bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects on Immunogenicity by Formulations of Emulsion-Based Adjuvants for Malaria Vaccines
Authors: Fox Christopher B. , Baldwin Susan L. , Vedvick Thomas S. , Angov Evelina , Reed Steven G.
Published: August 2012

New malaria vaccines are urgently needed to improve vaccine protective efficacy. PfCelTOS is a recombinant malaria vaccine antigen that has shown protective efficacy in a small-animal challenge model when combined with a water-in-oil emulsion adjuvant (Montanide ISA 720). In this report, we show that PfCelTOS vaccines containing GLA-SE (a stable oil-in-water emulsion combined with a Toll-like receptor 4 [TLR4] agonist) elicit strong Th1-type immune responses in BALB/c mice. These responses include higher antigen-specific IgG2a antibody titers and more gamma interferon (IFN-γ) production than those seen with a PfCelTOS vaccine containing Montanide ISA 720. Furthermore, reducing the emulsion dose from 2% to 1% or 0.5% (vol/vol) squalene in GLA-SE did not compromise immunogenicity. Emulsion dose titration in the absence of formulated GLA caused some reduction in humoral and cellular immune responses compared to those with the 2% squalene emulsion dose.
Prosthetic Joint Infection Diagnosis Using Broad-Range PCR of Biofilms Dislodged from Knee and Hip Arthroplasty Surfaces Using Sonication
Authors: Gomez Eric , Cazanave Charles , Cunningham Scott A. , Greenwood-Quaintance Kerryl E. , Steckelberg James M. , Uhl James R. , Hanssen Arlen D. , Karau Melissa J. , Schmidt Suzannah M. , Osmon Douglas R. , Berbari Elie F. , Mandrekar Jayawant , Patel Robin
Published: August 2012

Periprosthetic tissue and/or synovial fluid PCR has been previously studied for prosthetic joint infection (PJI) diagnosis; however, few studies have assessed the utility of PCR on biofilms dislodged from the surface of explanted arthroplasties using vortexing and sonication (i.e., sonicate fluid PCR). We compared sonicate fluid 16S rRNA gene real-time PCR and sequencing to culture of synovial fluid, tissue, and sonicate fluid for the microbiologic diagnosis of PJI. PCR sequences generating mixed chromatograms were decatenated using RipSeq Mixed. We studied sonicate fluids from 135 and 231 subjects with PJI and aseptic failure, respectively. Synovial fluid, tissue, and sonicate fluid culture and sonicate fluid PCR had similar sensitivities (64.7, 70.4, 72.6, and 70.4%, respectively;
P
> 0.05) and specificities (96.9, 98.7, 98.3, and 97.8%, respectively;
P
> 0.05). Combining sonicate fluid culture and PCR, the sensitivity was higher (78.5%,
P
< 0.05) than those of individual tests, with similar specificity (97.0%). Thirteen subjects had positive sonicate fluid culture but negative PCR, and 11 had negative sonicate fluid culture but positive PCR (among which 7 had prior use of antimicrobials). Broad-range PCR and culture of sonicate fluid have equivalent performance for PJI diagnosis.
Echinocandin Resistance in Two Candida haemulonii Isolates from Pediatric Patients
Authors: Dominguez Muro Marisol , Motta Fábio de Araújo , Burger Marion , Melo Analy Salles de Azevedo , Dalla-Costa Líbera Maria
Published: August 2012

We report 3 cases of patients with
Candida haemulonii
isolates that were obtained from hemocultures. In 2 of the 3 cases, isolates exhibited resistance to echinocandins and fluconazole. This is the first report of an echinocandin-resistant species of this fungus in pediatric patients.
Molecular Epidemiological Study of Enteroviruses Associated with Encephalitis in Children from India
Authors: Kumar Arvind , Shukla Deepti , Kumar Rashmi , Idris Mohammad Z. , Misra Usha K. , Dhole Tapan N.
Published: August 2012

Enteroviruses have been reported in encephalitis cases. However, clinical and epidemiological characteristics of enteroviruses in encephalitis are not fully established. We prospectively investigated 204 children with encephalitis over a period of 2 years (2009 to 2010) for enterovirus. Enterovirus was detected in 45 specimens (22.1%); of these, 40 were typed by seminested reverse transcription-PCR (RT-PCR) and sequencing of the VP1 gene. Molecular typing of enterovirus revealed the predominance of echovirus 21 associated with an epidemic during the rainy seasons of 2010 and the circulation of echovirus 1, coxsackievirus B1, enterovirus 75, enterovirus 76, coxsackievirus B5, and echovirus 19. The nucleotide divergence among echovirus 21 strains was 0 to 2% at the nucleotide level. This study suggests that enterovirus is an important cause of encephalitis in children from India. To our knowledge, this is the first report of echovirus 21 in encephalitis cases worldwide.
Prospective Genotyping of Hospital-Acquired Methicillin-Resistant Staphylococcus aureus Isolates by Use of a Novel, Highly Discriminatory Binary Typing System
Authors: O'Sullivan Matthew V. N. , Zhou Fei , Sintchenko Vitali , Gilbert Gwendolyn L.
Published: August 2012

In settings of high methicillin-resistant
Staphylococcus aureus
(MRSA) prevalence, detection of nosocomial transmission events can be difficult without strain typing. Prospective typing of all MRSA isolates could potentially identify transmission in a timely fashion, making infection control responses to outbreaks more effective. We describe the development and evaluation of a novel 19-target binary typing system for MRSA using the multiplex-PCR/reverse line blot hybridization platform. Pulse-field gel electrophoresis (PFGE),
spa
typing, and phage-derived open reading frame (PDORF) typing were performed for comparison. The system was utilized to identify transmission events in three general surgical wards over a 12-month period. Initial MRSA isolates from 273 patients were differentiated into 55 unique binary types. One or more potential contacts colonized with the same MRSA strain were identified in 69 of 87 cases (79%) in which definite or possible nosocomial MRSA acquisition had occurred. The discriminatory power of the typing system was similar to that of PFGE (Simpson's index of diversity [
D
] = 0.994, versus 0.987) and higher than that of
spa
typing (
D
= 0.926). Strain typing reduced the total number of potential MRSA-colonized source contacts from 859 to 212 and revealed temporal clustering of transmission events. Prospective MRSA typing using this novel binary typing method can rapidly identify nosocomial transmission events, even in high-prevalence settings, which allows timely infection control interventions. The system is rapid, inexpensive, discriminatory, and suitable for routine, high-throughput use in the hospital microbiology laboratory.
Molecular Epidemiology of Acinetobacter baumannii Bloodstream Isolates Obtained in the United States from 1995 to 2004 Using rep-PCR and Multilocus Sequence Typing
Authors: Higgins Paul G. , Janßen Katharina , Fresen Maximilian M. , Wisplinghoff Hilmar , Seifert Harald
Published: August 2012

Using a repetitive-sequence-based (rep)-PCR (DiversiLab), we have molecularly typed
Acinetobacter
nosocomial bloodstream isolates (
Acinetobacter
baumannii
[
n
= 187],
Acinetobacter
pittii
[
n
= 23], and
Acinetobacter
nosocomialis
[
n
= 61]) obtained from patients hospitalized in U.S. hospitals over a 10-year period (1995-2004) during a nationwide surveillance study (Surveillance and Control of Pathogens of Epidemiological Importance [SCOPE]). Patterns of
A. baumannii
rep-PCR were compared to those of previously identified international clonal lineages (ICs) and were further investigated by multilocus sequence typing (MLST) to compare the two typing methods. Forty-seven of the
A. baumannii
isolates clustered with the previously defined IC 2. ICs 1, 3, 6, and 7 were also detected. The remaining 81 isolates were unrelated to the described ICs. In contrast,
A. pittii
and
A. nosocomialis
isolates were more heterogeneous, as determined by rep-PCR. Our MLST results were in good correlation with the rep-PCR clusters. Our study confirms previous data indicating the predominance of a few major clonal
A. baumannii
lineages in the United States, particularly IC 2. The presence in the United States of
A. baumannii
ICs 1, 2, and 3 from as early as 1995 suggests that global dissemination of these lineages was an early event.
First Human Case of Pulmonary Fungal Ball Due to a Perenniporia Species (a Basidiomycete)
Authors: Chowdhary Anuradha , Agarwal Kshitij , Kathuria Shallu , Singh Pradeep Kumar , Roy P. , Gaur S. N. , Rodrigues Anderson M. , de Hoog G. S. , Meis Jacques F.
Published: August 2012

Perenniporia
species are basidiomycetes, resupinate shelf fungi responsible for white rot decay of wood. Here, we report for the first time an intracavitary pulmonary fungal ball due to a species of
Perenniporia
that has not been recognized so far as a human pathogen. The fungus was identified by sequencing of the partial ribosomal operon of a culture from a clinical specimen.
Proteomic Characterization of Bovine Herpesvirus 4 Extracellular Virions
Authors: Lété Céline , Palmeira Leonor , Leroy Baptiste , Mast Jan , Machiels Bénédicte , Wattiez Ruddy , Vanderplasschen Alain , Gillet Laurent
Published: August 2012

Gammaherpesviruses are important pathogens in human and animal populations. During early events of infection, these viruses manipulate preexisting host cell signaling pathways to allow successful infection. The different proteins that compose viral particles are therefore likely to have critical functions not only in viral structures and in entry into target cell but also in evasion of the host's antiviral response. In this study, we analyzed the protein composition of bovine herpesvirus 4 (BoHV-4), a close relative of the human Kaposi's sarcoma-associated herpesvirus. Using mass spectrometry-based approaches, we identified 37 viral proteins associated with extracellular virions, among which 24 were resistant to proteinase K treatment of intact virions. Analysis of proteins associated with purified capsid-tegument preparations allowed us to define protein localization. In parallel, in order to identify some previously undefined open reading frames, we mapped peptides detected in whole virion lysates onto the six frames of the BoHV-4 genome to generate a proteogenomic map of BoHV-4 virions. Furthermore, we detected important glycosylation of three envelope proteins: gB, gH, and gp180. Finally, we identified 38 host proteins associated with BoHV-4 virions; 15 of these proteins were resistant to proteinase K treatment of intact virions. Many of these have important functions in different cellular pathways involved in virus infection. This study extends our knowledge of gammaherpesvirus virions composition and provides new insights for understanding the life cycle of these viruses.
HIV Control through a Single Nucleotide on the HLA-B Locus
Authors: Kløverpris Henrik N. , Harndahl Mikkel , Leslie Alasdair J. , Carlson Jonathan M. , Ismail Nasreen , van der Stok Mary , Huang Kuan-Hsiang Gary , Chen Fabian , Riddell Lynn , Steyn Dewald , Goedhals Dominique , van Vuuren Cloete , Frater John , Walker Bruce D. , Carrington Mary , Ndung'u Thumbi , Buus Søren , Goulder Philip
Published: August 2012

Genetic variation within the HLA-B locus has the strongest impact on HIV disease progression of any polymorphisms within the human genome. However, identifying the exact mechanism involved is complicated by several factors. HLA-Bw4 alleles provide ligands for NK cells and for CD8 T cells, and strong linkage disequilibrium between HLA class I alleles complicates the discrimination of individual HLA allelic effects from those of other HLA and non-HLA alleles on the same haplotype. Here, we exploit an experiment of nature involving two recently diverged HLA alleles, HLA-B*42:01 and HLA-B*42:02, which differ by only a single amino acid. Crucially, they occur primarily on identical HLA class I haplotypes and, as Bw6 alleles, do not act as NK cell ligands and are therefore largely unconfounded by other genetic factors. We show that in an outbred cohort (n= 2,093) of HIV C-clade-infected individuals, a single amino acid change at position 9 of the HLA-B molecule critically affects peptide binding and significantly alters the cytotoxic T lymphocyte (CTL) epitopes targeted, measured directlyex vivoby gamma interferon (IFN-γ) enzyme-linked immunospot (ELISPOT) assay (P= 2 × 10−10) and functionally through CTL escape mutation (P= 2 × 10−8). HLA-B*42:01, which presents multiple Gag epitopes, is associated with a 0.52 log10lower viral-load set point than HLA-B*42:02 (P= 0.02), which presents no p24 Gag epitopes. The magnitude of this effect from a single amino acid difference in the HLA-A*30:01/B*42/Cw*17:01 haplotype is equivalent to 75% of that of HLA-B*57:03, the most protective HLA class I allele in this population. This naturally controlled experiment represents perhaps the clearest demonstration of the direct impact of a particular HIV-specific CTL on disease control.
Antibody-Dependent Cellular Cytotoxicity-Mediating Antibodies from an HIV-1 Vaccine Efficacy Trial Target Multiple Epitopes and Preferentially Use the VH1 Gene Family
Authors: Bonsignori Mattia , Pollara Justin , Moody M. Anthony , Alpert Michael D. , Chen Xi , Hwang Kwan-Ki , Gilbert Peter B. , Huang Ying , Gurley Thaddeus C. , Kozink Daniel M. , Marshall Dawn J. , Whitesides John F. , Tsao Chun-Yen , Kaewkungwal Jaranit , Nitayaphan Sorachai , Pitisuttithum Punnee , Rerks-Ngarm Supachai , Kim Jerome H. , Michael Nelson L. , Tomaras Georgia D. , Montefiori David C. , Lewis George K. , DeVico Anthony , Evans David T. , Ferrari Guido , Liao Hua-Xin , Haynes Barton F.
Published: August 2012

The ALVAC-HIV/AIDSVAX-B/E RV144 vaccine trial showed an estimated efficacy of 31%. RV144 secondary immune correlate analysis demonstrated that the combination of low plasma anti-HIV-1 Env IgA antibodies and high levels of antibody-dependent cellular cytotoxicity (ADCC) inversely correlate with infection risk. One hypothesis is that the observed protection in RV144 is partially due to ADCC-mediating antibodies. We found that the majority (73 to 90%) of a representative group of vaccinees displayed plasma ADCC activity, usually (96.2%) blocked by competition with the C1 region-specific A32 Fab fragment. Using memory B-cell cultures and antigen-specific B-cell sorting, we isolated 23 ADCC-mediating nonclonally related antibodies from 6 vaccine recipients. These antibodies targeted A32-blockable conformational epitopes (n= 19), a non-A32-blockable conformational epitope (n= 1), and the gp120 Env variable loops (n= 3). Fourteen antibodies mediated cross-clade target cell killing. ADCC-mediating antibodies displayed modest levels of V-heavy (VH) chain somatic mutation (0.5 to 1.5%) and also displayed a disproportionate usage of VH1 family genes (74%), a phenomenon recently described for CD4-binding site broadly neutralizing antibodies (bNAbs). Maximal ADCC activity of VH1 antibodies correlated with mutation frequency. The polyclonality and low mutation frequency of these VH1 antibodies reveal fundamental differences in the regulation and maturation of these ADCC-mediating responses compared to VH1 bNAbs.
Kaposi's Sarcoma-Associated Herpesvirus MicroRNAs Target IRAK1 and MYD88, Two Components of the Toll-Like Receptor/Interleukin-1R Signaling Cascade, To Reduce Inflammatory-Cytokine Expression
Authors: Abend Johanna R. , Ramalingam Dhivya , Kieffer-Kwon Philippe , Uldrick Thomas S. , Yarchoan Robert , Ziegelbauer Joseph M.
Published: August 2012

Kaposi's sarcoma (KS)-associated herpesvirus (KSHV) is the causative agent of KS, an important AIDS-associated malignancy. KSHV expresses at least 18 different mature microRNAs (miRNAs). We identified interleukin-1 receptor (IL-1R)-associated kinase 1 (IRAK1) as a potential target of miR-K12-9 (miR-K9) in an array data set examining changes in cellular gene expression levels in the presence of KSHV miRNAs. Using 3′-untranslated region (3′UTR) luciferase reporter assays, we confirmed that miR-K9 and other miRNAs inhibit IRAK1 expression. In addition, IRAK1 expression is downregulated in cells transfected with miR-K9 and duringde novoKSHV infection. IRAK1 is an important component of the Toll-like receptor (TLR)/IL-1R signaling cascade. The downregulation of IRAK1 by miR-K9 resulted in the decreased stimulation of NF-κB activity in endothelial cells treated with IL-1α and in B cells treated with a TLR7/8 agonist. Interestingly, miR-K9 had a greater effect on NF-κB activity than did a small interfering RNA (siRNA) targeting IRAK1 despite the more efficient downregulation of IRAK1 expression with the siRNA. We hypothesized that KSHV miRNAs may also be regulating a second component of the TLR/IL-1R signaling cascade, resulting in a stronger phenotype. Reanalysis of the array data set identified myeloid differentiation primary response protein 88 (MYD88) as an additional potential target. 3′UTR luciferase reporter assays and Western blot analysis confirmed the targeting of MYD88 by miR-K5. The presence of miR-K9 and miR-K5 inhibited the production of IL-6 and IL-8 upon the IL-1α stimulation of endothelial cells. These results demonstrate KSHV-encoded miRNAs regulating the TLR/IL-1R signaling cascade at two distinct points and suggest the importance of these pathways during viral infection.
Identification of the HIV-1 NC Binding Interface in Alix Bro1 Reveals a Role for RNA
Authors: Sette Paola , Dussupt Vincent , Bouamr Fadila
Published: August 2012

HIV-1 recruits members of ESCRT, the cell membrane fission machinery that promotes virus exit. HIV-1 Gag protein gains access to ESCRT directly by binding Alix, an ESCRT-associated protein that promotes budding. The Alix Bro1 and V domains bind Gag NC and p6 regions, respectively. Whereas V-p6 binding and function are well characterized, residues in Bro1 that interact with NC and their functional contribution to Alix-mediated HIV-1 budding are unknown. We mapped Bro1 residues that constitute the NC binding interface and found that they are critical for function. Intriguingly, residues involved in interactions on both sides of the Bro1-NC interface are positively charged, suggesting the involvement of a negatively charged cellular factor serving as a bridge. Nuclease treatment eliminated Bro1-NC interactions, revealing the involvement of RNA. These findings establish a direct role for NC in mediating interactions with ESCRT necessary for virus release and report the first evidence of RNA involvement in such recruitments.
Packaging Accessory Protein P7 and Polymerase P2 Have Mutually Occluding Binding Sites inside the Bacteriophage ϕ6 Procapsid
Authors: Nemecek Daniel , Qiao Jian , Mindich Leonard , Steven Alasdair C. , Heymann J. Bernard
Published: August 2012

Bacteriophage ϕ6 is a double-stranded RNA (dsRNA) virus whose genome is packaged sequentially as three single-stranded RNA (ssRNA) segments into an icosahedral procapsid which serves as a compartment for genome replication and transcription. The procapsid shell consists of 60 copies each of P1
A
and P1
B
, two nonequivalent conformers of the P1 protein. Hexamers of the packaging ATPase P4 are mounted over the 5-fold vertices, and monomers of the RNA-dependent RNA polymerase (P2) attach to the inner surface, near the 3-fold axes. A fourth protein, P7, is needed for packaging and also promotes assembly. We used cryo-electron microscopy to localize P7 by difference mapping of procapsids with different protein compositions. We found that P7 resides on the interior surface of the P1 shell and appears to be monomeric. Its binding sites are arranged around the 3-fold axes, straddling the interface between two P1
A
subunits. Thus, P7 may promote assembly by stabilizing an initiation complex. Only about 20% of the 60 P7 binding sites were occupied in our preparations. P7 density overlaps P2 density similarly mapped, implying mutual occlusion. The known structure of the ϕ12 homolog fits snugly into the P7 density. Both termini—which have been implicated in RNA binding—are oriented toward the adjacent 5-fold vertex, the entry pathway of ssRNA segments. Thus, P7 may promote packaging either by interacting directly with incoming RNA or by modulating the structure of the translocation pore.
Memory CD4
+
T Lymphocytes in the Gastrointestinal Tract Are a Major Source of Cell-Associated Simian Immunodeficiency Virus in Chronic Nonpathogenic Infection of African Green Monkeys
Authors: Schmitz Joern E. , Ma Zhong-Min , Hagan Emily A. , Wilks Andrew B. , Furr Kathryn L. , Linde Caitlyn H. , Zahn Roland C. , Brenchley Jason M. , Miller Christopher J. , Permar Sallie R.
Published: August 2012

Simian immunodeficiency virus (SIV) infection of natural hosts is characterized by nonpathogenic chronic viremia, maintenance of gastrointestinal epithelial barrier integrity, and low numbers of target cells. Assessment of cell-associated virus load in T cell subsets in multiple anatomic compartments of chronically SIV-infected sabeus African green monkeys (AGMs) revealed that gastrointestinal memory CD4
+
T lymphocytes are a major source of cell-associated virus and a significant contributor to SIV viremia in AGMs.
Modulation of Ribosomal Frameshifting Frequency and Its Effect on the Replication of Rous Sarcoma Virus
Authors: Nikolić Emily I. C. , King Louise M. , Vidakovic Marijana , Irigoyen Nerea , Brierley Ian
Published: August 2012

Programmed −1 ribosomal frameshifting is widely used in the expression of RNA virus replicases and represents a potential target for antiviral intervention. There is interest in determining the extent to which frameshifting efficiency can be modulated before virus replication is compromised, and we have addressed this question using the alpharetrovirus Rous sarcoma virus (RSV) as a model system. In RSV, frameshifting is essential in the production of the Gag-Pol polyprotein from the overlapping
gag
and
pol
coding sequences. The frameshift signal is composed of two elements, a heptanucleotide slippery sequence and, just downstream, a stimulatory RNA structure that has been proposed to be an RNA pseudoknot. Point mutations were introduced into the frameshift signal of an infectious RSV clone, and virus replication was monitored following transfection and subsequent infection of susceptible cells. The introduced mutations were designed to generate a range of frameshifting efficiencies, yet with minimal impact on encoded amino acids. Our results reveal that point mutations leading to a 3-fold decrease in frameshifting efficiency noticeably reduce virus replication and that further reduction is severely inhibitory. In contrast, a 3-fold stimulation of frameshifting is well tolerated. These observations suggest that small-molecule inhibitors of frameshifting are likely to have potential as agents for antiviral intervention. During the course of this work, we were able to confirm, for the first time
in vivo
, that the RSV stimulatory RNA is indeed an RNA pseudoknot but that the pseudoknot
per se
is not absolutely required for virus viability.
Intensity and correlates of multidimensional problems in HIV patients receiving integrated palliative care in sub-Saharan Africa
Authors: Harding Richard , Selman Lucy , Agupio Godfrey , Dinat Natalya , Downing Julia , Gao Wei , Gwyther Liz , Mashao Thandi , Mmoledi Keletso , Moll Anthony , Mpanga Sebuyira Lydia , Ikin Barbara , Higginson Irene J
Published: August 2012

Background

Despite global clinical guidance that HIV patients should have multidimensional care integrated into their management, there has been very limited data to guide practice since the advent of treatment. This study aimed to determine the three-day period intensity of problems (physical, psychological, social and spiritual) among HIV patients receiving integrated palliative care in sub-Saharan Africa, and to identify associations with problem severity.

Methods

A sample of 230 consecutive adult patients attending five sites in South Africa and Uganda gave self-report data using a well-validated outcome scale. Multivariable regression models determine the association of patient characteristics with intensity of three scale factors.

Results

The most burdensome problems were (in descending order) pain, worry, symptoms, and adequate information to plan for the future. Interestingly, CD4 counts were available on file for only 59.1% of patients. In multivariate analyses, being cared for at home was associated with poorer physical/psychological factor score (B=−0.192, 95% CI −2.566 -0.464, p=0.005), while being on ART was associated with better factor score (B=0.187, 95% CI=0.424 23.80, p=0.005). For the existential/spiritual factor, being cared for at home was associated with a worse factor score (B=−0.306, 95% CI −2.776 −1.128, p<0.001). ART use was not associated with either the interpersonal or spiritual/existential factors.

Discussion

These self-report data reveal a high burden of both physical and psychological problems, and that communication from professionals is insufficient. Patients receiving home care may require additional support to enhance wellbeing, and treatment may not affect interpersonal and existential/spiritual wellbeing.
Identification of two stably expressed QTLs for fat content in rice (Oryza sativa)
Authors: Shen Yingyue , Zhang Wenwei , Liu Xi , Chen Liangming , Liu Shijia , Zheng Leina , Li Jingjing , Chen Yilin , Wu Tao , Yu Yang , Zhong Zhengzheng , Jiang Ling , Wan Jianmin
Published: August 2012

Fat content (FC) is an important component of the nutritional quality of the rice ( Oryza sativa L.) grain and a partial determinant of grain quality. Three FC QTLs were identified from an analysis of a set of rice ‘Kasalath’/‘Koshihikari’ backcross inbred lines, which were grown in three independent environments. Two of these QTLs (qFC7.1 and qFC7.2) were located on chromosome 7, and they were detected in all three environments. The presence of qFC7.1 and qFC7.2 was further confirmed by testing a set of ‘Kasalath’ (donor) / ‘Koshihikari’ (recipient) chromosome segment substitution lines (CSSLs) across six environments. Both QTLs significantly increased grain FC and they might be involved in lipid metabolism. The two QTLs were stably expressed in a number of environments and populations, making them suitable candidates for the improvement of FC via marker assisted breeding.
Genomic characteristics of a diploid F4festulolium hybrid (Lolium multiflorum×Festuca arundinacea)
Authors: Akiyama Yukio , Kimura Kenji , Yamada-Akiyama Hitomi , Kubota Akito , Takahara Yoshinori , Ueyama Yasufumi
Published: August 2012

The grass festulolium, a hybrid between the genera Festuca and Lolium , has a variety of beneficial agronomic attributes derived from both parents. Compared with high-ploidy festulolium, diploid festulolium is well suited to stabilizing ploidy and for studying agronomic traits and genetic relationships. We sought to produce a diploid festulolium hybrid that was resistant to summer depression, by hybridizing diploid Lolium multiflorum Lam. and hexaploid Festuca arundinacea Schreb., which has a high tolerance to summer depression. We obtained seven diploid F4plants that were capable of surviving the extremely hot summer in Morioka, Japan, in 2010, which was 2.7 °C higher than the average summer temperature. The observed resistance to summer depression in these plants was likely due to heat stress tolerance. The genomic constitutions of these seven hybrids were analyzed by GISH, and the chromosomal characteristics of a single diploid F4was analyzed by FISH using rDNA probes. The results showed that although no Festuca-specific genome remained in any of the seven diploid F4plants, extensive chromosomal rearrangement was observed in one of them. Our findings suggested that hybridizing diploid L. multiflorum and hexaploid F. arundinacea may be useful for modifying chromosome architecture in the Lolium genome with potential applications in chromosome engineering.
Homing endonucleases: DNA scissors on a mission
Authors: Hafez Mohamed , Hausner Georg
Published: August 2012

Buried within the genomes of many microorganisms are genetic elements that encode rare-cutting homing endonucleases that assist in the mobility of the elements that encode them, such as the self-splicing group I and II introns and in some cases inteins. There are several different families of homing endonucleases and their ability to initiate and target specific sequences for lateral transfers makes them attractive reagents for gene targeting. Homing endonucleases have been applied in promoting DNA modification or genome editing such as gene repair or “gene knockouts”. This review examines the categories of homing endonucleases that have been described so far and their possible applications to biotechnology. Strategies to engineer homing endonucleases to alter target site specificities will also be addressed. Alternatives to homing endonucleases such as zinc finger nucleases, transcription activator-like effector nucleases, triplex forming oligonucleotide nucleases, and targetrons are also briefly discussed.
Rapid identification of Amaranthus caudatus and Amaranthus hypochondriacus by sequencing and PCR–RFLP analysis of two starch synthase genes
Authors: Park Young-Jun , Nishikawa Tomotaro
Published: August 2012

The objective of this study was to develop a PCR–RFLP method to identity the cultivated species of grain amaranth based on variations in the sequences of their starch synthase genes. We sequenced the SSSI and GBSSI loci in 126 accessions of cultivated grain amaranth collected from diverse locations around the world. We aligned the gene sequences and searched for restriction enzyme cleavage sites specific to each species for use in the PCR–RFLP analysis. Our analyses indicated that EcoRI would recognize the sequence 5′-GAATT/C-3′ in the SSSI gene from Amaranthus caudatus L., and TaqI would recognize the sequence 5′-T/CGA-3′ in the GBSSI gene from Amaranthus hypochondriacus L. The PCR products obtained using gene-specific primers were 423 bp (SSSI) and 627 or 635 bp (GBSSI) in length. These products were cut with different restriction enzymes resulting in species-specific RFLP patterns that could be used to distinguish among the cultivated grain amaranths. The results clearly showed that A. caudatus and A. hypochondriacus were easily differentiated at the species level using this method. Therefore, the PCR–RFLP method targeting amaranth starch synthase genes is simple and rapid, and it will be a useful tool for the identification of cultivated species of grain amaranth.
Tweaking the cholesterol efflux capacity of reconstituted HDL
Authors: Ma Cheng-I J. , Beckstead Jennifer A. , Thompson Airlia , Hafiane Anouar , Wang Rui Hao Leo , Ryan Robert O. , Kiss Robert S.
Published: August 2012

Mechanisms to increase plasma high-density lipoprotein (HDL) or to promote egress of cholesterol from cholesterol-loaded cells (e.g., foam cells from atherosclerotic lesions) remain an important target to regress heart disease. Reconstituted HDL (rHDL) serves as a valuable vehicle to promote cellular cholesterol efflux in vitro and in vivo. rHDL were prepared with wild type apolipoprotein (apo) A-I and the rare variant, apoA-I Milano (M), and each apolipoprotein was reconstituted with phosphatidylcholine (PC) or sphingomyelin (SM). The four distinct rHDL generated were incubated with CHO cells, J774 macrophages, and BHK cells in cellular cholesterol efflux assays. In each cell type, apoA-I(M) SM-rHDL promoted the greatest cholesterol efflux. In BHK cells, the cholesterol efflux capacities of all four distinct rHDL were greatly enhanced by increased expression of ABCG1. Efflux to PC-containing rHDL was stimulated by transfection of a nonfunctional ABCA1 mutant (W590S), suggesting that binding to ABCA1 represents a competing interaction. This interpretation was confirmed by binding experiments. The data show that cholesterol efflux activity is dependent upon the apoA-I protein employed, as well as the phospholipid constituent of the rHDL. Future studies designed to optimize the efflux capacity of therapeutic rHDL may improve the value of this emerging intervention strategy.
Identification of regulatory regions and regulatory protein complexes of theSpirulinadesDgene under temperature stress conditions: Role of thioredoxin as an inactivator of a transcriptional repressor GntR under low-temperature stress
Authors: Kurdrid Pavinee , Phuengcharoen Phuttawadee , Yutthanasirikul Rayakorn , Roytrakul Sittiruk , Paemanee Atchara , Cheevadhanarak Supapon , Hongsthong Apiradee
Published: August 2012

In the present study, electrophoretic mobility shift assays were used to identify temperature responsive elements in the 5′ upstream region (5′ UTR) of the Spirulina desD gene. Overlapping, synthetic oligonucleotides of both sense and anti-sense strands that spanned the entire 5′ UTR of the gene were analyzed. The responsive DNA-binding protein complexes were identified using liquid chromatography–tandem mass spectrometry. The results indicated that the cold-responsive elements were located at –453 to –247, –197 to –151, –105 to –76, and –50 to –1, whereas the low-temperature specific regulatory regions were located at –372 to –352. Moreover, the heat-responsive elements were located at –347 to –243, –197 to –151, and –124 to –1, whereas the high-temperature specific elements were located between –130 to –101 and –30 to –1. In terms of regulatory protein complexes under the two stress conditions, Trx was only detected in the low-temperature responsive protein complex, and divalent cations were essential for the binding of the protein complex to the regulatory elements. Furthermore, Trx was shown to play a critical role as a reducing agent that inactivates the Spirulina desD repressor, GntR. Consequently, the desD gene expression is induced under the low-temperature condition.
An exon-centric perspective1Canadian Society of Molecular Biosciences (CSMB) Senior Investigator Award
Authors: Blencowe Benjamin J.
Published: August 2012

During the past ten years, remarkable progress has been made in our understanding of the complexity and regulation of alternative splicing. The generation of large datasets of quantitative alternative splicing profiling information has revealed that transcripts from at least 95% of multi-exon human genes undergo alternative splicing, and that thousands of exons in mammalian transcriptomes are subject to striking regulatory patterns. Together with advanced computational methods, these datasets have enabled the inference of a predictive code for tissue-dependent alternative splicing. This code has further provided new insight into splicing regulatory mechanisms. Collectively, these approaches are revealing the existence of discrete networks of exons that are coordinately regulated in diverse biologically normal and disease contexts. A major challenge ahead is to systematically determine the functions of exons comprising these exon networks as well as the factors and mechanisms responsible for their regulation. This perspective provides an account of progress in these areas and also discusses future avenues of exon-centric exploration.
Biophysical and structural studies of the human calcium- and integrin-binding protein family: understanding their functional similarities and differences
Authors: Huang Hao , Bogstie Joel N. , Vogel Hans J.
Published: August 2012

The human calcium- and integrin-binding protein 1 (CIB1) plays important roles in various cellular functions. In this study, three other members of this protein family (CIB2–4: CIB2, CIB3, and CIB4) were purified and subsequently characterized using biophysical and structural approaches. As expected from sequence alignments, CIB2–4 were shown to bind calcium (Ca2+) and magnesium (Mg2+) ions. Binding of Ca2+ or Mg2+ ions changes the secondary structure of CIB2–4 and the exposure of hydrophobic surface area. Ca2+ and Mg2+ ions also stabilize the tertiary structures for CIB2 and CIB3. Through in vitro binding experiments, we show that CIB2 can interact with the integrin αIIb cytoplasmic domain and the integrin α7b membrane-proximal fragment. Fluorescence experiments using a 7-azatryptophan labeled peptide demonstrate that CIB2, CIB3, and CIB4 are binding partners for the integrin αIIb subunit, which suggests that they are potentially involved in regulating integrin αIIb subunit activation. The distinct responses of αIIb to the different CIB3 and CIB4 metal (Ca2+ and Mg2+) binding states imply a potential connection between the calcium and integrin signaling pathways.
Repetitive mechanical stretching modulates transforming growth factor-β induced collagen synthesis and apoptosis in human patellar tendon fibroblasts
Authors: Jiang Chaoyin , Shao Lei , Wang Qiaojie , Dong Yang
Published: August 2012

The cellular and molecular mechanisms underlying the development of tendinopathy are not clear, but inflammatory mediators produced by tendon fibroblasts in response to repetitive mechanical loading may be an important factor for this illness. In this study, we explored the effect of cyclic mechanical stretching on collagen synthesis and apoptosis of human patellar tendon fibroblasts (HPTFs). The role of a candidate inflammatory mediator, transforming growth factor-β1 (TGFβ1), which we identified in a cytokine antibody array, in collagen synthesis and apoptosis during repetitive mechanical stretching was also investigated. Our results showed that there was a significant increase in collagen type I synthesis at 4% and 8% stretch. Significantly, enhancement of apoptosis may account for the observed decrease in fibroblast numbers after 8% stretching. Furthermore, the exogenous addition of an anti-TGFβ1 antibody or gene silencing by si-TGFβ1 eliminated the increase in collagen type I production and activities of caspases during apoptosis under cyclic uniaxial stretching conditions. These results suggest that TGFβ1 may take part in the increase of cellular production of collagen type I and apoptosis during the development of tendinopathy. Furthermore, caspase 8 mediates activation of caspase 3 and poly ADP-ribose polymerase (PARP) cleavage during TGFβ1-induced apoptosis in stretching HPTFs.
HEAVY PSEUDOSCALAR-MESON DECAY CONSTANTS WITH STRANGENESS FROM THE EXTENDED NONLOCAL CHIRAL-QUARK MODEL
Authors: NAM SEUNG-IL
Published: August 2012

We study the weak-decay constants for the heavy pseudoscalar mesons, D, Ds, B and Bs. For this purpose, we employ the extended nonlocal chiral-quark model (ExNLChQM), motivated by the heavy-quark effective field theory as well as the instanton-vacuum configuration. In addition to the heavy-quark symmetry and the nonlocal interactions between quarks and pseudoscalar mesons in ExNLChQM, a correction for the strange-quark content inside Ds and Bs is also taken into account and found to be crucial to reproduce the empirical values. From those numerical results, we obtain fD, Ds, B, Bs = (207.53, 262.56, 208.13, 262.39) MeV , which are in good agreement with experimental data and other theoretical estimations. Using those numerical results, we estimate the CKM matrix elements and the Cabibbo angle with the various mesonic and leptonic heavy-meson decay channels, resulting in (|Vcd|, |Vcs|, |Vub|, |Vtd|/|Vts|) = (0.224, 0.968, <5.395×10-3, 0.215) and θC = 12.36° which are well compatible with available data.
SCALAR MODULI, WALL CROSSING AND PHENOMENOLOGICAL PREDICTIONS
Authors: BELLUCCI STEFANO , TIWARI BHUPENDRA NATH
Published: August 2012

We present the scalar moduli stabilization from the perspective of the real intrinsic geometry. In this paper, we describe the physical nature of the vacuum moduli fluctuations of an arbitrary Fayet configuration. For finitely many Abelian scalar fields, we show that the framework of the real intrinsic geometry investigates the mixing between the marginal and threshold vacua. Interestingly, we find that the phenomena of wall crossing and the search of the stable vacuum configurations, pertaining to D-term and F-term scalar moduli, can be accomplished for the Abelian charges. For given vacuum expectation values of the moduli scalars, we provide phenomenological aspects of the vacuum fluctuations and phase transitions in the supersymmetry breaking configurations.
PARAMETRIC DOWN CONVERSION OF A BOSONIC THERMOFIELD VACUUM
Authors: PRUDÊNCIO THIAGO
Published: August 2012

We consider a process of parametric down conversion where the input state is a bosonic thermofield vacuum. This state leads to a parametric down conversion, generating an output of two excited photons. Following a thermofield dynamics scheme, the input state, initially in a bosonic thermofield vacuum, and the output states, initially in vacuum states, evolve under a Liouville–von Neumann equation.
UNSUPERVISED DISCOVERY OF VISUAL FACE CATEGORIES
Authors: YANG SHICAI , BEBIS GEORGE , HUSSAIN MUHAMMAD , MUHAMMAD GHULAM , MIRZA ANWAR M.
Published: August 2012

Human faces can be arranged into different face categories using information from common visual cues such as gender, ethnicity, and age. It has been demonstrated that using face categorization as a precursor step to face recognition improves recognition rates and leads to more graceful errors. Although face categorization using common visual cues yields meaningful face categories, developing accurate and robust gender, ethnicity, and age categorizers is a challenging issue. Moreover, it limits the overall number of possible face categories and, in practice, yields unbalanced face categories which can compromise recognition performance. This paper investigates ways to automatically discover a categorization of human faces from a collection of unlabeled face images without relying on predefined visual cues. Specifically, given a set of face images from a group of known individuals (i.e., gallery set), our goal is finding ways to robustly partition the gallery set (i.e., face categories). The objective is being able to assign novel images of the same individuals (i.e., query set) to the correct face category with high accuracy and robustness. To address the issue of face category discovery, we represent faces using local features and apply unsupervised learning (i.e., clustering). To categorize faces in novel images, we employ nearest-neighbor algorithms or learn the separating boundaries between face categories using supervised learning (i.e., classification). To improve face categorization robustness, we allow face categories to share local features as well as to overlap. We demonstrate the performance of the proposed approach through extensive experiments and comparisons using the FERET database.
MONTE-CARLO EXPRESSION DISCOVERY
Authors: CAZENAVE TRISTAN
Published: August 2012

Monte-Carlo Tree Search is a general search algorithm that gives good results in games. Genetic Programming evaluates and combines trees to discover expressions that maximize a given fitness function. In this paper Monte-Carlo Tree Search is used to generate expressions that are evaluated in the same way as in Genetic Programming. Monte-Carlo Tree Search is transformed in order to search expression trees rather than lists of moves. We compare Nested Monte-Carlo Search to UCT (Upper Confidence Bounds for Trees) for various problems. Monte-Carlo Tree Search achieves state of the art results on multiple benchmark problems. The proposed approach is simple to program, does not suffer from expression growth, has a natural restart strategy to avoid local optima and is extremely easy to parallelize.
CP NONCONSERVATION
Authors: HENLEY ERNEST M.
Published: August 2012

CP symmetry is defined and examined. The failure of CP symmetry in the kaon, D and B systems is outlined and discussed. The discussion is extended to leptons.
Inhibition of apelin expression by BMP signaling in endothelial cells
Authors: Poirier Odette , Ciumas Mariana , Eyries Mélanie , Montagne Kevin , Nadaud Sophie , Soubrier Florent
Published: August 2012

The transforming growth factor-β/bone morphogenic protein (BMP) system is a major pathway for angiogenesis and is involved in hereditary vascular diseases. Here we report that the gene encoding the vasoactive and vascular cell growth-regulating peptide apelin is a target of the BMP pathway. We demonstrate that apelin expression is strongly downregulated by BMP in an endothelial cell line as well as in lung endothelial microvascular cells. We show that BMP signals through the BMPR2-SMAD pathway to downregulate apelin expression and that a transcriptional direct and indirect mechanism is required. The BMP-induced downregulation of apelin expression was found to be critical for hypoxia-induced growth of endothelial cells, because the growth inhibitory effect of BMP in this condition is suppressed by enforced expression of apelin. Thus, we describe an important link between a signaling pathway involved in angiogenesis and vascular diseases and a peptide regulating vascular homeostasis.
Lipopolysaccharide prolongs action potential duration in HL-1 mouse cardiomyocytes
Authors: Wondergem Robert , Graves Bridget M. , Li Chuanfu , Williams David L.
Published: August 2012

Sepsis has deleterious effects on cardiac function including reduced contractility. We have shown previously that lipopolysaccharides (LPS) directly affect HL-1 cardiac myocytes by inhibiting Ca2+ regulation and by impairing pacemaker “funny” current, If. We now explore further cellular mechanisms whereby LPS inhibits excitability in HL-1 cells. LPS (1 μg/ml) derived from Salmonella enteritidis decreased rate of firing of spontaneous action potentials in HL-1 cells, and it increased their pacemaker potential durations and decreased their rates of depolarization, all measured by whole cell current clamp. LPS also increased action potential durations and decreased their amplitude in cells paced at 1 Hz with 0.1 nA, and 20 min were necessary for maximal effect. LPS decreased the amplitude of a rapidly inactivating inward current attributed to Na+ and of an outward current attributed to K+; both were measured by whole cell voltage clamp. The K+ currents displayed a resurgent outward tail current, which is characteristic of the rapid delayed-rectifier K+ current, IKr. LPS accordingly reduced outward currents measured with pipette Cs+ substituted for K+ to isolate IKr. E-4031 (1 μM) markedly inhibited IKr in HL-1 cells and also increased action potential duration; however, the direct effects of E-4031 occurred minutes faster than the slow effects of LPS. We conclude that LPS increases action potential duration in HL-1 mouse cardiomyocytes by inhibition of IKr and decreases their rate of firing by inhibition of INa. This protracted time course points toward an intermediary metabolic event, which either decreases available mouse ether-a-go-go (mERG) and Na+ channels or potentiates their inactivation.
Left ventricular output and aortic blood flow in response to changes in preload and afterload in the preterm piglet heart
Authors: Eiby Yvonne A. , Lumbers Eugenie R. , Headrick John P. , Lingwood Barbara E.
Published: August 2012

Low systemic blood flow occurs in up to 30% of infants born at less than 30 wk gestation. It is associated with increased morbidity and mortality, and current treatments are ineffective in 40% of cases. The aim of this study was to assess the ability of the preterm heart to respond to the acute shifts in preload and afterload that occur at the time of birth. Myocardial and coronary vascular function was assessed using an isolated working heart model in term (115 days) and preterm (92 days) piglets. Cardiac output/kg body wt in preterm hearts was ∼50% lower than that of term hearts ( P = 0.001). Pressure development was similar in term and preterm hearts. Elevations in preload increased cardiac output and aortic flow similarly in term and preterm hearts, demonstrating significant preload “reserve”. By contrast, elevations in afterload markedly depressed aortic flow, with a greater proportion of cardiac output being distributed to coronary flow in preterm hearts at high afterloads. The demands of increased workload were associated with greater increases in coronary flow in preterm hearts compared with term hearts. In preterm hearts, exposure to maternal glucocorticoids resulted in increased aortic flow when afterload was below 25 mmHg. These data suggest the preterm heart lacks the functional capacity to acutely adapt to postnatal afterload. To maximize systemic blood flow in preterm infants, treatments limiting afterload, while harnessing significant preload reserve, should be further explored.