bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic diversity, population structure, pollen morphology and cross‐compatibility among Chinese Cymbidiums
Authors: Li Xiaobai , Xiang Lin , Wang Yan , Luo Jie , Wu Chao , Sun Chongbo , Xie Ming 
Published: December 2013

AbstractA total of 85 Chinese Cymbidiums and one Zygopetalum were collected and analysed using 29 simple sequence repeats (SSRs) and 12 intersimple sequence repeats (ISSRs). These Chinese Cymbidiums are some of the most popular cultivars in market. The pairwise genetic distance between these accessions averaged 0.897, ranging from 0.259 to 1.000. A model‐based clustering analysis revealed five genetic groups with serious admixture ancestry, as indicated by a fixation index of 0.156 and only 10.67% genetic variation among groups. By analysing the cross‐compatibility and pollen morphology, Chinese Cymbidiums are revealed to have high compatibility for intra‐ and interspecific crosses. Notably, Zygopetalum mackayi had high compatibility with Chinese Cymbidiums and shared similar morphologies in terms of pollinia and pollen grain. This study is the first to report a successful cross between Zygopetalum and Chinese Cymbidiums. The high compatibility offers the potential for introducing Zygopetalum mackayi's superior traits into Chinese Cymbidiums. The similar pollen morphology as well as the low genetic differentiation might be related to the high cross‐compatibility among these accessions.
Scrambled Self‐Assembly of Bacteriochlorophylls c and e in Aqueous Triton X‐100 Micelles
Authors: Saga Yoshitaka , Saiki Tatsuya , Takahashi Naoya , Shibata Yutaka , Tamiaki Hitoshi 
Published: December 2013

AbstractBacteriochlorophyll (BChl) e was coassembled with BChl c in Triton X‐100 micelles in aqueous solutions. The Qy absorption bands of the coaggregates were positioned between those of aggregates consisting solely of BChl c or e. The electronic absorption spectra of the coaggregates could not be reproduced by linear combinations of the spectra of the aggregates consisting solely of each pigment, but they were in line with the simulated spectra for the self‐aggregates in which both BChls were randomly distributed. These suggest that BChls c and e are not spatially separated; they are homogenously distributed over the self‐aggregates to give electronic spectra that are different from those of the aggregate consisting solely of each pigment. Deaggregation of the scrambled self‐aggregates by excess Triton X‐100 did not produce any spectral components assigned to an aggregate consisting solely of either BChl c or e. Acid‐induced decomposition of the scrambled aggregates showed different kinetics from those of the aggregates consisting solely of each pigment. These also support the homogeneous distribution of BChls c and e in the scrambled self‐aggregates. These results will be useful to investigate the major light‐harvesting antenna systems of green photosynthetic bacteria that contain two kinds of chlorosomal BChls.
Storage of Bovine Reproductive Tissues and RNA Extracts on Ice for 24 h or Repeated Freeze–Thaw Cycles do not Affect RNA Integrity
Authors: França MR , Mesquita FS , Binelli M 
Published: December 2013

ContentsThe aims of this study were to test (i) the effect of time of tissue and RNA extracts storage on ice and (ii) the effect of repeated freeze–thaw cycles on RNA integrity and gene expression of bovine reproductive tissues. Fragments of endometrium (ENDO), corpus luteum (CL) and ampulla (AMP) were subdivided and incubated for 0, 1, 3, 6, 12 or 24 h on ice. RNA extracts were incubated on ice for 0, 3, 12 or 24 h, or exposed to 1, 2, 4 or 6 freeze–thaw cycles. RNA integrity number (RIN) was estimated. Expression of progesterone receptor (PGR) and cyclophilin genes from RNA extracts stored on ice for 0 or 24 h, and 1 or 6 freeze–thaw cycles was measured by qPCR. Tissue and RNA extract incubation on ice, and repeated freeze–thaw cycles did not affect RIN values of RNA from ENDO, CL or AMP. Storage on ice or exposure to freeze–thaw cycles did not affect Cq values for PGR or cyclophilin genes. In conclusion, neither generalized RNA degradation nor specific RNA degradation was affected by storage of tissue or RNA extracts on ice for up to 24 h, or by up to 6 freeze–thaw cycles of RNA extracts obtained from bovine ENDO, CL and AMP.
Flutamide Influences Placental Aldo–Keto Reductase Family 1 Member C1 (AKR1C1) Expression in Pigs
Authors: Grzesiak M , Knapczyk‐Stwora K , Wieciech I , Golas A , Slomczynska M 
Published: December 2013

ContentsAldo–keto reductase family 1 member C1 (AKR1C1) catalyses the conversion of progesterone into inactive 20α‐dihydroxyprogesterone. It is suggested that AKR1C1 expression in the placenta prevents from the cytotoxic effect of progesterone on foetuses during late pregnancy. The aim of the study was to determine whether the anti‐androgen flutamide administered during late pregnancy (83–89 days of gestation) or before parturition (101–107 days of gestation) influences AKR1C1 expression in the porcine placenta. AKR1C1 mRNA and protein levels were measured using real‐time PCR and western blotting, respectively. Immunolocalization of AKR1C1 within placentas was also performed. Flutamide significantly increased AKR1C1 mRNA (p = 0.008) and protein (p = 0.019) expression only during the pre‐parturient period in pigs. AKR1C1 protein was immunolocalized in the epithelial and stromal cells of foetal and maternal part of placenta at both stages of gestation. Following flutamide treatment, the intensity of staining was higher (p = 0.045) on day 108 of gestation. In conclusion, porcine placental AKR1C1 expression seems to be regulated by an androgen signalling pathway and may be involved in foetal survival by preventing the detrimental effect of progesterone.
Fabrication of high quality factor GaAs/InAsSb photonic crystal microcavities by inductively coupled plasma etching and fast wet etching
Authors: González Iván Prieto , Muñoz Camuñez Luis Enrique , Taboada Alfonso González , Robles Urdiales Carmen , Ripalda Cobián Jose María , Postigo Resa Pablo Aitor 
Published: December 2013

The authors demonstrate high quality factor GaAs-based L9 photonic crystal microcavities (PCMs) with embedded InAsSb quantum dots with emission in 1.3 μm at room temperature. The fabrication process uses reactive ion beam etching with a CHF3/N2 gas mixture and reactive ion etching with a BCl3/N2 gas mixture to form PCMs on air-suspended slabs. An optimum N2 partial flux content of 0.65 and a successful removal of deposits formed during the membrane release by a fast wet etching in HF provide optical quality factors (Q-factors) as high as ∼30 000.
Antibody Responses to Bordetella pertussis Fim2 or Fim3 following Immunization with a Whole-Cell, Two-Component, or Five-Component Acellular Pertussis Vaccine and following Pertussis Disease in Children in Sweden in 1997 and 2007
Authors: Hallander Hans , Advani Abdolreza , Alexander Frances , Gustafsson Lennart , Ljungman Margaretha , Pratt Catherine , Hall Ian , Gorringe Andrew R. 
Published: December 2013

ABSTRACTBordetella pertussisfimbriae (Fim2 and Fim3) are components of a five-component acellular pertussis vaccine (diphtheria–tetanus–acellular pertussis vaccine [DTaP5]), and antibody responses to fimbriae have been associated with protection. We analyzed the IgG responses to individual Fim2 and Fim3 in sera remaining from a Swedish placebo-controlled efficacy trial that compared a whole-cell vaccine (diphtheria-tetanus-whole-cell pertussis vaccine [DTwP]), a two-component acellular pertussis vaccine (DTaP2), and DTaP5. One month following three doses of the Fim-containing vaccines (DTwP or DTaP5), anti-Fim2 geometric mean IgG concentrations were higher than those for anti-Fim3, with a greater anti-Fim2/anti-Fim3 IgG ratio elicited by DTaP5. We also determined the responses in vaccinated children following an episode of pertussis. Those who received DTaP5 showed a large rise in anti-Fim2 IgG, reflecting the predominant Fim2 serotype at the time. In contrast, those who received DTwP showed an equal rise in anti-Fim2 and anti-Fim3 IgG concentrations, indicating that DTwP may provide a more efficient priming effect for a Fim3 response following contact withB. pertussis. Anti-Fim2 and anti-Fim3 IgG concentrations were also determined in samples from two seroprevalence studies conducted in Sweden in 1997, when no pertussis vaccine was used and Fim2 isolates predominated, and in 2007, when either DTaP2 or DTaP3 without fimbriae was used and Fim3 isolates predominated. Very similar distributions of anti-Fim2 and anti-Fim3 IgG concentrations were obtained in 1997 and 2007, except that anti-Fim3 concentrations in 1997 were lower. This observation, together with the numbers of individuals with both anti-Fim2 and anti-Fim3 IgG concentrations, strongly suggests thatB. pertussisexpresses both Fim2 and Fim3 during infection.
Epidemiology and Molecular Characterization of Macrolide-Resistant Streptococcus pyogenes in Taiwan
Authors: Huang Chia-Ying , Lai Jui-Fen , Huang I-Wen , Chen Pei-Chen , Wang Hui-Ying , Shiau Yih-Ru , Cheng Ya-Wen , Hsieh Li-Yun , Chang Shan-Chwen , Lauderdale Tsai-Ling Yang 
Published: December 2013

ABSTRACT

Our multicenter nationwide surveillance data indicated that erythromycin (ERY) resistance among group A
Streptococcus
(GAS) isolates in Taiwan declined from 53.1% in 1998 and 2000 to 14.6% in 2002 and 2004 and 10.7% in 2006 to 2010 (
P
< 0.01). The present study aimed to assess the epidemiology of GAS in Taiwan and identify factors associated with ERY resistance. All 127 ERY-resistant (ERY
r
) isolates and 128 randomly selected ERY-susceptible (ERY
s
) isolates recovered from 1998 to 2010 were
emm
typed. ERY
r
isolates were also characterized by ERY resistance phenotype and mechanisms and pulsed-field gel electrophoresis (PFGE). Multilocus sequence typing was performed on selected ERY
r
isolates. The predominant
emm
types in ERY
r
isolates were
emm
22 (
n
= 33, 26.0%),
emm
12 (
n
= 24, 18.9%),
emm
4 (
n
= 21, 16.5%), and
emm
106 (
n
= 15, 11.8%). In ERY
s
isolates,
emm
12 (
n
= 27, 21.9%),
emm
1 (
n
= 18, 14.1%),
emm
106 (
n
= 16, 12.5%), and
emm
11 (
n
= 9, 7.1%) predominated. The most common ERY resistance phenotype was the M phenotype (resistant to macrolides) (70.9%), with all but one isolate carrying
mef
(A), followed by the constitutive macrolide-lincosamide-streptogramin B resistance (cMLS
B
) phenotype (26.8%), with isolates carrying
erm
(B) or
erm
(TR). ERY
r
isolates of the
emm
12-sequence type 36 (ST36) lineage with the cMLS
B
phenotype were mostly present before 2004, while those of the
emm
22-ST46 lineage with the M phenotype predominated in later years. Recovery from respiratory (throat swab) specimens was an independent factor associated with ERY resistance.
emm
1 and
emm
11 GAS isolates were significantly associated with ERY
s
, while
emm
22 was detected only in ERY
r
GAS. In addition,
emm
106 isolates were prevalent among the abscess/pus isolates, whereas
emm
12 isolates were strongly associated with a respiratory (throat) origin. In addition to identifying factors associated with ERY resistance in GAS, our study provides helpful information on the changing GAS epidemiology in Taiwan.
Comparative Performances of HIV-1 RNA Load Assays at Low Viral Load Levels: Results of an International Collaboration
Authors: Swenson Luke C. , Cobb Bryan , Geretti Anna Maria , Harrigan P. Richard , Poljak Mario , Seguin-Devaux Carole , Verhofstede Chris , Wirden Marc , Amendola Alessandra , Boni Jurg , Bourlet Thomas , Huder Jon B. , Karasi Jean-Claude , Zidovec Lepej Snjezana , Lunar Maja M. , Mukabayire Odette , Schuurman Rob , Tomažič Janez , Van Laethem Kristel , Vandekerckhove Linos , Wensing Annemarie M. J. 
Published: December 2013

ABSTRACT
Low-level viremia during antiretroviral therapy and its accurate measurement are increasingly relevant. Here, we present an international collaboration of 4,221 paired blood plasma viral load (pVL) results from four commercial assays, emphasizing the data with low pVL. The assays compared were the Abbott RealTime assay, the Roche Amplicor assay, and the Roche TaqMan version 1 and version 2 assays. The correlation between the assays was 0.90 to 0.97. However, at a low pVL, the correlation fell to 0.45 to 0.85. The observed interassay concordance was higher when detectability was defined as 200 copies/ml than when it was defined as 50 copies/ml. A pVL of ∼100 to 125 copies/ml by the TaqMan version 1 and version 2 assays corresponded best to a 50-copies/ml threshold with the Amplicor assay. Correlation and concordance between the viral load assays were lower at a low pVL. Clear guidelines are needed on the clinical significance of low-level viremia.
Ease and Comfort of Cervical and Vaginal Sampling for Chlamydia trachomatis and Trichomonas vaginalis with a New Aptima Specimen Collection and Transportation Kit
Authors: Chernesky Max , Jang Dan , Gilchrist Jodi , Randazzo Joan , Elit Laurie , Lytwyn Alice , Smieja Marek , Reid Jennifer , Hill Craig 
Published: December 2013

ABSTRACT

Use of a new collection kit for vaginal and cervical sampling was reported as easy by the majority of 692 women and not uncomfortable (by 87.4% of those ≥25 years old and 78.8% of those <25 years old). By Aptima testing, patient- and physician-collected samples agreed strongly for
Chlamydia trachomatis
(99.6% to 99.3%; κ = 0.93 to 0.89) and
T. vaginalis
(99.6% to 98.9%; κ = 0.97 to 0.78).
De Novo
Prion Aggregates Trigger Autophagy in Skeletal Muscle
Authors: Joshi-Barr Shivanjali , Bett Cyrus , Chiang Wei-Chieh , Trejo Margarita , Goebel Hans H. , Sikorska Beata , Liberski Pawel , Raeber Alex , Lin Jonathan H. , Masliah Eliezer , Sigurdson Christina J. 
Published: December 2013

ABSTRACT

In certain sporadic, familial, and infectious prion diseases, the prion protein misfolds and aggregates in skeletal muscle in addition to the brain and spinal cord. In myocytes, prion aggregates accumulate intracellularly, yet little is known about clearance pathways. Here we investigated the clearance of prion aggregates in muscle of transgenic mice that develop prion disease
de novo
. In addition to neurodegeneration, aged mice developed a degenerative myopathy, with scattered myocytes containing ubiquitinated, intracellular prion inclusions that were adjacent to myocytes lacking inclusions. Myocytes also showed elevated levels of the endoplasmic reticulum chaperone Grp78/BiP, suggestive of impaired protein degradation and endoplasmic reticulum stress. Additionally, autophagy was induced, as indicated by increased levels of beclin-1 and LC3-II. In C2C12 myoblasts, inhibition of autophagosome maturation or lysosomal degradation led to enhanced prion aggregation, consistent with a role for autophagy in prion aggregate clearance. Taken together, these findings suggest that the induction of autophagy may be a central strategy for prion aggregate clearance in myocytes.

IMPORTANCE
In prion diseases, the prion protein misfolds and aggregates in the central nervous system and sometimes in other organs, including muscle, yet the cellular pathways of prion aggregate clearance are unclear. Here we investigated the clearance of prion aggregates in the muscle of a transgenic mouse model that develops profound muscle degeneration. We found that endoplasmic reticulum stress pathways were activated and that autophagy was induced. Blocking of autophagic degradation in cell culture models led to an accumulation of aggregated prion protein. Collectively, these findings suggest that autophagy has an instrumental role in prion protein clearance.
Quantification of Entry Phenotypes of Macrophage-Tropic HIV-1 across a Wide Range of CD4 Densities
Authors: Joseph Sarah B. , Arrildt Kathryn T. , Swanstrom Adrienne E. , Schnell Gretja , Lee Benhur , Hoxie James A. , Swanstrom Ronald 
Published: December 2013

ABSTRACT

Defining a macrophage-tropic phenotype for HIV-1 to assess a role in pathogenesis is complicated by the fact that HIV-1 isolates vary continuously in their ability to enter monocyte-derived macrophages (MDMs)
in vitro
, and MDMs vary in their ability to support HIV-1 entry. To overcome these limitations, we identified consistent differences in entry phenotypes between five paired blood-derived, T cell-tropic HIV-1
env
genes, four of which are CCR5-using (R5) and one of which is CXCR4-using (X4), and cerebrospinal fluid (CSF)-derived, R5 macrophage-tropic
env
genes. We performed entry assays using the CD4- and CCR5-inducible Affinofile cell line, expressing a range of CD4 levels that approximates the range from MDMs to CD4
+
T cells. The macrophage-tropic viruses were significantly better at infecting cells expressing low levels of CD4 than the T cell-tropic viruses from the same subjects, with the titration of CD4 providing a distinctive and quantitative phenotype. This difference in CD4 utilization was not due to macrophage-tropic viruses being CD4 independent. Furthermore, macrophage-tropic viruses did not differ from paired T cell-tropic viruses in their ability to use low levels of CCR5 (
t
paired
= −1.39;
P
= 0.24) or their use of an alternative conformation of CCR5. We also infected MDMs with a panel of viruses and observed that infectivity of each virus differed across four donors and between three preparations from a single donor. We concluded that the evolutionary transition from replication in T cells to that in macrophages involves a phenotypic transition to acquire the ability to infect cells expressing low levels of CD4 and that this phenotype is more reliably measured in Affinofile cells than in macrophages.

IMPORTANCE
HIV-1 typically infects memory T cells by using CD4 and CCR5 to enter cells. The virus evolves to infect new cell types by changing the coreceptor from CCR5 to CXCR4 to infect naive T cells or adapting to the use of low levels of CD4 to infect macrophages. However, defining the phenotype of macrophage tropism has been difficult due to inherent variability in the use of macrophages generated in culture to support entry of HIV-1. We describe the use of Affinofile cells with inducible and variable levels of CD4 to identify a signature phenotype for macrophage-tropic HIV-1. The ability to define HIV-1 variants that have evolved an entry phenotype that allows more efficient entry into cells with low levels of CD4 sets the stage for a clearer placement of these variants in HIV-associated pathogenesis.
Stable, High-Level Expression of Reporter Proteins from Improved Alphavirus Expression Vectors To Track Replication and Dissemination during Encephalitic and Arthritogenic Disease
Authors: Sun Chengqun , Gardner Christina L. , Watson Alan M. , Ryman Kate D. , Klimstra William B. 
Published: December 2013

ABSTRACT

Engineered alphavirus vectors expressing reporters of infection have been used for a number of years due to their relatively low costs for analysis of virus replication and the capacity to utilize imaging systems for longitudinal measurements of growth within single animals. In general, these vectors have been derived from Old World alphaviruses using a second viral subgenomic promoter to express the transgenes, placed either immediately after the nonstructural proteins or at the 3′ end of the viral coding sequences. However, the relevance of these vectors to natural infections is questionable, as they have not been rigorously tested for virulence
in vivo
in comparison with parental viruses or for the retention of the reporter during replication. Here, we report construction of new expression vectors for two Old World arthritogenic alphaviruses (Sindbis and Chikungunya viruses) and two New World encephalitic alphaviruses (eastern and Venezuelan equine encephalitis viruses) based upon either fusion of the reporter protein in frame within nonstructural protein 3 (nsP3) or insertion of the reporter as a cleavable element between the capsid and PE2 structural proteins. We have compared these with a traditional 3′ double subgenomic promoter virus expressing either a large, firefly luciferase (fLuc; 1,650 nucleotides), or small, NanoLuc (nLuc; 513 nucleotides), luminescent reporter protein. Results indicate that the nLuc is substantially more stable than fLuc during repeated rounds of infection regardless of the transgene location. However, the capsid-PE2 insertion and nsP3 fusion viruses exhibit the most authentic mimicking of parental virus infection regardless of expressed protein.

IMPORTANCE
As more antiviral therapeutics and vaccines are developed, rapid and accurate
in vivo
modeling of their efficacy will be required. However, current alphavirus vectors expressing reporters of infection have not been extensively tested for accurate mimicking of the infection characteristics of unmodified parental viruses. Additionally, use of
in vivo
imaging systems detecting light emitted from luciferase reporters can significantly decrease costs associated with efficacy studies by minimizing numbers of animals. Herein we report development and testing of new expression vectors for Sindbis, Chikungunya, and eastern and Venezuelan equine encephalitis viruses and demonstrate that a small (∼500-nucleotide) reporter gene (NanoLuc; Promega) is very stable and causes a disease severity similar to that caused by unmodified parental viruses. In contrast, expression of larger reporters is very rapidly lost with virus replication and can be significantly attenuating. The utility of NanoLuc for
in vivo
imaging is also demonstrated.
Inhibition of Hepatitis C Virus Production by Aptamers against the Core Protein
Authors: Shi Shali , Yu Xiaoyan , Gao Yimin , Xue Binbin , Wu Xinjiao , Wang Xiaohong , Yang Darong , Zhu Haizhen 
Published: December 2013

ABSTRACT
Hepatitis C virus (HCV) core protein is essential for virus assembly. HCV core protein was expressed and purified. Aptamers against core protein were raised through the selective evolution of ligands by the exponential enrichment approach. Detection of HCV infection by core aptamers and the antiviral activities of aptamers were characterized. The mechanism of their anti-HCV activity was determined. The data showed that selected aptamers against core specifically recognize the recombinant core protein but also can detect serum samples from hepatitis C patients. Aptamers have no effect on HCV RNA replication in the infectious cell culture system. However, the aptamers inhibit the production of infectious virus particles. Beta interferon (IFN-β) and interferon-stimulated genes (ISGs) are not induced in virally infected hepatocytes by aptamers. Domains I and II of core protein are involved in the inhibition of infectious virus production by the aptamers. V31A within core is the major resistance mutation identified. Further study shows that the aptamers disrupt the localization of core with lipid droplets and NS5A and perturb the association of core protein with viral RNA. The data suggest that aptamers against HCV core protein inhibit infectious virus production by disrupting the localization of core with lipid droplets and NS5A and preventing the association of core protein with viral RNA. The aptamers for core protein may be used to understand the mechanisms of virus assembly. Core-specific aptamers may hold promise for development as early diagnostic reagents and potential therapeutic agents for chronic hepatitis C.
Expression of Herpes Simplex Virus 1 MicroRNAs in Cell Culture Models of Quiescent and Latent Infection
Authors: Jurak Igor , Hackenberg Michael , Kim Ju Youn , Pesola Jean M. , Everett Roger D. , Preston Chris M. , Wilson Angus C. , Coen Donald M. 
Published: December 2013

ABSTRACT

To facilitate studies of herpes simplex virus 1 latency, cell culture models of quiescent or latent infection have been developed. Using deep sequencing, we analyzed the expression of viral microRNAs (miRNAs) in two models employing human fibroblasts and one using rat neurons. In all cases, the expression patterns differed from that in productively infected cells, with the rat neuron pattern most closely resembling that found in latently infected human or mouse ganglia
in vivo
.