bluuebunny/crossref_metadata_2025 huggingface dataset:
Efficient Depletion of Host DNA Contamination in Malaria Clinical Sequencing
Authors: Oyola Samuel O. , Gu Yong , Manske Magnus , Otto Thomas D. , O'Brien John , Alcock Daniel , MacInnis Bronwyn , Berriman Matthew , Newbold Chris I. , Kwiatkowski Dominic P. , Swerdlow Harold P. , Quail Michael A.
Published: December 2012

The cost of whole-genome sequencing (WGS) is decreasing rapidly as next-generation sequencing technology continues to advance, and the prospect of making WGS available for public health applications is becoming a reality. So far, a number of studies have demonstrated the use of WGS as an epidemiological tool for typing and controlling outbreaks of microbial pathogens. Success of these applications is hugely dependent on efficient generation of clean genetic material that is free from host DNA contamination for rapid preparation of sequencing libraries. The presence of large amounts of host DNA severely affects the efficiency of characterizing pathogens using WGS and is therefore a serious impediment to clinical and epidemiological sequencing for health care and public health applications. We have developed a simple enzymatic treatment method that takes advantage of the methylation of human DNA to selectively deplete host contamination from clinical samples prior to sequencing. Using malaria clinical samples with over 80% human host DNA contamination, we show that the enzymatic treatment enriches
Plasmodium falciparum
DNA up to ∼9-fold and generates high-quality, nonbiased sequence reads covering >98% of 86,158 catalogued typeable single-nucleotide polymorphism loci.
Isolation of a Novel Strain of Mycobacterium iranicum from a Woman in the United States
Authors: Balakrishnan Nandhakumar , Tortoli Enrico , Engel Susan L. , Breitschwerdt Edward B.
Published: December 2012

A novel strain of
Mycobacterium iranicum
, a recently described nontuberculous
Mycobacterium
species, was isolated from the sputum of a woman. The source of infection was not determined; however, fomite transmission of inhaled aerosolized secretions from her husband's sleep apnea equipment was historically possible.
Genotypic Characterization of Enterotoxigenic Escherichia coli Strains Causing Traveler's Diarrhea
Authors: Rivera Fulton P. , Medina Anicia M. , Aldasoro Edelweiss , Sangil Anna , Gascon Joaquim , Ochoa Theresa J. , Vila Jordi , Ruiz Joaquim
Published: December 2012

This study aims to characterize the presence of virulence factors of enterotoxigenic
Escherichia coli
(ETEC) causing traveler's diarrhea. Among 52 ETEC isolates, the most common toxin type was STh, and the most frequent colonization factors (CFs) were CS21, CS6, and CS3. On the other hand, the nonclassical virulence factors EAST1 and EatA were frequently present.
Comparison of Droplet Digital PCR to Real-Time PCR for Quantitative Detection of Cytomegalovirus
Authors: Hayden R. T. , Gu Z. , Ingersoll J. , Abdul-Ali D. , Shi L. , Pounds S. , Caliendo A. M.
Published: December 2012

Quantitative real-time PCR (QRT-PCR) has been widely implemented for clinical viral load testing, but a lack of standardization and relatively poor precision have hindered its usefulness. Digital PCR offers highly precise, direct quantification without requiring a calibration curve. Performance characteristics of real-time PCR were compared to those of droplet digital PCR (ddPCR) for cytomegalovirus (CMV) load testing. Tenfold serial dilutions of the World Health Organization (WHO) and the National Institute of Standards and Technology (NIST) CMV quantitative standards were tested, together with the AcroMetrix CMV tc panel (Life Technologies, Carlsbad, CA) and 50 human plasma specimens. Each method was evaluated using all three standards for quantitative linearity, lower limit of detection (LOD), and accuracy. Quantitative correlation, mean viral load, and variability were compared. Real-time PCR showed somewhat higher sensitivity than ddPCR (LODs, 3 log
10
versus 4 log
10
copies/ml and IU/ml for NIST and WHO standards, respectively). Both methods showed a high degree of linearity and quantitative correlation for standards (
R
2
≥ 0.98 in each of 6 regression models) and clinical samples (
R
2
= 0.93) across their detectable ranges. For higher concentrations, ddPCR showed less variability than QRT-PCR for the WHO standards and AcroMetrix standards (
P
< 0.05). QRT-PCR showed less variability and greater sensitivity than did ddPCR in clinical samples. Both digital and real-time PCR provide accurate CMV load data over a wide linear dynamic range. Digital PCR may provide an opportunity to reduce the quantitative variability currently seen using real-time PCR, but methods need to be further optimized to match the sensitivity of real-time PCR.
Enterovirus 68 in Pediatric Patients Hospitalized for Acute Airway Diseases
Authors: Renois Fanny , Bouin Alexis , Andreoletti Laurent
Published: December 2012

Enterovirus 68 was detected in 10 respiratory specimens from pediatric patients hospitalized for acute wheezing or bronchitis during 2009 in the northeast of France. Viral loads ranged from 2 × 10
5
to 7.2 × 10
7
copies/ml. Alignment of 5′ nontranslated regions and phylogenetic analysis of partial VP1 gene sequences show that these viruses clustered and belonged to clade C.
Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry for Rapid Identification of Tick Vectors
Authors: Yssouf Amina , Flaudrops Christophe , Drali Rezak , Kernif Tahar , Socolovschi Cristina , Berenger Jean-Michel , Raoult Didier , Parola Philippe
Published: December 2012

A method for rapid species identification of ticks may help clinicians predict the disease outcomes of patients with tick bites and may inform the decision as to whether to administer postexposure prophylactic antibiotic treatment. We aimed to establish a matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) spectrum database based on the analysis of the legs of six tick vectors:
Amblyomma variegatum
,
Rhipicephalus sanguineus
,
Hyalomma marginatum rufipes
,
Ixodes ricinus
,
Dermacentor marginatus
, and
Dermacentor reticulatus
. A blind test was performed on a trial set of ticks to identify specimens of each species. Subsequently, we used MALDI-TOF MS to identify ticks obtained from the wild or removed from patients. The latter tick samples were also identified by 12S ribosomal DNA (rDNA) sequencing and were tested for bacterial infections. Ticks obtained from the wild or removed from patients (
R. sanguineus
,
I. ricinus
, and
D. marginatus
) were accurately identified using MALDI-TOF MS, with the exception of those ticks for which no spectra were available in the database. Furthermore, one damaged specimen was correctly identified as
I. ricinus
, a vector of Lyme disease, using MALDI-TOF MS only. Six of the 14 ticks removed from patients were found to be infected by pathogens that included
Rickettsia
,
Anaplasma
, and
Borrelia
spp. MALDI-TOF MS appears to be an effective tool for the rapid identification of tick vectors that requires no previous expertise in tick identification. The benefits for clinicians include the more targeted surveillance of patients for symptoms of potentially transmitted diseases and the ability to make more informed decisions as to whether to administer postexposure prophylactic treatment.
Molecular Characterization of Mycoplasma agalactiae Reveals the Presence of an Endemic Clone in Spain
Authors: Ariza-Miguel Jaime , Rodríguez-Lázaro David , Hernández Marta
Published: December 2012

Mycoplasma agalactiae
isolates from Spain were genetically characterized to investigate their genomic diversity and to better understand their relationship to isolates from other countries. Molecular typing revealed a high genomic homogeneity in Spanish
M. agalactiae
isolates, which clearly shows the circulation of one endemic clonal population.
Urease Operon and Urease Activity in Commensal and Disease-Causing Nontypeable Haemophilus influenzae
Authors: Zhang Lixin , Patel Mayuri , Xie Jingping , Davis Gregg S. , Marrs Carl F. , Gilsdorf Janet R.
Published: December 2012

The
ure
operon was significantly more prevalent in
Haemophilus influenzae
isolates causing otitis media and chronic obstructive pulmonary disease (COPD)-associated bronchitis than in those from throats of healthy individuals (97% versus 78.1%,
P
< 0.001). Strains lacking the
ure
operon are over 8 times more likely to be from the throat than either otitis media or COPD isolates.
The Use of the Ames Test as a Tool for Addressing Problem-Based Learning in the Microbiology Lab
Authors: Rodríguez Eliana , Piccini Claudia , Sosa Vanessa , Zunino Pablo
Published: December 2012

Our environment is full of potential carcinogens such as UV light, industrial pollutants, pesticides, and food additives, among others. It is estimated that 90% of all carcinogens are also mutagens. The Ames test is one of the most common tests for mutagens. In this problem-based learning activity, undergraduate biology students used the Ames test to screen a substance they provided, to see if it could be considered a mutagen. The idea of surveying substances used in everyday life appealed to our students, and helped engage them in this activity.
Determination of the Antibiotic Resistance Profile of Student Cell Phones
Authors: Blankinship Lisa Ann
Published: December 2012

Sampling of common use items (e.g., student cell phones) for bacterial presence, identification, and antibiotic resistance profiling helps students to recognize the need for routine cleaning of personal items and encourages thoughtful use of currently available medications. This multilab period project can be used to teach or reinforce several methods from general microbiology including aseptic technique, isolation streak, serial dilution, spread plating, Kirby Bauer testing, unknown identification, and media production. The data generated can be saved and added to each semester, thus providing a data set that reflects a local trend of antibiotic resistance.
Printed Identification Key or Web-Based Identification Guide: An Effective Tool for Species Identification?
Authors: dela Cruz Thomas Edison E. , Pangilinan Ma. Victoria B. , Litao Rodrigo A.
Published: December 2012

Species identification is often done with the aid of traditional dichotomous keys. This printed material is based on one’s decision between two alternatives, which is followed by another pair of alternatives until the final species name is reached. With the advent of internet technology, the use of an online database offers an updatable and accumulative approach to species identification. It can also be accessed anytime, and this is very useful for fast-changing groups of organisms. In this paper, we report the preference of sophomore Bachelor of Science (B.Sc.) in Microbiology students to two identification guides as a tool in taxonomy. We wish to test our hypothesis that today’s students will prefer to use web-based ID guides over printed dichotomous keys. We also describe how these printed dichotomous key and web-based ID guides were used by the students as one of their laboratory activities in the course Biology of Algae and Fungi.
Learner-Centered Teaching in Nonmajors Introductory Biology: The Impact of Giving Students Choices
Authors: Hurney Carol A.
Published: December 2012

Learner-centered teaching represents more than creating a course where students are actively engaged. Rather it is articulated by a shift in the balance of power, function of content, role of the instructor, purpose of assessment, and/or responsibility for learning in a course. To make the learning environment in a large-enrollment nonmajors Biology course more learner-centered, students were given the responsibility to: 1) select course topics, 2) determine the types and weights of course assignments used to assess learning, and 3) individually decide, prior to being assigned work, the weight of exams and projects. Combined survey results from two learner-centered sections of the course (n = 137) indicate that a majority of the students found that choosing the topics enhanced their learning of course material. Students also reported that they put more effort into the parts of the course that they had weighted more heavily. In addition, results support that students are reflective of the learner-centered environment, confident in their ability to learn biological topics and more interested in biology than they thought they would be. Finally, course averages from the learner-centered courses were significantly higher than course grades from instructor-centered versions of the course.
Almost All that You Need to Know about Fungal PathogensReview of:	Fundamental Medical Mycology;	ReissErrolJean ShadomyH.Marshall LyonG.III; (	2012).	John Wiley and Sons,	Hoboken, NJ.	624 pages.
Authors: Harrington Brian J.
Published: December 2012

Review of:
Fundamental Medical Mycology:
Errol Reiss, H. Jean Shadomy, and G. Marshall Lyon, III; (2012). John Wiley & Sons, Hoboken, NJ. 624 pages.
Food Microbiology 101Review of:	Food Microbiology: an Introduction,	3rd ed.;	MontvilleThomas J.MatthewsKarl R.KnielKalmia E.; (	2012).	ASM Press,	Washington, DC.	570 pages.
Authors: Liao Min-Ken
Published: December 2012

Review of:
Food Microbiology: an Introduction, 3rd ed.;
Thomas J. Montville, Karl R. Matthews, and Kalmia E. Kniel; (2012). ASM Press, Washington, DC. 570 pages.
Helpful Resources for Mentoring Novice ResearchersReview of:	Lab Ref, Volume 1: A Handbook of Recipes, Reagents, and Other Reference Tools for Use at the Bench;	RoskamsJane, ed.; (	2002).	Cold Spring Harbor Press,	Cold Spring Harbor, NY.	272 pages.	Lab Dynamics: Management and Leadership Skills for Scientists,	2nd ed.;	CohenCarl M.CohenSuzanne L.; (	2012).	Cold Spring Harbor Press,	Cold Spring Harbor, NY.	280 pages
Authors: Trujillo Monica
Published: December 2012

Review of:
Two resources for laboratory students:
Lab Ref, Volume 1: A Handbook of Recipes, Reagents, and Other Reference Tools for Use at the Bench;
Jane Roskams, ed.; (2002). Cold Spring Harbor Press, Cold Spring Harbor, NY. 272 pages; and
Lab Dynamics: Management and Leadership Skills for Scientists, 2nd ed.;
Carl M. Cohen and Suzanne L. Cohen; (2012). Cold Spring Harbor Press, Cold Spring Harbor, NY. 280 pages.
Myeloid-Derived Suppressor Cells in Murine Retrovirus-Induced AIDS Inhibit T- and B-Cell ResponsesIn VitroThat Are Used To Define the Immunodeficiency
Authors: Green Kathy A. , Cook W. James , Green William R.
Published: December 2012

Myeloid-derived suppressor cells (MDSCs) have been characterized in several disease settings, especially in many tumor systems. Compared to their involvement in tumor microenvironments, however, MDSCs have been less well studied in their responses to infectious disease processes, in particular to retroviruses that induce immunodeficiency. Here, we demonstrate for the first time the development of a highly immunosuppressive MDSC population that is dependent on infection by the LP-BM5 retrovirus, which causes murine acquired immunodeficiency. These MDSCs express a cell surface marker signature (CD11b+Gr-1+Ly6C+) characteristic of monocyte-type MDSCs. Such MDSCs profoundly inhibit immune responsiveness by a cell dose- and substantially inducible nitric oxide synthase (iNOS)-dependent mechanism that is independent of arginase activity, PD-1–PD-L1 expression, and interleukin 10 (IL-10) production. These MDSCs display levels of immunosuppressive function in parallel with the extent of disease in LP-BM5-infected wild-type (w.t.) versus knockout mouse strains that are differentially susceptible to pathogenesis. These MDSCs suppressed not only T-cell but also B-cell responses, which are an understudied target for MDSC inhibition. The MDSC immunosuppression of B-cell responses was confirmed by the use of purified B responder cells, multiple B-cell stimuli, and independent assays measuring B-cell expansion. Retroviral load measurements indicated that the suppressive Ly6Glow/±Ly6C+CD11b+-enriched MDSC subset was positive for LP-BM5, albeit at a significantly lower level than that of nonfractionated splenocytes from LP-BM5-infected mice. These results, including the strong direct MDSC inhibition of B-cell responsiveness, are novel for murine retrovirus-induced immunosuppression and, as this broadly suppressive function mirrors that of the LP-BM5-induced disease syndrome, support a possible pathogenic effector role for these retrovirus-induced MDSCs.
ATF6 Signaling Is Required for Efficient West Nile Virus Replication by Promoting Cell Survival and Inhibition of Innate Immune Responses
Authors: Ambrose Rebecca L. , Mackenzie Jason M.
Published: December 2012

West Nile virus strain Kunjin (WNV
KUN
) is an enveloped, positive-sense RNA virus within the virus family
Flaviviridae
. Many flaviviruses have been shown to manipulate multiple signaling pathways, including autophagic, innate immune, and stress responses, in order to benefit replication. In particular, we have demonstrated that WNV
KUN
regulates the unfolded protein response (UPR), skewing the downstream effectors toward chaperone expression and Xbp-1 activation while preventing PERK-mediated translation attenuation and C/EBP homologous protein (CHOP) upregulation. WNV
KUN
-regulated UPR signaling can then be hijacked in order to affect type I interferon (IFN) responses, preventing IFN-mediated STAT1 phosphorylation and nuclear translocation. To extend our previous observations, we aimed to investigate the contribution of ATF6- and IRE1-mediated signaling during WNV
KUN
replication and how the two sensors contribute to the inhibition of IFN signaling. ATF6-deficient cells infected with WNV
KUN
showed decreased protein and virion production. These cells also demonstrated increased eIF2α phosphorylation and CHOP transcription, absent in infected matched control cells. Thus, we propose that in the absence of ATF6, WNV
KUN
is incapable of manipulating the PERK-mediated response to infection. In contrast, infection of IRE1
−/−
knockout cells showed no discernible differences compared to IRE1
+/+
cells. However, both ATF6 and IRE1 were required for WNV
KUN
-induced inhibition of STAT1 phosphorylation. We suggest that the combination of abhorrent UPR signaling, promotion of cell death, and increased innate immune responses contributes to the replication defects in ATF6-deficient cells, thus demonstrating the dual importance of ATF6 in maintaining cell viability and modulating immune responses during WNV
KUN
infection.
Poly(C)-Binding Protein 1, a Novel N
pro
-Interacting Protein Involved in Classical Swine Fever Virus Growth
Authors: Li Dan , Li Su , Sun Yuan , Dong Hong , Li Yongfeng , Zhao Bibo , Guo Dongwei , Weng Changjiang , Qiu Hua-Ji
Published: December 2012

N
pro
is a multifunctional autoprotease unique to pestiviruses. The interacting partners of the N
pro
protein of classical swine fever virus (CSFV), a swine pestivirus, have been insufficiently defined. Using a yeast two-hybrid screen, we identified poly(C)-binding protein 1 (PCBP1) as a novel interacting partner of the CSFV N
pro
protein and confirmed this by coimmunoprecipitation, glutathione
S
-transferase (GST) pulldown, and confocal assays. Knockdown of PCBP1 by small interfering RNA suppressed CSFV growth, while overexpression of PCBP1 promoted CSFV growth. Furthermore, we showed that type I interferon was downregulated by PCBP1, as well as N
pro
. Our results suggest that cellular PCBP1 positively modulates CSFV growth.
2G12-Expressing B Cell Lines May Aid in HIV Carbohydrate Vaccine Design Strategies
Authors: Doores Katie J. , Huber Michael , Le Khoa M. , Wang Sheng-Kai , Doyle-Cooper Colleen , Cooper Anthony , Pantophlet Ralph , Wong Chi-Huey , Nemazee David , Burton Dennis R.
Published: December 2012

The highly conserved cluster of high-mannose glycans on the HIV-1 envelope glycoprotein, gp120, has been highlighted as a target for neutralizing antibodies. 2G12, the first HIV-1 antiglycan neutralizing antibody described, binds with an unusual domain-exchanged structure that creates a high-affinity multivalent binding surface. It is an interesting challenge for rational vaccine design to generate immunogens capable of eliciting domain-exchanged 2G12-like responses. We recently showed that di-mannose recognition by the variable domains of 2G12 is independent of domain exchange but that exchange is critical for virus neutralization. Carbohydrate-based immunogens aimed at inducing 2G12-like antibodies may need to drive both di-mannose recognition and domain exchange through interactions with B cell receptors. Here we assessed the ability of such immunogens to activate mouse B cell lines displaying domain-exchanged wild-type 2G12 (2G12 WT), a non-domain-exchanged Y-shaped variant (2G12 I19R), and germ line 2G12 (2G12 gl). We show that several immunogens, including heat-killed yeast and bacteria, can activate both 2G12 WT and 2G12 I19R B cells. However, only discrete clusters of high-mannose glycans, as on recombinant forms of the HIV-1 envelope trimer and oligodendrons, activate 2G12 WT B cells. Furthermore, no immunogen tested activated 2G12 gl cells. Our results support the hypothesis that in order to drive domain exchange of an antimannose antibody response, a boost with an immunogen displaying discrete clusters of high-mannose glycans not recognized by conventional Y-shaped antibodies will be required. Additionally, a molecule capable of activating 2G12 gl cells might also be required. The results highlight broadly neutralizing antibody-expressing mouse B cells as potentially useful tools for carbohydrate immunogen screening.
Hepatitis B Virus mRNA-Mediated miR-122 Inhibition Upregulates PTTG1-Binding Protein, Which Promotes Hepatocellular Carcinoma Tumor Growth and Cell Invasion
Authors: Li Changfei , Wang Yanzhong , Wang Saifeng , Wu Bo , Hao Junli , Fan Hongxia , Ju Ying , Ding Yuping , Chen Lizhao , Chu Xiaoyu , Liu Wenjun , Ye Xin , Meng Songdong
Published: December 2012

As the most abundant liver-specific microRNA, miR-122 is involved in diverse aspects of hepatic function and neoplastic transformation. Our previous study showed that miR-122 levels are significantly decreased in hepatitis B virus (HBV)-infected patients, which may facilitate viral replication and persistence (S. Wang, L. Qiu, X. Yan, W. Jin, Y. Wang, L. Chen, E. Wu, X. Ye, G. F. Gao, F. Wang, Y. Chen, Z. Duan, and S. Meng, Hepatology
55:
730–741, 2012). Loss of miR-122 expression in patients with hepatitis B enhances hepatitis B virus replication through cyclin G1-modulated P53 activity.). In this study, we provide evidence that all HBV mRNAs harboring an miR-122 complementary site act as sponges to bind and sequester endogenous miR-122, indicating that the highly redundant HBV transcripts are involved in HBV-mediated miR-122 suppression. We next identified pituitary tumor-transforming gene 1 (PTTG1) binding factor (PBF) as a target of miR-122 and demonstrated that HBV replication causes an obvious increase in PBF levels. Furthermore, we observed that the miR-122 levels were decreased and PBF was upregulated in chronic hepatitis B (CHB) and hepatocellular carcinoma (HCC). Overexpression and knockdown studies both revealed that PBF enhances proliferation and invasion of HCC cells, and silencing PBF resulted in a dramatic reduction of HCC tumor growth
in vivo
. Mechanistic analysis demonstrated that PBF interacts with PTTG1 and facilitates PTTG1 nuclear translocation, subsequently increasing its transcriptional activities. Therefore, we identified a novel HBV mRNA-miR-122-PBF regulatory pathway that facilitates malignant hepatocyte growth and invasion in CHB which may contribute to CHB-induced HCC development and progression. Our work underscores the reciprocal interplay of host miRNA sequestration and depletion by viral mRNAs, which may contribute to chronic-infection-related cancer.
Pseudoinfectious Venezuelan Equine Encephalitis Virus: a New Means of Alphavirus Attenuation
Authors: Atasheva Svetlana , Kim Dal Young , Akhrymuk Maryna , Morgan David G. , Frolova Elena I. , Frolov Ilya
Published: December 2012

Venezuelan equine encephalitis virus (VEEV) is a reemerging virus that causes a severe and often fatal disease in equids and humans. In spite of a continuous public health threat, to date, no vaccines or antiviral drugs have been developed for human use. Experimental vaccines demonstrate either poor efficiency or severe adverse effects. In this study, we developed a new strategy of alphavirus modification aimed at making these viruses capable of replication and efficient induction of the immune response without causing a progressive infection, which might lead to disease development. To achieve this, we developed a pseudoinfectious virus (PIV) version of VEEV. VEE PIV mimics natural viral infection in that it efficiently replicates its genome, expresses all of the viral structural proteins, and releases viral particles at levels similar to those found in wild-type VEEV-infected cells. However, the mutations introduced into the capsid protein make this protein almost incapable of packaging the PIV genome, and most of the released virions lack genetic material and do not produce a spreading infection. Thus, VEE PIV mimics viral infection in terms of antigen production but is safer due to its inability to incorporate the viral genome into released virions. These genome-free virions are referred to as virus-like particles (VLPs). Importantly, the capsid-specific mutations introduced make the PIV a very strong inducer of the innate immune response and add self-adjuvant characteristics to the designed virus. This unique strategy of virus modification can be applied for vaccine development against other alphaviruses.
Components of Promyelocytic Leukemia Nuclear Bodies (ND10) Act Cooperatively To Repress Herpesvirus Infection
Authors: Glass Mandy , Everett Roger D.
Published: December 2012

Upon the entry of the viral genome into the nucleus, herpes simplex virus type 1 (HSV-1) gene expression is rapidly repressed by constitutively expressed cellular proteins. This intrinsic antiviral defense is normally counteracted by ICP0, which allows virus infection to proceed efficiently. Replication of ICP0-null mutant HSV-1, however, is severely repressed by mechanisms that are conferred, at least in part, by nuclear domain 10 (ND10) components, including hDaxx, the promyelocytic leukemia (PML) protein, and Sp100. To investigate if these ND10 components repress viral gene expression in a cooperative manner, we simultaneously depleted host cells for hDaxx, PML, and Sp100 by multiple short hairpin RNA (shRNA) knockdown from a single lentivirus vector. We found that replication and gene expression of ICP0-null mutant HSV-1 were cooperatively repressed by hDaxx, PML, and Sp100 immediately upon infection, and all stages of virus replication were inhibited. Plaque-forming efficiency was enhanced at least 50-fold in the triple-depleted cells, a much larger increase than achieved by depletion of any single ND10 protein. Similar effects were also observed during infection of triple-depleted cells with human cytomegalovirus (HCMV). Moreover, using a cell culture model of quiescent infection, we found that triple depletion resulted in a much larger number of viral genomes escaping repression. However, triple depletion was unable to fully overcome the ICP0-null phenotype, implying the presence of additional repressive host factors, possibly components of the SUMO modification or DNA repair pathways. We conclude that several ND10 components cooperate in an additive manner to regulate HSV-1 and HCMV infection.
Insights into a Viral Lytic Pathway from an Archaeal Virus-Host System
Authors: Snyder Jamie C. , Brumfield Susan K. , Kerchner Keshia M. , Quax Tessa E. F. , Prangishvili David , Young Mark J.
Published: December 2012

Archaeal host cells infected by
Sulfolobus
turreted icosahedral virus (STIV) and
Sulfolobus islandicus
rod-shaped virus 2 (SIRV2) produce unusual pyramid-like structures on the cell surface prior to virus-induced cell lysis. This viral lysis process is distinct from known viral lysis processes associated with bacterial or eukaryal viruses. The STIV protein C92 and the SIRV2 protein 98 are the only viral proteins required for the formation of the pyramid lysis structures of STIV and SIRV2, respectively. Since SIRV2 and STIV have fundamentally different morphotypes and genome sequences, it is surprising that they share this lysis system. In this study, we have constructed a collection of C92/P98 chimeric proteins and tested their abilities, both in the context of virus replication and alone, to form pyramid lysis structures in
S. solfataricus
. The results of this study illustrate that these proteins are functionally homologous when expressed as individual chimeric proteins but not when expressed in the context of complete STIV infection.
Identification of a Noncanonically Transcribed Subgenomic mRNA of Infectious Bronchitis Virus and Other Gammacoronaviruses
Authors: Bentley Kirsten , Keep Sarah May , Armesto Maria , Britton Paul
Published: December 2012

Coronavirus subgenomic mRNA (sgmRNA) synthesis occurs via a process of discontinuous transcription involving transcription regulatory sequences (TRSs) located in the 5′ leader sequence (TRS-L) and upstream of each structural and group-specific gene (TRS-B). Several gammacoronaviruses including infectious bronchitis virus (IBV) contain a putative open reading frame (ORF), localized between the M gene and gene 5, which is controversial due to the perceived absence of a TRS. We have studied the transcription of a novel sgmRNA associated with this potential ORF and found it to be transcribed via a previously unidentified noncanonical TRS-B. Using an IBV reverse genetics system, we demonstrated that the template-switching event during intergenic region (IR) sgmRNA synthesis occurs at the 5′ end of the noncanonical TRS-B and recombines between nucleotides 5 and 6 of the 8-nucleotide consensus TRS-L. Introduction of a complete TRS-B showed that higher transcription levels are achieved by increasing the number of nucleotide matches between TRS-L and TRS-B. Translation of a protein from the sgmRNA was demonstrated using enhanced green fluorescent protein, suggesting the translation of a fifth, novel, group-specific protein for IBV. This study has resolved an issue concerning the number of ORFs expressed by members of the
Gammacoronavirus
genus and proposes the existence of a fifth IBV accessory protein. We confirmed previous reports that coronaviruses can produce sgmRNAs from noncanonical TRS-Bs, which may expand their repertoire of proteins. We also demonstrated that noncanonical TRS-Bs may provide a mechanism by which coronaviruses can control protein expression levels by reducing sgmRNA synthesis.
Misleading presentation of acute Lyme neuroborreliosis
Authors: Winter Elizabeth Martha , Rothbarth Philip H , Delfos Nathalie M
Published: December 2012

A young man presented with recent-onset non-specific symptoms like headache, sleepiness and weight loss, interfering with normal daily life. Physical and biochemical irregularities were absent. Because extensive examination by neurologist and psychiatrist including brain imaging did not reveal any clues, the complaints were initially considered psychosomatic. As the symptoms deteriorated with ongoing weight loss, the patient was re-admitted to the hospital. Again, extensive additional investigation did not reveal any abnormalities. Because of previous exposition to the woods Lyme serology was determined. Surprisingly, it appeared to be a remarkable presentation of acute Lyme neuroborreliosis which was successfully treated with ceftriaxon. Clinicians must be aware of the fact that this severe illness can present without any typical symptoms.
Association between sepsis and Rocky Mountain spotted fever
Authors: Bacci Marcelo Rodrigues , Namura José Jorge
Published: December 2012

Rocky Mountain spotted fever (RMSF) is a disease caused by the Gram-negative coccobacillusRickettsia ricketsiiwhich has been on the rise since the last decade in the USA. The symptoms are common to the many viral diseases, and the classic triad of fever, rash and headache is not always present when RMSF is diagnosed. It may progress to severe cases such as renal failure, disseminated intravascular coagulation and septicaemia. This report aims to present a fulminant case of RMSF associated with sepsis. It describes a female patient's case that quickly progressed to sepsis and death. The patient showed non-specific symptoms for 5 days before being admitted to a hospital. The fact that she lived in an area highly infested with Amblyomma aureolatum ticks was unknown to the medical staff until the moment she died.
Metastatic leiomyosarcoma presenting as bilateral, multifocal breast masses
Authors: Vasan Neil , Saglam Ozlen , Killelea Brigid K
Published: December 2012

Here we describe a case of metastatic leiomyosarcoma presenting as bilateral, multifocal breast masses. This case represents the convergence of three rare entities: leiomyosarcoma of unknown primary origin, metastases to the breast and bilateral, multicentric breast disease.
Duodenal dissection secondary to intramural haematoma after endoscopic therapy for a bleeding duodenal ulcer in a patient on long-term haemodialysis with liver cirrhosis
Authors: Chen Chi-Yi , Yan Yuan-Horng
Published: December 2012

We report a case of intestinal obstruction and duodenal dissection resulting from an intramural haematoma after therapeutic upper digestive endoscopy with injection therapy for a bleeding duodenal ulcer in a patient on long-term haemodialysis with liver cirrhosis.
Childlessness, parental mortality and psychiatric illness: a natural experiment based on in vitro fertility treatment and adoption
Authors: Agerbo Esben , Mortensen Preben Bo , Munk-Olsen Trine
Published: December 2012

Background

Childlessness increases the risk of premature mortality and psychiatric illness. These results might, however, be confounded by factors that affect both the chance of parenthood as well as the risk of premature death and psychiatric illness.

Methods

Using population-based health and social registers, we conducted a follow-up study of 21 276 childless couples in in vitro fertility treatment.

Results

The crude death rate ratio in women who become mothers to a biological child is 0.25 (95% CI 0.16 to 0.39). In other words, childless women experience a fourfold higher rate of death, that is, 4.02 (2.56 to 6.31). The analogous death rate in fathers is approximately halved: 0.51 (0.39 to 0.68) and 0.55 (0.32 to 0.96) associated with having a biological child and an adopted child, respectively. With substance use disorders being the exception, none of the crude rates of psychiatric illness in parents of a biological child were statistically distinguishable from the rates in the childless. These findings were slightly confounded by age, calendar year, income, education, somatic comorbidity and marital breakup.

Conclusions

Mindful that association is not causation, our results suggest that the mortality rates are higher in the childless. Rates of psychiatric illness do not appear to vary with childlessness, but the rate of psychiatric illness in parents who adopt is decreased.
Inclusion of a Coulomb interaction potential in a variational model for positronium–helium scattering
Authors: DiRienzi Joseph , Drachman Richard J.
Published: December 2012

While carrying out investigations on Ps–He scattering it was discovered that it would be possible to improve the results of a previous work on zero-energy scattering of ortho-positronium by helium atoms. The previous work used a model to account for exchange and also attempted to include the effect of short-range Coulomb interactions in the close-coupling approximation. The three terms that were then included did not produce a well-converged result but served to give some justification to the model. Now we improve the calculation by using a simple variational wave function, and derive a much better value of the scattering length. The new result is compared with other computed values, and when an approximate correction due to the van der Waals potential is included the total is consistent with an earlier conjecture.
The interaction of diamines and polyamines with the peroxidase-catalyzed metabolism of aromatic amines: a potential mechanism for the modulation of aniline toxicity
Authors: Michail Karim , Aljuhani Naif , Siraki Arno G.
Published: December 2012

Synthetic and biological amines such as ethylenediamine (EDA), spermine, and spermidine have not been previously investigated in free-radical biochemical systems involving aniline-based drugs or xenobiotics. We aimed to study the influence of polyamines in the modulation of aromatic amine radical metabolites in peroxidase-mediated free radical reactions. The aniline compounds tested caused a relatively low oxidation rate of glutathione in the presence of horseradish peroxidase (HRP), and H2O2; however, they demonstrated marked oxygen consumption when a polyamine molecule was present. Next, we characterized the free-radical products generated by these reactions using spin-trapping and electron paramagnetic resonance (EPR) spectrometry. Primary and secondary but not tertiary polyamines dose-dependently enhanced the N-centered radicals of different aniline compounds catalyzed by either HRP or myeloperoxidase, which we believe occurred via charge transfer intermediates and subsequent stabilization of aniline-derived radical species as suggested by isotopically labeled aniline. Aniline/peroxidase reaction product(s) were monitored at 435 nm by kinetic spectrophotometry in the presence and absence of a polyamine additive. Using gas chromatography – mass spectrometry, the dimerziation product of aniline, azobenzene, was significantly amplified when EDA was present. In conclusion, di- and poly-amines are capable of enhancing the formation of aromatic-amine-derived free radicals, a fact that is expected to have toxicological consequences.
Identification of QTLs for capsaicinoids, fruit quality, and plant architecture-related traits in an interspecific Capsicum RIL population
Authors: Yarnes Shawn C. , Ashrafi Hamid , Reyes-Chin-Wo Sebastian , Hill Theresa A. , Stoffel Kevin M. , Van Deynze Allen
Published: December 2012

Quantitative trait loci (QTL) analyses in pepper are common for horticultural, disease resistance, and fruit quality traits; although none of the studies to date have used sequence-based markers associated with genes. In this study we measured plant architectural, phenological, and fruit quality traits in a pepper mapping population consisting of 92 recombinant inbred lines derived from a cross between Capsicum frutescens acc. 2814-6 and C. annuum var. NuMexRNAKY. Phenotypic measurements were correlated to loci in a high-density EST-based genetic map. In total, 96 QTL were identified for 38 traits, including 12 QTL associated with capsaicinoid levels. Twenty-one loci showed correlation among seemingly unrelated phenotypic categories, highlighting tight linkage or shared genetics between previously unassociated traits in pepper.
EXACT SOLUTIONS TO THE SPIN-2 GROSS–PITAEVSKII EQUATIONS
Authors: ZHANG ZHI-HAI , LIU YONG-KAI , YANG SHI-JIE
Published: December 2012

We present several exact solutions to the coupled nonlinear Gross–Pitaevskii equations which describe the motion of the one-dimensional spin-2 Bose–Einstein condensates. The nonlinear density–density interactions are decoupled by making use of the properties of Jacobian elliptical functions. The distinct time factors in each hyperfine state implies a "Lamor" procession in these solutions. Furthermore, exact time-evolving solutions to the time-dependent Gross–Pitaevskii equations are constructed through the spin-rotational symmetry of the Hamiltonian. The spin-polarizations and density distributions in the spin-space are analyzed.
RECONSTRUCTING GROUP ACTIONS
Authors: CARBONE LISA , RIPS ELIYAHU
Published: December 2012

We give a general structure theory for reconstructing non-trivial group actions on sets without any further assumptions on the group, the action, or the set on which the group acts. Using certain "local data" [Formula: see text] from the action we build a group [Formula: see text] of the data and a space [Formula: see text] with an action of [Formula: see text] on [Formula: see text] that arise naturally from the data [Formula: see text]. We use these to obtain an approximation to the original group G, the original space X and the original action G × X → X. The data [Formula: see text] is distinguished by the property that it may be chosen from the action locally. For a large enough set of local data [Formula: see text], our definition of [Formula: see text] in terms of generators and relations allows us to obtain a presentation for the group G. We demonstrate this on several examples. When the local data [Formula: see text] is chosen from a graph of groups, the group [Formula: see text] is the fundamental group of the graph of groups and the space [Formula: see text] is the universal covering tree of groups. For general non-properly discontinuous group actions our local data allows us to imitate a fundamental domain, quotient space and universal covering for the quotient. We exhibit this on a non-properly discontinuous free action on ℝ. For a certain class of non-properly discontinuous group actions on the upper half-plane, we use our local data to build a space on which the group acts discretely and cocompactly. Our combinatorial approach to reconstructing abstract group actions on sets is a generalization of the Bass–Serre theory for reconstructing group actions on trees. Our results also provide a generalization of the notion of developable complexes of groups by Haefliger.
DESIGN AND ANALYSIS OF THERMOACOUSTIC REFRIGERATOR
Authors: PRASHANTHA B. G. , GOVINDE GOWDA M. S. , SEETHARAMU S. , NARASIMHAM G. S. V. L.
Published: December 2012

This paper deals with the design and analysis of a quarter-wavelength, 10 W capacity, thermoacoustic refrigerator using short stack boundary layer approximation assumptions. The effect of operating frequency on the performance of the refrigerator is studied using dimensional normalization technique. The variation of stack diameter with average gas pressure and cooling power is discussed. The resonator optimization is discussed and the calculation results show a 9% improvement in the coefficient of performance and 201% improvement in power density for the optimized quarter-wavelength resonator compared to published optimization studies. The optimized resonator design is tested with DeltaEC software and the results show better performance compared to past established resonator designs.
Prostaglandin and myokine involvement in the cyclooxygenase-inhibiting drug enhancement of skeletal muscle adaptations to resistance exercise in older adults
Authors: Trappe Todd A. , Standley Robert A. , Jemiolo Bozena , Carroll Chad C. , Trappe Scott W.
Published: December 2012

Twelve weeks of resistance training (3 days/wk) combined with daily consumption of the cyclooxygenase-inhibiting drugs acetaminophen (4.0 g/day; n = 11, 64 ± 1 yr) or ibuprofen (1.2 g/day; n = 13, 64 ± 1 yr) unexpectedly promoted muscle mass and strength gains 25–50% above placebo ( n = 12, 67 ± 2 yr). To investigate the mechanism of this adaptation, muscle biopsies obtained before and ∼72 h after the last training bout were analyzed for mRNA levels of prostaglandin (PG)/cyclooxygenase pathway enzymes and receptors [arachidonic acid synthesis: cytosolic phospholipase A2(cPLA2) and secreted phospholipase A2(sPLA2); PGF2αsynthesis: PGF2αsynthase and PGE2to PGF2αreductase; PGE2synthesis: PGE2synthase-1, -2, and -3; PGF2αreceptor and PGE2receptor-4], cytokines and myokines involved in skeletal muscle adaptation (TNF-α, IL-1β, IL-6, IL-8, IL-10), and regulators of muscle growth [myogenin, myogenic regulatory factor-4 (MRF4), myostatin] and atrophy [Forkhead box O3A (FOXO3A), atrogin-1, muscle RING finger protein 1 (MuRF-1), inhibitory κB kinase β (IKKβ)]. Training increased ( P < 0.05) cPLA2, PGF2αsynthase, PGE2to PGF2αreductase, PGE2receptor-4, TNF-α, IL-1β, IL-8, and IKKβ. However, the PGF2αreceptor was upregulated ( P < 0.05) only in the drug groups, and the placebo group upregulation ( P < 0.05) of IL-6, IL-10, and MuRF-1 was eliminated in both drug groups. These results highlight prostaglandin and myokine involvement in the adaptive response to exercise in older individuals and suggest two mechanisms underlying the enhanced muscle mass gains in the drug groups: 1) The drug-induced PGF2αreceptor upregulation helped offset the drug suppression of PGF2α-stimulated protein synthesis after each exercise bout and enhanced skeletal muscle sensitivity to this stimulation. 2) The drug-induced suppression of intramuscular PGE2production increased net muscle protein balance after each exercise bout through a reduction in PGE2-induced IL-6 and MuRF-1, both promoters of muscle loss.
Intercalated cell-specific Rh B glycoprotein deletion diminishes renal ammonia excretion response to hypokalemia
Authors: Bishop Jesse M. , Lee Hyun-Wook , Handlogten Mary E. , Han Ki-Hwan , Verlander Jill W. , Weiner I. David
Published: December 2012

The ammonia transporter family member, Rh B Glycoprotein (Rhbg), is an ammonia-specific transporter heavily expressed in the kidney and is necessary for the normal increase in ammonia excretion in response to metabolic acidosis. Hypokalemia is a common clinical condition in which there is increased renal ammonia excretion despite the absence of metabolic acidosis. The purpose of this study was to examine Rhbg's role in this response through the use of mice with intercalated cell-specific Rhbg deletion (IC-Rhbg-KO). Hypokalemia induced by feeding a K+-free diet increased urinary ammonia excretion significantly. In mice with intact Rhbg expression, hypokalemia increased Rhbg protein expression in intercalated cells in the cortical collecting duct (CCD) and in the outer medullary collecting duct (OMCD). Deletion of Rhbg from intercalated cells inhibited hypokalemia-induced changes in urinary total ammonia excretion significantly and completely prevented hypokalemia-induced increases in urinary ammonia concentration, but did not alter urinary pH. We conclude that hypokalemia increases Rhbg expression in intercalated cells in the cortex and outer medulla and that intercalated cell Rhbg expression is necessary for the normal increase in renal ammonia excretion in response to hypokalemia.
Genetic basis of the impaired renal myogenic response in FHH rats
Authors: Burke Marilyn , Pabbidi Malikarjuna , Fan Fan , Ge Ying , Liu Ruisheng , Williams Jan Michael , Sarkis Allison , Lazar Jozef , Jacob Howard J. , Roman Richard J.
Published: December 2012

This study examined the effect of substitution of a 2.4-megabase pair (Mbp) region of Brown Norway (BN) rat chromosome 1 (RNO1) between 258.8 and 261.2 Mbp onto the genetic background of fawn-hooded hypertensive (FHH) rats on autoregulation of renal blood flow (RBF), myogenic response of renal afferent arterioles (AF-art), K+channel activity in renal vascular smooth muscle cells (VSMCs), and development of proteinuria and renal injury. FHH rats exhibited poor autoregulation of RBF, while FHH.1BN congenic strains with the 2.4-Mbp BN region exhibited nearly perfect autoregulation of RBF. The diameter of AF-art from FHH rats increased in response to pressure but decreased in congenic strains containing the 2.4-Mbp BN region. Protein excretion and glomerular and interstitial damage were significantly higher in FHH rats than in congenic strains containing the 2.4-Mbp BN region. K+channel current was fivefold greater in VSMCs from renal arterioles of FHH rats than cells obtained from congenic strains containing the 2.4-Mbp region. Sequence analysis of the known and predicted genes in the 2.4-Mbp region of FHH rats revealed amino acid-altering variants in the exons of three genes: Add3, Rbm20, and Soc-2. Quantitative PCR studies indicated that Mxi1 and Rbm20 were differentially expressed in the renal vasculature of FHH and FHH.1BN congenic strain F. These data indicate that transfer of this 2.4-Mbp region from BN to FHH rats restores the myogenic response of AF-art and autoregulation of RBF, decreases K+current, and slows the progression of proteinuria and renal injury.