identify novel eggshell proteins by examining the transcriptome of the uterus during calcification of the eggshell. An extensive bioinformatic analysis on genes over-expressed in the uterus allowed us to identify novel eggshell proteins that contribute to the egg's natural defenses.ResultsOur 14 K Del-Mar Chicken Integrated Systems microarray was used for transcriptional profiling in the hen's uterus during eggshell deposition. A total of 605 transcripts were over-expressed in the uterus compared with the magnum or white isthmus across a wide range of abundance (1.1- to 79.4-fold difference). The 605 highly-expressed uterine transcripts correspond to 469 unique genes, which encode 437 different proteins. Gene Ontology (GO) analysis was used for interpretation of protein function. The most over-represented GO terms are related to genes encoding ion transport proteins, which provide eggshell mineral precursors. Signal peptide sequence was found for 54 putative proteins secreted by the uterus during eggshell formation. Many functional proteins are involved in calcium binding or biomineralization--prerequisites for interacting with the mineral phase during eggshell fabrication. While another large group of proteins could be involved in proper folding of the eggshell matrix. Many secreted uterine proteins possess antibacterial properties, which would protect the egg against microbial invasion. A final group includes proteases and protease inhibitors that regulate protein activity in the acellular uterine fluid where eggshell formation takes place.ConclusionsOur original study provides the first detailed description of the chicken uterus transcriptome during formation of the eggshell. We have discovered a cache of about 600 functional genes and identified a large number of encoded proteins secreted into uterine fluid for fabrication of the eggshell and chemical protection of the egg. Some of these uterine genes could prove useful as biological markers for genetic improvement of phenotypic traits (i.e., egg and eggshell quality).