bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of an Alu‐mediated 12.2‐kb deletion of the complete LPAR6 (P2RY5) gene in a Turkish family with hypotrichosis and woolly hair
Authors: Mahmoudi Hassnaa , Tug Esra , Parlak Ali Haydar , Atasoy Halil Ibrahim , Ludwig Michael , Polat Mualla , Pasternack Sandra M. , Betz Regina C. 
Published: April 2012

AbstractHypotrichosis is a rare form of progressive hair loss characterized by sparse and occasionally woolly hair that is curly and breaks easily. Disease‐causing mutations in LIPH, LPAR6 and KRT74 have recently been identified. We describe a four‐generation pedigree from Turkey following an autosomal recessive pattern, in which the four affected members had hypotrichosis and woolly hair. By sequencing LPAR6 and the use of SNP arrays, we revealed a homozygous loss of the entire LPAR6 gene in the affected individuals. We hypothesize that the 12‐kb deletion resulted from illegitimate recombination secondary to slip‐replication. The orientation of three Alu repeats around LPAR6 may have provoked the formation of a ‘triple‐barrel’ structure during replication, thereby allowing strand slipping. This first report of complete LPAR6 loss expands the spectrum of known LPAR6 mutations and suggests a novel mechanism for this gene and for the formation of DNA rearrangements in general.
In vitro research on vitiligo: strategies, principles, methodological options and common pitfalls
Authors: Dell'Anna Maria Lucia , Cario‐André Muriel , Bellei Barbara , Taieb Alain , Picardo Mauro 
Published: April 2012

AbstractUnderstanding the cellular and molecular mechanisms leading to melanocyte loss in vitiligo is a mandatory step in improving the overall management of vitiligo patients. Until now, the study of vitiligo was characterised by a fragmented approach, and it is very hard to share and compare the data obtained by the different teams. The scenario mirrors the pathogenic puzzle, but it delays a true productive focus on the disease. The in vitro research is based on different models, ranging from monolayer cell culture of epidermal and dermal cells or 3D reconstructed skin to histological data, gene expression, computer simulation profile. For each model, several different (biochemical, phenotypic, immunological) aspects have been considered, increasing the mass of data difficult to be merged. Our purpose was to provide a practical synopsis of consolidated and advanced possibilities in the study of vitiligo, showing how data have been poorly shared until now. Following a short overview of the background of the disease, the approaches, ranging from basic cell biology to molecular and ‘omics’ studies, are summarised. New fluorescent probes and techniques open new possibilities for functional studies. Next, intracellular and superficial markers of the melanocytes, the main involved cells, are listed. Moving the focus from the epidermal level to the systemic and subcellular ones, this review aims to propose innovative multidisciplinary options for the vitiligo understanding. This paper focuses on the major practical and theoretical questions to be solved. It may be the basis for a more coordinated and productive approach to the biological question.
The DSL1 Complex: The Smallest but Not the Least CATCHR
Authors: Spang Anne 
Published: April 2012

AbstractThe DSL1 complex is a conserved tethering complex at the endoplasmic reticulum that recognizes Golgi‐derived COPI vesicles and hands them over to the fusion machinery. The DSL1 complex is the simplest tethering complex of the complexes associated with tethering containing helical rods (CATCHR) family. CATCHR tethering complexes play a role at compartments along the exocytic and endocytic pathways. In this review, different functions of the DSL1 complex are discussed, some open questions with the seemingly straightforward picture are pointed out and alternative functions of the DSL1 complex members are mentioned.
Observations and Modeling of Stream Plunging in an Urban Lake1
Authors: Owens Emmet M. , Effler Steven W. , Prestigiacomo Anthony R. , Matthews David A. , O’Donnell Susan M. 
Published: April 2012

Owens, Emmet M., Steven W. Effler, Anthony R. Prestigiacomo, David A. Matthews, and Susan M. O’Donnell, 2012. Observations and Modeling of Stream Plunging in an Urban Lake. Journal of the American Water Resources Association (JAWRA) 48(4): 707‐721. DOI: 10.1111/j.1752‐1688.2012.00646.xAbstract:  The plunging behavior of two tributaries in Onondaga Lake, New York, is quantified based on a program of monitoring, process studies, and modeling. The dynamics of buoyancy of the tributaries are resolved with hourly measurements of temperature (T), specific conductance (SC), and turbidity (Tn) at the mouths, and observations every 6 h in the lake. Negative buoyancy of the tributaries is found to diminish and change rapidly during runoff events compared to dry periods. In‐lake patterns of the transport of plunging inflow are resolved for dry weather conditions using a dye tracer, and following a runoff event through measurements of T, SC, and Tn. The hydrodynamic/transport model ELCOM (Estuary Lake and Coastal Ocean Model) is demonstrated to perform well in simulating these patterns. Analyses conducted with the model establish the importance of diurnal effects and in‐lake mixing mediated by wind, the need for temporally detailed measurements during runoff events, and modifications of the plunging behavior of the urban tributary as it passes through a harbor. The model provides critical information to support rehabilitation programs for the lake by quantifying the transport of the two largest tributaries, particularly the distribution of the loads between the upper waters and stratified layers. The model predicts that 10% of the urban tributary load enters the upper waters of the lake within 24 h for a dry weather period; this portion increases to 30% for a runoff event.
How indeterminism shapes ecologists’ contributions to managing socio‐ecological systems
Authors: Michaels Sarah , Tyre Andrew J. 
Published: April 2012

AbstractTo make a difference in policy making about socio‐ecological systems, ecologists must grasp when decision makers are amenable to acting on ecological expertise and when they are not. To enable them to do so we present a matrix for classifying a socio‐ecological system by the extent of what we don't know about its natural components and the social interactions that affects them. We use four examples, Midcontinent Mallards, Laysan Ducks, Pallid Sturgeon, and Rocky Mountain Grey Wolves to illustrate how the combination of natural and social source of indeterminism matters. Where social indeterminism is high, ecologists can expand the range of possible science‐based options decision makers might consider even while recognizing societal‐based concerns rather than science will dominate decision making. In contrast, where natural indeterminism is low, ecologists can offer reasonably accurate predictions that may well serve as inputs into decision making. Depending on the combination of natural and social indeterminism characterizing a particular circumstance, ecologists have different roles to play in informing socio‐ecological system management.
Analysis of Viral and Cellular Factors Influencing Herpesvirus-Induced Nuclear Envelope Breakdown
Authors: Grimm Katharina S. , Klupp Barbara G. , Granzow Harald , Müller Frederik M. , Fuchs Walter , Mettenleiter Thomas C. 
Published: April 2012

ABSTRACTHerpesvirus nucleocapsids are translocated from their assembly site in the nucleus to the cytosol by acquisition of a primary envelope at the inner nuclear membrane which subsequently fuses with the outer nuclear membrane. This transport through the nuclear envelope requires homologs of the conserved herpesviral pUL31 and pUL34 proteins which form the nuclear egress complex (NEC). In its absence, 1,000-fold less virus progeny is produced. We isolated a UL34-negative mutant of the alphaherpesvirus pseudorabies virus (PrV), PrV-ΔUL34Pass, which regained replication competence after serial passages in cell culture by inducing nuclear envelope breakdown (NEBD) (B. G. Klupp, H. Granzow, and T. C. Mettenleiter, J. Virol. 85:8285–8292, 2011). To test whether this phenotype is unique, passaging experiments were repeated with a UL31 deletion mutant. After 60 passages, the resulting PrV-ΔUL31Pass replicated similarly to wild-type PrV. Ultrastructural analyses confirmed escape from the nucleus via NEBD, indicating an inherent genetic disposition in herpesviruses. To identify the mutated viral genes responsible for this phenotype, the genome of PrV-ΔUL34Pass was sequenced and compared to the genomes of parental PrV-Ka and PrV-ΔUL34. Targeted sequencing of PrV-ΔUL31Pass disclosed congruent mutations comprising genes encoding tegument proteins (pUL49, pUL46, pUL21, pUS2), envelope proteins (gI, pUS9), and protease pUL26. To investigate involvement of cellular pathways, different inhibitors of cellular kinases were tested. While induction of apoptosis or inhibition of caspases had no specific effect on the passaged mutants, roscovitine, a cyclin-dependent kinase inhibitor, and U0126, an inhibitor of MEK1/2, specifically impaired replication of the passaged mutants, indicating involvement of mitosis-related processes in herpesvirus-induced NEBD.
The Number of Toll-Like Receptor 9-Agonist Motifs in the Adenovirus Genome Correlates with Induction of Dendritic Cell Maturation by Adenovirus Immune Complexes
Authors: Perreau Matthieu , Welles Hugh C. , Pellaton Celine , Gjoksi Bebeka , Potin Lambert , Martin Ricardo , Harari Alexandre , Bett Andrew , Casimiro Danilo , Gall Jason , Barouch Dan H. , Kremer Eric J. , Pantaleo Giuseppe 
Published: April 2012

ABSTRACT
Adenovirus serotype 5 (Ad5) vectors and specific neutralizing antibodies (NAbs) generate immune complexes (ICs) which are potent inducers of dendritic cell (DC) maturation. Here we show that ICs generated with rare Ad vector serotypes, such as Ad26 and Ad35, which are lead candidates in HIV vaccine development, are poor inducers of DC maturation and that their potency in inducing DC maturation strongly correlated with the number of Toll-like receptor 9 (TLR9)-agonist motifs present in the Ad vector's genome. In addition, we showed that antihexon but not antifiber antibodies are responsible for the induction of Ad IC-mediated DC maturation.
Rescue of a Porcine Anellovirus (Torque Teno Sus Virus 2) from Cloned Genomic DNA in Pigs
Authors: Huang Yao-Wei , Patterson Abby R. , Opriessnig Tanja , Dryman Barbara A. , Gallei Andreas , Harrall Kylie K. , Vaughn Eric M. , Roof Michael B. , Meng Xiang-Jin 
Published: April 2012

ABSTRACT

Anelloviruses are a group of single-stranded circular DNA viruses infecting humans and other animal species. Animal models combined with reverse genetic systems of anellovirus have not been developed. We report here the construction and initial characterization of full-length DNA clones of a porcine anellovirus, torque teno sus virus 2 (TTSuV2),
in vitro
and
in vivo
. We first demonstrated that five cell lines, including PK-15 cells, are free of TTSuV1 or TTSuV2 contamination, as determined by a real-time PCR and an immunofluorescence assay (IFA) using anti-TTSuV antibodies. Recombinant plasmids harboring monomeric or tandem-dimerized genomic DNA of TTSuV2 from the United States and Germany were constructed. Circular TTSuV2 genomic DNA with or without introduced genetic markers and tandem-dimerized TTSuV2 plasmids were transfected into PK-15 cells, respectively. Splicing of viral mRNAs was identified in transfected cells. Expression of TTSuV2-specific open reading frame 1 (ORF1) in cell nuclei, especially in nucleoli, was detected by IFA. However, evidence of productive TTSuV2 infection was not observed in 12 different cell lines transfected with the TTSuV2 DNA clones. Transfection with circular DNA from a TTSuV2 deletion mutant did not produce ORF1 protein, suggesting that the observed ORF1 expression is driven by TTSuV2 DNA replication in cells. Pigs inoculated with either the tandem-dimerized clones or circular genomic DNA of U.S. TTSuV2 developed viremia, and the introduced genetic markers were retained in viral DNA recovered from the sera of infected pigs. The availability of an infectious DNA clone of TTSuV2 will facilitate future study of porcine anellovirus pathogenesis and biology.
Serology-Enabled Discovery of Genetically Diverse Hepaciviruses in a New Host
Authors: Burbelo Peter D. , Dubovi Edward J. , Simmonds Peter , Medina Jan L. , Henriquez Jose A. , Mishra Nischay , Wagner Jason , Tokarz Rafal , Cullen John M. , Iadarola Michael J. , Rice Charles M. , Lipkin W. Ian , Kapoor Amit 
Published: April 2012

ABSTRACT
Genetic and biological characterization of new hepaciviruses infecting animals contributes to our understanding of the ultimate origins of hepatitis C virus (HCV) infection in humans and dramatically enhances our ability to study its pathogenesis using tractable animal models. Animal homologs of HCV include a recently discovered canine hepacivirus (CHV) and GB virus B (GBV-B), both viruses with largely undetermined natural host ranges. Here we used a versatile serology-based approach to determine the natural host of the only known nonprimate hepacivirus (NPHV), CHV, which is also the closest phylogenetic relative of HCV. Recombinant protein expressed from the helicase domain of CHV NS3 was used as antigen in the luciferase immunoprecipitation system (LIPS) assay to screen several nonprimate animal species. Thirty-six samples from 103 horses were immunoreactive, and viral genomic RNA was present in 8 of the 36 seropositive animals and none of the seronegative animals. Complete genome sequences of these 8 genetically diverse NPHVs showed 14% (range, 6.4% to 17.2%) nucleotide sequence divergence, with most changes occurring at synonymous sites. RNA secondary structure prediction of the 383-base 5′ untranslated region of NPHV was refined and extended through mapping of polymorphic sites to unpaired regions or (semi)covariant pairings. Similar approaches were adopted to delineate extensive RNA secondary structures in the coding region of the genome, predicted to form 27 regularly spaced, thermodynamically stable stem-loops. Together, these findings suggest a promising new nonprimate animal model and provide a database that will aid creation of functional NPHV cDNA clones and other novel tools for hepacivirus studies.
Identification of a Divalent Metal Cation Binding Site in Herpes Simplex Virus 1 (HSV-1) ICP8 Required for HSV Replication
Authors: Bryant Kevin F. , Yan Zhipeng , Dreyfus David H. , Knipe David M. 
Published: April 2012

ABSTRACT

Herpes simplex virus 1 (HSV-1) ICP8 is a single-stranded DNA-binding protein that is necessary for viral DNA replication and exhibits recombinase activity
in vitro
. Alignment of the HSV-1 ICP8 amino acid sequence with ICP8 homologs from other herpesviruses revealed conserved aspartic acid (D) and glutamic acid (E) residues. Amino acid residue D1087 was conserved in every ICP8 homolog analyzed, indicating that it is likely critical for ICP8 function. We took a genetic approach to investigate the functions of the conserved ICP8 D and E residues in HSV-1 replication. The E1086A D1087A mutant form of ICP8 failed to support the replication of an ICP8 mutant virus in a complementation assay. E1086A D1087A mutant ICP8 bound DNA, albeit with reduced affinity, demonstrating that the protein is not globally misfolded. This mutant form of ICP8 was also recognized by a conformation-specific antibody, further indicating that its overall structure was intact. A recombinant virus expressing E1086A D1087A mutant ICP8 was defective in viral replication, viral DNA synthesis, and late gene expression in Vero cells. A class of enzymes called DDE recombinases utilize conserved D and E residues to coordinate divalent metal cations in their active sites. We investigated whether the conserved D and E residues in ICP8 were also required for binding metal cations and found that the E1086A D1087A mutant form of ICP8 exhibited altered divalent metal binding in an
in vitro
iron-induced cleavage assay. These results identify a novel divalent metal cation-binding site in ICP8 that is required for ICP8 functions during viral replication.
Multifunctional CD4 Cells Expressing Gamma Interferon and Perforin Mediate Protection against Lethal Influenza Virus Infection
Authors: Brown Deborah M. , Lee Sarah , Garcia-Hernandez Maria de la Luz , Swain Susan L. 
Published: April 2012

ABSTRACTCD4 effectors generatedin vitrocan promote survival against a highly pathogenic influenza virus via an antibody-independent mechanism involving class II-restricted, perforin-mediated cytotoxicity. However, it is not known whether CD4 cells activated during influenza virus infection can acquire cytolytic activity that contributes to protection against lethal challenge. CD4 cells isolated from the lungs of infected mice were able to confer protection against a lethal dose of H1N1 influenza virus A/Puerto Rico 8/34 (PR8). Infection of BALB/c mice with PR8 induced a multifunctional CD4 population with proliferative capacity and ability to secrete interleukin-2 (IL-2) and tumor necrosis factor alpha (TNF-α) in the draining lymph node (DLN) and gamma interferon (IFN-γ) and IL-10 in the lung. IFN-γ-deficient CD4 cells produced larger amounts of IL-17 and similar levels of TNF-α, IL-10, and IL-2 compared to wild-type (WT) CD4 cells. Both WT and IFN-γ−/−CD4 cells exhibit influenza virus-specific cytotoxicity; however, IFN-γ-deficient CD4 cells did not promote recovery after lethal infection as effectively as WT CD4 cells. PR8 infection induced a population of cytolytic CD4 effectors that resided in the lung but not the DLN. These cells expressed granzyme B (GrB) and required perforin to lyse peptide-pulsed targets. Lethally infected mice given influenza virus-specific CD4 cells deficient in perforin showed greater weight loss and a slower time to recovery than mice given WT influenza virus-specific CD4 cells. Taken together, these data strengthen the concept that CD4 T cell effectors are broadly multifunctional with direct roles in promoting protection against lethal influenza virus infection.
The association between jockey experience and race-day falls in flat racing in Australia
Authors: Hitchens Peta L , Blizzard C Leigh , Jones Graeme , Day Lesley M , Fell James 
Published: April 2012

ObjectivesApprentice thoroughbred racing jockeys have a higher fall rate than their more experienced counterparts. The authors describe rates of occurrence and investigate risk factors for falls among less-experienced thoroughbred flat racing jockeys in Australia who commenced their race riding career between August 2002 and July 2009.MethodsData on race-day falls were extracted from stewards' reports. Denominator data were provided by Racing Information Services Australia on races conducted in Australia. HRs were estimated using time-to-event (survival analysis) methods.ResultsFactors found to be associated with falls by less-experienced jockeys (as indicated by number of career rides or career stage) were older jockey age at commencement of career (p=0.001), fewer previous rides this meeting (p<0.001), fewer previous starts by the horse (p<0.001), younger horse age (p<0.001), lower race grade (p<0.001), lower prize money (p<0.001), shorter race distance (p<0.001) and drier track rating (p<0.001). Apprentice experience was inversely and strongly associated with increased rates of falls (p<0.001). Three indicators of less accomplished horses (lower race grade, fewer previous starts by the horse and less prize money at stake) and two race conditions (drier tracks and shorter race distance) were found to be associated with a progressively higher hazard of falls for less-experienced jockeys.ConclusionsThis study identified factors that preferentially contribute to falls by inexperienced jockeys. The authors suggest that consideration be given to restricting apprentice jockeys with little race-riding experience from riding horses that have not yet won a race (maiden) or that have had few previous race starts.
Antitumor Mechanisms of Targeting the PDK1 Pathway in Head and Neck Cancer
Authors: Bhola Neil E. , Freilino Maria L. , Joyce Sonali C. , Sen Malabika , Thomas Sufi M. , Sahu Anirban , Cassell Andre , Chen Ching-Shih , Grandis Jennifer R. 
Published: April 2012

Abstract
G-protein–coupled receptors (GPCR) activate the epidermal growth factor receptor (EGFR) and mediate EGFR-independent signaling pathways to promote the growth of a variety of cancers, including head and neck squamous cell carcinoma (HNSCC). Identification of the common signaling mechanisms involved in GPCR-induced EGFR-dependent and EGFR-independent processes will facilitate the development of more therapeutic strategies. In this study, we hypothesized that phosphoinositide-dependent kinase 1 (PDK1) contributes to GPCR–EGFR cross-talk and signaling in the absence of EGFR and suggests that inhibition of the PDK1 pathway may be effective in the treatment of HNSCC. The contribution of PDK1 to the EGFR-dependent and EGFR-independent signaling in HNSCC was determined using RNA interference, a kinase-dead mutant, and pharmacologic inhibition. In vivo xenografts studies were also carried out to determine the efficacy of targeting PDK1 alone or in combination with the U.S. Food and Drug Administration–approved EGFR inhibitor cetuximab. PDK1 contributed to both GPCR-induced EGFR activation and cell growth. PDK1 also mediated activation of p70S6K in the absence of EGFR. Blockade of PDK1 with a small molecule inhibitor (AR-12) abrogated HNSCC growth, induced apoptosis, and enhanced the antiproliferative effects of EGFR tyrosine kinase inhibitors in vitro. HNSCC xenografts expressing kinase-dead PDK1 showed increased sensitivity to cetuximab compared with vector-transfected controls. Administration of AR-12 substantially decreased HNSCC tumor growth in vivo. These cumulative results show that PDK1 is a common signaling intermediate in GPCR–EGFR cross-talk and EGFR-independent signaling, and in which targeting the PDK1 pathway may represent a rational therapeutic strategy to enhance clinical responses to EGFR inhibitors in HNSCC. Mol Cancer Ther; 11(6); 1236–46. ©2012 AACR.
Combination of Rad001 (Everolimus) and Propachlor Synergistically Induces Apoptosis through Enhanced Autophagy in Prostate Cancer Cells
Authors: Tai Sheng , Sun Yin , Liu Nan , Ding Boxiao , Hsia Elaine , Bhuta Sunita , Thor Ryan K. , Damoiseaux Robert , Liang Chaozhao , Huang Jiaoti 
Published: April 2012

Abstract
PI3K/AKT/mTOR pathway plays a key role in the tumorigenesis of many human cancers including prostate cancer. However, inhibitors of this pathway, such as Rad001, have not shown therapeutic efficacy as a single agent. Through a high-throughput screen of 5,000 widely used small molecules, we identified compounds that can synergize with Rad001 to inhibit prostate cancer cells. One of the compounds, propachlor, synergizes with Rad001 to induce apoptosis of castration-resistant prostate cancer cells via enhanced autophagy. This enhanced autophagic cell death is accompanied by increased Beclin1 expression as well as upregulation of Atg5–Atg12 conjugate and LC3-2. Rad001 and propachlor can also synergistically inhibit tumors in a xenograft animal model of prostate cancer. These findings provide a novel direction to develop combination therapies for advanced and metastatic prostate cancer that has failed the currently available therapies. Mol Cancer Ther; 11(6); 1320–31. ©2012 AACR.