bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Promotion Analysis of Wolof Clefts
Authors: Torrence Harold 
Published: November 2012

Abstract. This article investigates the syntax of cleft clauses in Wolof. I argue that Wolof clefts are derived by the movement of the clefted constituent to the cleft position. Evidence for the movement anlaysis comes from several general and language‐specific reconstruction tests: island sensitivity, idiom chunk reconstruction, reconstruction for Principle A and Principle C, quantifier binding, negative polarity item reconstruction, and the properties of Wolof subjunctive clauses and clitics. I compare Wolof clefts to English clefts throughout and, following work going back toSchachter 1973, suggest that English clefts are also derived by overt movement of the clefted item. Using quantifier float, clausal pied piping and awh‐copy construction, I argue that movement of the clefted item in Wolof is successive cyclic. Finally, I examine the relation between movement, Superiority, and (Strong and Weak) Crossover by comparing Wolof, English, and Yoruba.
Extensive polymorphism and evidence of selection pressure on major histocompatibility complex DLA‐DRB1, DQA1 and DQB1 class II genes in Croatian grey wolves
Authors: Arbanasić H. , Huber Đ. , Kusak J. , Gomerčić T. , Hrenović J. , Galov A. 
Published: November 2012

AbstractThe genes of the major histocompatibility complex (MHC) are a key component of the mammalian immune system and have become important molecular markers for measuring fitness‐related genetic variation in wildlife populations. Because of human persecution and habitat fragmentation, the grey wolf has become extinct from a large part of Western and Central Europe, and remaining populations have become isolated. In Croatia, the grey wolf population, part of the Dinaric–Balkan population, shrank nearly to extinction during the 20th century, and is now legally protected. Using the cloning–sequencing method, we investigated the genetic diversity and evolutionary history of exon 2 of MHC class II DLA‐DRB1, DQA1 and DQB1 genes in 77 individuals. We identified 13 DRB1, 7 DQA1 and 11 DQB1 highly divergent alleles, and 13 DLA‐DRB1/DQA1/DQB1 haplotypes. Selection analysis comparing the relative rates of non‐synonymous to synonymous mutations (dN/dS) showed evidence of positive selection pressure acting on all three loci. Trans‐species polymorphism was found, suggesting the existence of balancing selection. Evolutionary codon models detected considerable difference between alpha and beta chain gene selection patterns: DRB1 and DQB1 appeared to be under stronger selection pressure, while DQA1 showed signs of moderate selection. Our results suggest that, despite the recent contraction of the Croatian wolf population, genetic variability in selectively maintained immune genes has been preserved.
Oryza sativa actin‐interacting protein 1 is required for rice growth by promoting actin turnover
Authors: Shi Meng , Xie Yurong , Zheng Yiyan , Wang Junmin , Su Yi , Yang Qiuying , Huang Shanjin 
Published: November 2012

SummaryRapid actin turnover is essential for numerous actin‐based processes. However, how it is precisely regulated remains poorly understood. Actin‐interacting protein 1 (AIP1) has been shown to be an important factor by acting coordinately with actin‐depolymerizing factor (ADF)/cofilin in promoting actin depolymerization, the rate‐limiting factor in actin turnover. However, the molecular mechanism by which AIP1 promotes actin turnover remains largely unknown in plants. Here, we provide a demonstration that AIP1 promotes actin turnover, which is required for optimal growth of rice plants. Specific down‐regulation of OsAIP1 increased the level of filamentous actin and reduced actin turnover, whereas over‐expression of OsAIP1 induced fragmentation and depolymerization of actin filaments and enhanced actin turnover. In vitro biochemical characterization showed that, although OsAIP1 alone does not affect actin dynamics, it enhances ADF‐mediated actin depolymerization. It also caps the filament barbed end in the presence of ADF, but the capping activity is not required for their coordinated action. Real‐time visualization of single filament dynamics showed that OsAIP1 enhanced ADF‐mediated severing and dissociation of pointed end subunits. Consistent with this, the filament severing frequency and subunit off‐rate were enhanced in OsAIP1 over‐expressors but decreased in RNAi protoplasts. Importantly, OsAIP1 acts coordinately with ADF and profilin to induce massive net actin depolymerization, indicating that AIP1 plays a major role in the turnover of actin, which is required to optimize F‐actin levels in plants.
Nuclear gene targeting in Chlamydomonas using engineered zinc‐finger nucleases
Authors: Sizova Irina , Greiner Andre , Awasthi Mayanka , Kateriya Suneel , Hegemann Peter 
Published: November 2012

SummaryThe unicellular green alga Chlamydomonas reinhardtii is a versatile model for fundamental and biotechnological research. A wide range of tools for genetic manipulation have been developed for this alga, but specific modification of nuclear genes is still not routinely possible. Here, we present a nuclear gene targeting strategy for Chlamydomonas that is based on the application of zinc‐finger nucleases (ZFNs). Our approach includes (i) design of gene‐specific ZFNs using available online tools, (ii) evaluation of the designed ZFNs in a Chlamydomonas in situ model system, (iii) optimization of ZFN activity by modification of the nuclease domain, and (iv) application of the most suitable enzymes for mutagenesis of an endogenous gene. Initially, we designed a set of ZFNs to target the COP3 gene that encodes the light‐activated ion channel channelrhodopsin‐1. To evaluate the designed ZFNs, we constructed a model strain by inserting a non‐functional aminoglycoside 3′‐phosphotransferase VIII (aphVIII) selection marker interspaced with a short COP3 target sequence into the nuclear genome. Upon co‐transformation of this recipient strain with the engineered ZFNs and an aphVIII DNA template, we were able to restore marker activity and select paromomycin‐resistant (Pm‐R) clones with expressing nucleases. Of these Pm‐R clones, 1% also contained a modified COP3 locus. In cases where cells were co‐transformed with a modified COP3 template, the COP3 locus was specifically modified by homologous recombination between COP3 and the supplied template DNA. We anticipate that this ZFN technology will be useful for studying the functions of individual genes in Chlamydomonas.
Genetic and biochemical basis for alternative routes of tocotrienol biosynthesis for enhanced vitaminEantioxidant production
Authors: Zhang Chunyu , Cahoon Rebecca E. , Hunter Sarah C. , Chen Ming , Han Jixiang , Cahoon Edgar B. 
Published: November 2012

SummaryVitamin E tocotrienol synthesis in monocots requires homogentisate geranylgeranyl transferase (HGGT), which catalyzes the condensation of homogentisate and the unsaturated C20 isoprenoid geranylgeranyl diphosphate (GGDP). By contrast, vitamin E tocopherol synthesis is mediated by homogentisate phytyltransferase (HPT), which condenses homogentisate and the saturated C20 isoprenoid phytyl diphosphate (PDP). AnHGGT‐independent pathway for tocotrienol synthesis has also been shown to occur by de‐regulation of homogentisate synthesis. In this paper, the basis for this pathway and its impact on vitamin E production when combined withHGGTare explored. An Arabidopsis line was initially developed that accumulates tocotrienols and homogentisate by co‐expression of Arabidopsis hydroxyphenylpyruvate dioxygenase (HPPD) andEscherichia colibi‐functional chorismate mutase/prephenate dehydrogenase (TyrA). When crossed into thevte2–1HPTnull mutant, tocotrienol production was lost, indicating thatHPTcatalyzes tocotrienol synthesis inHPPD/TyrA‐expressing plants by atypical use ofGGDPas a substrate. Consistent with this, recombinant ArabidopsisHPTpreferentially catalyzedin vitroproduction of the tocotrienol precursor geranylgeranyl benzoquinol only when presented with high molar ratios ofGGDP:PDP. In addition, tocotrienol levels were highest in early growth stages inHPPD/TyrA lines, but decreased strongly relative to tocopherols during later growth stages whenPDPis known to accumulate. Collectively, these results indicate thatHPPD/TyrA‐induced tocotrienol production requiresHPTand occurs upon enrichment ofGGDPrelative toPDPin prenyl diphosphate pools. Finally, combined expression ofHPPD/TyrA andHGGTin Arabidopsis leaves and seeds resulted in large additive increases in vitamin E production, indicating that homogentisate concentrations limitHGGT‐catalyzed tocotrienol synthesis.
An unusual case of ocular melanosis and limbal melanocytoma with benign intraorbital extension in a dog
Authors: Dees D. Dustin , MacLaren Nicole E. , Teixeira Leandro , Dubielzig Richard R. 
Published: November 2012

AbstractThis case report describes concurrent ocular melanosis and limbal melanocytoma in a 6‐year‐old Golden Retriever dog. Three years prior, the pet was examined for progressive corneal pigmentation and started on topical Tacrolimus but was subsequently lost to followup. Current ophthalmic examination revealed a large pigmented limbal mass and severe corneal pigmentation of the left eye as well as a small focal raised pigmented mass of the right third eyelid. Due to extent and rapidity of tumor growth, the left eye was removed via transconjunctival enucleation and submitted for histopathologic examination. At the time of surgery, numerous orbital structures including intraorbital fat, extraocular muscles, and portions of the proximal nasolacrimal drainage apparatus contained multifocal areas of black pigmentation. These tissues were subsequently removed and submitted for microscopic analysis. The pigmented mass of the right third eyelid was also excised. Histopathology of the left eye and orbital contents revealed a limbal melanocytoma extending to the bulbar conjunctiva and orbital space forming a large, markedly necrotic mass. Diffuse, severe ocular melanosis, abnormal stromal pigmentation of the sclera and orbital tissues, and corneal stromal pigmentation were noted. The mass of the right third eyelid was confirmed to be a conjunctival melanocytoma. To the authors' knowledge, this is the first report of concurrent ocular melanosis and limbal melanocytoma with orbital infiltration. The peculiar multifocal distribution of melanocytes throughout ocular connective tissues may explain the development of multiple melanocytic lesions in this patient.
Standards Meetings Calendar–National
Authors: Blaeser Susan B. , Schomer Paul D. 
Published: November 2012

American National Standards (ANSI Standards) developed by Accredited Standards Committees S1, S2, S3, and S12 in the areas of acoustics, mechanical vibration and shock, bioacoustics, and noise, respectively, are published by the Acoustical Society of America (ASA). In addition to these standards, ASA publishes catalogs of Acoustical Standards, both National and International. To receive copies of the latest Standards catalogs, please contact Susan B. Blaeser.
Comments are welcomed on all material in Acoustical Standards News.
This Acoustical Standards News section in JASA, as well as the National and International Catalogs of Acoustical Standards, and other information on the Standards Program of the Acoustical Society of America, are available via the ASA home page: http://acousticalsociety.org.
Genetic Analysis of Non-Hydrogen Sulfide-Producing Salmonella enterica Serovar Typhimurium and S. enterica Serovar Infantis Isolates in Japan
Authors: Sakano Chieko , Kuroda Makoto , Sekizuka Tsuyoshi , Ishioka Taisei , Morita Yukio , Ryo Akihide , Tsukagoshi Hiroyuki , Kawai Yuko , Inoue Nobuko , Takada Hayato , Ogaswara Yumiko , Nishina Atsuyoshi , Shimoda Masa-aki , Kozawa Kunihisa , Oishi Kazunori , Kimura Hirokazu 
Published: November 2012

ABSTRACT

Whole-genome sequencing of non-H
2
S-producing
Salmonella enterica
serovar Typhimurium and
S. enterica
serovar Infantis isolates from poultry meat revealed a nonsense mutation in the
phsA
thiosulfate reductase gene and carriage of a CMY-2 β-lactamase. The lack of production of H
2
S might lead to the incorrect identification of
S. enterica
isolates carrying antimicrobial resistance genes.
Genetic Diversity of Burkholderia contaminans Isolates from Cystic Fibrosis Patients in Argentina
Authors: Martina Pablo , Bettiol Marisa , Vescina Cecilia , Montanaro Patricia , Mannino M. Constanza , Prieto Claudia I. , Vay Carlos , Naumann Dieter , Schmitt Juergen , Yantorno Osvaldo , Lagares Antonio , Bosch Alejandra 
Published: November 2012

ABSTRACT

A total of 120
Burkholderia cepacia
complex isolates collected during 2004–2010 from 66 patients in two cystic fibrosis reference centers in Argentina were analyzed.
Burkholderia contaminan
s was the species most frequently recovered (57.6%), followed by
Burkholderia cenocepacia
(15%), a species distribution not reported so far. The
recA
-PCR-based techniques applied to the
B. contaminans
isolates revealed that 85% of the population carried the
recA
-ST-71 allele. Our results showed the utility of BOX-PCR genotyping in analyzing
B. contaminans
diversity. This approach allowed us to address clonal transmission during an outbreak and the genetic changes occurring in infecting bacteria over the course of chronic infection.
Characterization of a Tsukamurella Pseudo-Outbreak by Phenotypic Tests, 16S rRNA Sequencing, Pulsed-Field Gel Electrophoresis, and Metabolic Footprinting
Authors: To Kelvin K. W. , Fung Ami M. Y. , Teng Jade L. L. , Curreem Shirly O. T. , Lee Kim-Chung , Yuen Kwok-Yung , Lam Ching-Wan , Lau Susanna K. P. , Woo Patrick C. Y. 
Published: November 2012

ABSTRACT

We report a pseudo-outbreak of
Tsukamurella
due to improperly wrapped scissors used for processing of tissue specimens. A polyphasic approach, involving biochemical, genetic, and metabolomic techniques, was used in the laboratory investigation. This report highlights that early recognition of pseudo-outbreaks is important in preventing unnecessary and incorrect treatment of patients.
Colonization Dynamics of Antibiotic-Resistant Coagulase-Negative Staphylococci in Neonates
Authors: Hira Vishal , Kornelisse René F. , Sluijter Marcel , Kamerbeek Alike , Goessens Wil H. F. , de Groot Ronald , Hermans Peter W. M. 
Published: November 2012

ABSTRACT

Coagulase-negative staphylococci (CoNS) isolated in neonatal late-onset sepsis are often antibiotic resistant. We analyzed CoNS from skin and feces of neonates during hospitalization. Antibiotic resistance of skin isolates increased during hospitalization, especially in
Staphylococcus haemolyticus
.
Staphylococcus warneri
showed low antibiotic resistance. Our data suggest that different CoNS species may play distinct roles in colonization.
Highly Attenuated Recombinant Vesicular Stomatitis Virus VSV-12′GFP Displays Immunogenic and Oncolytic Activity
Authors: van den Pol Anthony N. , Davis John N. 
Published: November 2012

ABSTRACT
Vesicular stomatitis virus (VSV) has shown considerable promise both as an immunization vector and as an oncolytic virus. In both applications, an important concern is the safety profile of the virus. To generate a highly attenuated virus, we added two reporter genes to the 3′ end of the VSV genome, thereby shifting the NPMGL genes from positions 1 to 5 to positions 3 to 7. The resulting virus (VSV-12′GFP) was highly attenuated, generating smaller plaques than four other attenuated VSVs. In one-step growth curves, VSV-12′GFP displayed the slowest growth kinetics. The mechanism of attenuation appears to be due to reduced expression of VSV genes downstream of the reporter genes, as suggested by a 10.4-fold reduction in L-protein RNA transcript. Although attenuated, VSV-12′GFP was highly effective at generating an immune response, indicated by a high-titer antibody response against the green fluorescent protein (GFP) expressed by the virus. Although VSV-12′GFP was more attenuated than other VSVs on both normal and cancer cells, it nonetheless showed a greater level of infection of human cancer cells (glioma and melanoma) than of normal cells, and this effect was magnified in glioma by interferon application, indicating selective oncolysis. Intravenous VSV-12′GFP selectively infected human gliomas implanted into SCID mice subcutaneously or intracranially. All postnatal day 16 mice given intranasal VSV-12′GFP survived, whereas only 10% of those given VSV-G/GFP survived, indicating reduced neurotoxicity. Intratumoral injection of tumors with VSV-12′GFP dramatically suppressed tumor growth and enhanced survival. Together these data suggest this recombinant virus merits further study for its oncolytic and vaccine potential.
HIV-1 Resistance to Maraviroc Conferred by a CD4 Binding Site Mutation in the Envelope Glycoprotein gp120
Authors: Ratcliff Annette N. , Shi Wuxian , Arts Eric J. 
Published: November 2012

ABSTRACT

Maraviroc (MVC) is a CCR5 antagonist that inhibits HIV-1 entry by binding to the coreceptor and inducing structural alterations in the extracellular loops. In this study, we isolated MVC-resistant variants from an HIV-1 primary isolate that arose after 21 weeks of tissue culture passage in the presence of inhibitor. gp120 sequences from passage control and MVC-resistant cultures were cloned into NL4-3 via yeast-based recombination followed by sequencing and drug susceptibility testing. Using 140 clones, three mutations were linked to MVC resistance, but none appeared in the V3 loop as was the case with previous HIV-1 strains resistant to CCR5 antagonists. Rather, resistance was dependent upon a single mutation in the C4 region of gp120. Chimeric clones bearing this N425K mutation replicated at high MVC concentrations and displayed significant shifts in 50% inhibitory concentrations (IC
50
s), characteristic of resistance to all other antiretroviral drugs but not typical of MVC resistance. Previous reports on MVC resistance describe an ability to use a drug-bound form of the receptor, leading to reduction in maximal drug inhibition. In contrast, our structural models on K425 gp120 suggest that this resistant mutation impacts CD4 interactions and highlights a novel pathway for MVC resistance.
Engagement of the ATR-Dependent DNA Damage Response at the Human Papillomavirus 18 Replication Centers during the Initial Amplification
Authors: Reinson Tormi , Toots Mart , Kadaja Meelis , Pipitch Regina , Allik Mihkel , Ustav Ene , Ustav Mart 
Published: November 2012

ABSTRACT

We have previously demonstrated that the human papillomavirus (HPV) genome replicates effectively in U2OS cells after transfection using electroporation. The transient extrachromosomal replication, stable maintenance, and late amplification of the viral genome could be studied for high- and low-risk mucosal and cutaneous papillomaviruses. Recent findings indicate that the cellular DNA damage response (DDR) is activated during the HPV life cycle and that the viral replication protein E1 might play a role in this process. We used a U2OS cell-based system to study E1-dependent DDR activation and the involvement of these pathways in viral transient replication. We demonstrated that the E1 protein could cause double-strand DNA breaks in the host genome by directly interacting with DNA. This activity leads to the induction of an ATM-dependent signaling cascade and cell cycle arrest in the S and G
2
phases. However, the transient replication of HPV genomes in U2OS cells induces the ATR-dependent pathway, as shown by the accumulation of γH2AX, ATR-interacting protein (ATRIP), and topoisomerase IIβ-binding protein 1 (TopBP1) in viral replication centers. Viral oncogenes do not play a role in this activation, which is induced only through DNA replication or by replication proteins E1 and E2. The ATR pathway in viral replication centers is likely activated through DNA replication stress and might play an important role in engaging cellular DNA repair/recombination machinery for effective replication of the viral genome upon active amplification.
Gangliosides Have a Functional Role during Rotavirus Cell Entry
Authors: Martínez Miguel Angel , López Susana , Arias Carlos F. , Isa Pavel 
Published: November 2012

ABSTRACT
Cell entry of rotaviruses is a complex process, which involves sequential interactions with several cell surface molecules. Among the molecules implicated are gangliosides, glycosphingolipids with one or more sialic acid (SA) residues. The role of gangliosides in rotavirus cell entry was studied by silencing the expression of two key enzymes involved in their biosynthesis—the UDP-glucose:ceramide glucosyltransferase (UGCG), which transfers a glucose molecule to ceramide to produce glucosylceramide GlcCer, and the lactosyl ceramide-α-2,3–sialyl transferase 5 (GM3-s), which adds the first SA to lactoceramide-producing ganglioside GM3. Silencing the expression of both enzymes resulted in decreased ganglioside levels (as judged by GM1a detection). Four rotavirus strains tested (human Wa, simian RRV, porcine TFR-41, and bovine UK) showed a decreased infectivity in cells with impaired ganglioside synthesis; however, their replication after bypassing the entry step was not affected, confirming the importance of gangliosides for cell entry of the viruses. Interestingly, viral binding to the cell surface was not affected in cells with inhibited ganglioside synthesis, but the infectivity of all strains tested was inhibited by preincubation of gangliosides with virus prior to infection. These data suggest that rotaviruses can attach to cell surface in the absence of gangliosides but require them for productive cell entry, confirming their functional role during rotavirus cell entry.
Humoral Immunity to Smallpox Vaccines and Monkeypox Virus Challenge: Proteomic Assessment and Clinical Correlations
Authors: Townsend M. B. , Keckler M. S. , Patel N. , Davies D. H. , Felgner P. , Damon I. K. , Karem K. L. 
Published: November 2012

ABSTRACT

Despite the eradication of smallpox, orthopoxviruses (OPV) remain public health concerns. Efforts to develop new therapeutics and vaccines for smallpox continue through their evaluation in animal models despite limited understanding of the specific correlates of protective immunity. Recent monkeypox virus challenge studies have established the black-tailed prairie dog (
Cynomys ludovicianus
) as a model of human systemic OPV infections. In this study, we assess the induction of humoral immunity in humans and prairie dogs receiving Dryvax, Acam2000, or Imvamune vaccine and characterize the proteomic profile of immune recognition using enzyme-linked immunosorbent assays (ELISA), neutralization assays, and protein microarrays. We confirm anticipated similarities of antigenic protein targets of smallpox vaccine-induced responses in humans and prairie dogs and identify several differences. Subsequent monkeypox virus intranasal infection of vaccinated prairie dogs resulted in a significant boost in humoral immunity characterized by a shift in reactivity of increased intensity to a broader range of OPV proteins. This work provides evidence of similarities between the vaccine responses in prairie dogs and humans that enhance the value of the prairie dog model system as an OPV vaccination model and offers novel findings that form a framework for examining the humoral immune response induced by systemic orthopoxvirus infection.
Expression of Prototype Foamy Virus Pol as a Gag-Pol Fusion Protein Does Not Change the Timing of Reverse Transcription
Authors: Jackson Dana L. , Lee Eun-Gyung , Linial Maxine L. 
Published: November 2012

ABSTRACT
Foamy viruses are retroviruses whose Pol protein is synthesized without Gag from a spliced mRNA. Unlike orthoretroviruses, reverse transcription occurs during viral assembly, leading to DNA-containing virions. When prototype foamy virus Pol is expressed as an orthoretroviral-like Gag-Pol fusion protein, reverse transcription also occurs late in viral replication, as measured by the timing of reverse transcriptase sensitivity to the inhibitor 3′-azido-3′deoxythymidine (AZT). Thus, timing of reverse transcription is intrinsic to Pol itself.