bluuebunny/crossref_metadata_2025 huggingface dataset:
Development of Neuraminidase Subtype-Specific Reference Antisera by Recombinant Protein Expressed in Baculovirus
Authors: Lee Kyu-Jun , Choi Jun-Gu , Kang Hyun-Mi , Kim Kwang-Il , Park Choi-Kyu , Lee Youn-Jeong
Published: December 2012

Outbreaks of avian influenza A virus infection, particularly the H5N1 strains that have affected birds and some humans for the past 15 years, have highlighted the need for increased surveillance and disease control. Such measures require diagnostic tests to detect and characterize the different subtypes of influenza virus. In the current study, a simple method for producing reference avian influenza virus antisera to be used in diagnostic tests was developed. Antisera of nine avian influenza A virus neuraminidases (NA) used for NA subtyping were produced using a recombinant baculovirus. The recombinant NA (rNA) proteins were expressed in Sf9 insect cells and inoculated intramuscularly into specific-pathogen-free chickens with the ISA70 adjuvant. The NA inhibition antibody titers of the rNA antiserum were in the ranges of 5 to 8 and 6 to 9 log2units after the primary and boost immunizations, respectively. The antisera were subtype specific, showing low cross-reactivity against every other NA subtype using the conventional thiobarbituric acid NA inhibition assay. These results suggest that this simple method for producing reference NA antisera without purification may be useful for the diagnosis and surveillance of influenza virus.
First Case of Cerebral Abscess Due to a Novel Nocardia Species in an Immunocompromised Patient
Authors: Flateau C. , Jurado V. , Lemaître N. , Loïez C. , Wallet F. , Saiz-Jimenez C. , Decoene C. , Bergeron E. , Boiron P. , Faure K. , Guery B. , Rodríguez-Nava V.
Published: December 2012

We report the first case of cerebral abscess due to a novel species of
Nocardia
in a heart transplant patient and describe the antimicrobial susceptibility of this isolate. As our patient was intolerant to trimethoprim-sulfamethoxazole, we also discuss alternative therapeutic options in brain abscess due to
Nocardia
sp.
Comparison of Commercial Real-Time Reverse Transcription-PCR Assays for Reliable, Early, and Rapid Detection of Heterologous Strains of Porcine Reproductive and Respiratory Syndrome Virus in Experimentally Infected or Noninfected Boars by Use of Different Sample Types
Authors: Gerber Priscilla F. , O'Neill Kevin , Owolodun Olajide , Wang Chong , Harmon Karen , Zhang Jianqiang , Halbur Patrick G. , Zhou Lei , Meng Xiang-Jin , Opriessnig Tanja
Published: December 2012

The aims of this study were to compare three commercial porcine reproductive and respiratory syndrome virus (PRRSV) real-time reverse transcription-PCR (RT-PCR) assays for detection of genetically diverse PRRSV isolates in serum, semen, blood swabs, and oral fluids collected from experimentally infected boars and to evaluate the effects of sample pooling. Six groups of three boars negative for PRRSV were each inoculated with one of six PRRSV isolates (sharing 55 to 99% nucleotide sequence identity in ORF5). Samples were collected on days −2, 1, 3, 5, 7, 14, and 21 postinoculation (p.i.) and tested by one of three commercially available real-time RT-PCR assays (VetMax from Applied Biosystems, Foster City, CA [abbreviated AB]; VetAlert from Tetracore, Rockville, MD [TC]; and AcuPig from AnDiaTec GmbH, Kornwestheim, Germany [AD]). At day 1 p.i., all assays detected at least one positive sample in each group. The highest detection rates were on days 3 and 5 p.i. Between days 1 and 7 p.i., serum samples had the highest detection rate (90%) with 100% agreement between tests, followed by blood swabs (kappa value of 0.97) and semen (kappa value of 0.80). Oral fluids had the lowest detection rates (AB, 55%; TC, 41%; AD, 46%) and the highest disagreement between kits (kappa value of 0.63). Pools of five samples did not reduce the detection rates if there was one positive sample with a large amount (cycle threshold, <30) of viral RNA in the pool. Serum and blood swab samples had shorter turnaround times for RNA extraction. The AB assay had a 1.6-times-shorter PCR time. In summary, serum and blood swabs had the best performance with highest detection rates and agreement between assays and the shortest turnaround times.
Dolphin Morbillivirus Infection in a Captive Harbor Seal (Phoca vitulina)
Authors: Mazzariol Sandro , Peletto Simone , Mondin Alessandra , Centelleghe Cinzia , Di Guardo Giovanni , Di Francesco Cristina Esmeralda , Casalone Cristina , Acutis Pier Luigi
Published: December 2012

During the second morbillivirus epidemic (2007 to 2011) in cetaceans along the Italian coastline, dolphin morbillivirus (DMV) was detected by molecular analyses in a captive harbor seal (
Phoca vitulina
), with pathological findings consistent with morbillivirus infection. This report confirms interspecies DMV transmission from cetaceans to pinnipeds.
How Many Sputum Culture Results Do We Need To Monitor Multidrug-Resistant-Tuberculosis (MDR-TB) Patients during Treatment?
Authors: Janssen Saskia , Padanilam Xavier , Louw Rianna , Mahanyele Russel , Coetzee Gerrit , Hänscheid Thomas , Leenstra Tjalling , Grobusch Martin P.
Published: December 2012

Discharge of a hospital patient after a single negative sputum culture may save money when treating multidrug-resistant tuberculosis. However, after initial sputum conversion in 336 South Africans, 11.6% and 5.4% reconverted after 1 and 2 months, respectively. These findings endorse the WHO definitions of 2 negative cultures taken ≥30 days apart after sputum culture conversion.
Long-Term Retention of Knowledge and Critical Thinking Skills in Developmental Biology
Authors: Darland Diane C. , Carmichael Jeffrey S.
Published: December 2012

The primary goal of this project was to assess long-term retention of concepts and critical thinking skills in individuals who completed a Developmental Biology course. Undergraduates who had completed the course between 2006 and 2009 were recently contacted and asked to complete a professional goals survey and a multiple-choice developmental biology assessment test (DBAT) targeting four levels of learning. The DBAT was designed to assess students’ retention of knowledge and skills related to factual recall, concept application, data analysis, and experimental design. Performance of the 2006–2009 cohorts was compared to that of students enrolled in 2010 who completed the DBAT at the beginning and the end of the semester. Participants from the 2010 course showed significant learning gains based on pre- and posttest scores overall and for each of the four levels of learning. No significant difference in overall performance was observed for students grouped by year from 2006–2010. Participants from the 2006–2009 cohorts scored slightly, but significantly, higher on average if they enrolled in graduate or professional training. However, performance on individual question categories revealed no significant differences between those participants with and without postundergraduate training. Scores on exams and a primary literature critique assignment were correlated with DBAT scores and thus represent predictors of long-term retention of developmental biology knowledge and skills.
Educating Medical Laboratory Technologists: Revisiting Our Assumptions in the Current Economic and Health-Care Environment
Authors: Linder Regina
Published: December 2012

Health care occupies a distinct niche in an economy struggling to recover from recession. Professions related to the care of patients are thought to be relatively resistant to downturns, and thus become attractive to students typically drawn to more lucrative pursuits. Currently, a higher profile for clinical laboratory technology among college students and those considering career change results in larger and better prepared applicant pools. However, after decades of contraction marked by closing of programs, prospective students encounter an educational system without the capacity or vigor to meet their needs. Here discussed are some principles and proposals to allow universities, partnering with health-care providers, government agencies, and other stake-holders to develop new programs, or reenergize existing ones to serve our students and patients. Principles include academic rigor in biomedical and clinical science, multiple points of entry for students, flexibility in format, cost effectiveness, career ladders and robust partnerships.
Using Small Group Debates to Actively Engage Students in an Introductory Microbiology Course
Authors: Shaw Joyce A.
Published: December 2012

Debates stimulate critical thinking and can be a highly effective way to actively engage students in the classroom. This paper describes a small group debate format in which groups of four to six students debated preassigned topics in microbiology in front of the rest of the class. Rapid advancements in science, especially in microbiology, provide the scaffolding for students to locate and share evidence-based information from a plethora of complex and often conflicting sources. Student-generated debate presentations can be a welcome respite from the lecture format. Debates were scheduled throughout the course to coincide with topics being covered. Questionnaires distributed immediately after each debate revealed that the debates were well received by students and were effective in changing student attitudes and misconceptions. Debate preparation provided students the opportunity to gain proficiency in accessing information from electronic databases, to use resources from professional organizations, and to synthesize and analyze information. In addition, the debate process gave students experience in developing oral communication skills.
The Genome Solver Website: A Virtual Space Fostering High Impact Practices for Undergraduate Biology
Authors: Rosenwald Anne G. , Russell Janet S. , Arora Gaurav
Published: December 2012

While the tools for analysis of prokaryotic genomes are available on the internet and are relatively easy for undergraduates to master, the challenge lies with faculty inexperienced in teaching bioinformatics. To meet this challenge we developed the Genome Solver (GS) website, a community of practice for faculty support and student learning. At the GS site, faculty can learn about face-to-face training opportunities or use the virtual training materials such as primers on the pertinent science, tools, and techniques. Faculty can also find colleagues engaged in similar work as well as relevant curricular materials. The GS site also helps facilitate sharing of student work, so that students can engage in peer-to-peer review. Finally, genomics experts also have a presence on GS and can weigh in on problems or discuss methods.
Using Bioinformatics to Develop and Test Hypotheses:
E. coli
-Specific Virulence Determinants
Authors: Klein Joanna R. , Gulsvig Theresa
Published: December 2012

Bioinformatics, the use of computer resources to understand biological information, is an important tool in research, and can be easily integrated into the curriculum of undergraduate courses. Such an example is provided in this series of four activities that introduces students to the field of bioinformatics as they design PCR based tests for pathogenic
E. coli
strains. A variety of computer tools are used including BLAST searches at NCBI, bacterial genome searches at the Integrated Microbial Genomes (IMG) database, protein analysis at Pfam and literature research at PubMed. In the process, students also learn about virulence factors, enzyme function and horizontal gene transfer. Some or all of the four activities can be incorporated into microbiology or general biology courses taken by students at a variety of levels, ranging from high school through college. The activities build on one another as they teach and reinforce knowledge and skills, promote critical thinking, and provide for student collaboration and presentation. The computer-based activities can be done either in class or outside of class, thus are appropriate for inclusion in online or blended learning formats. Assessment data showed that students learned general microbiology concepts related to pathogenesis and enzyme function, gained skills in using tools of bioinformatics and molecular biology, and successfully developed and tested a scientific hypothesis.
Enhancing Engineering Students’ Learning in an Environmental Microbiology Course
Authors: Zhou Zhi
Published: December 2012

While environmental engineering students have gained some knowledge of biogeochemical cycles and sewage treatment, most of them haven’t learned microbiology previously and usually have difficulty in learning environmental microbiology because microbiology deals with invisible living microorganisms instead of visible built environment. Many teaching techniques can be used to enhance students’ learning in microbiology courses, such as lectures, animations, videos, small-group discussions, and active learning techniques. All of these techniques have been applied in the engineering class, but the results indicate that these techniques are often inadequate for students. Learning difficulties have to be identified to enhance students’ learning.
Microorganisms Enhance Understanding of EvolutionReview of:	Microbes and Evolution: The World That Darwin Never Saw; edited by	KolterRobertoMaloyStanley; (	2012).	ASM Press,	Washington, DC.	299 pages.
Authors: Harbour Deborah V.
Published: December 2012

Review of:
Microbes and Evolution: The World That Darwin Never Saw;
edited by Roberto Kolter and Stanley Maloy; (2012). ASM Press, Washington, DC. 299 pages
Microbiologists Just Want to Have FunReview of:	A Selected Set of Non-Technical Online Microbial Resources.
Authors: Seitz Heather M.
Published: December 2012

Review of:
Non-technical online microbial resources that entertain, engage, and promote microbiology thorugh music, comics, and gaming. Resources include
Food Safety Music, Pandemic 2, Microbe Kombat,
and
The Great Flu.
Virulence Determinants of Pandemic A(H1N1)2009 Influenza Virus in a Mouse Model
Authors: Uraki Ryuta , Kiso Maki , Shinya Kyoko , Goto Hideo , Takano Ryo , Iwatsuki-Horimoto Kiyoko , Takahashi Kazuo , Daniels Rod S. , Hungnes Olav , Watanabe Tokiko , Kawaoka Yoshihiro
Published: December 2012

A novel swine-origin H1N1 influenza virus [A(H1N1)pdm09 virus] caused the 2009 influenza pandemic. Most patients exhibited mild symptoms similar to seasonal influenza, but some experienced severe clinical signs and, in the worst cases, died. Such differences in symptoms are generally associated with preexisting medical conditions, but recent reports indicate the possible involvement of viral factors in clinical severity. To better understand the mechanism of pathogenicity of the A(H1N1)pdm09 virus, here, we compared five viruses that are genetically similar but were isolated from patients with either severe or mild symptoms. In a mouse model, A/Norway/3487/2009 (Norway3487) virus exhibited greater pathogenicity than did A/Osaka/164/2009 (Osaka164) virus. By exploiting reassortant viruses between these two viruses, we found that viruses possessing the hemagglutinin (HA) gene of Norway3487 in the genetic background of Osaka164 were more pathogenic in mice than other reassortant viruses, indicating a role for HA in the high virulence of Norway3487 virus. Intriguingly, a virus possessing HA, NA, and NS derived from Norway3487 exhibited greater pathogenicity in mice in concert with PB2 and PB1 derived from Osaka164 than did the parental Norway3487 virus. These findings demonstrate that reassortment between A(H1N1)pdm09 viruses can lead to increased pathogenicity and highlight the need for continued surveillance of A(H1N1)pdm09 viruses.
Identification and Structural Characterization of a Broadly Neutralizing Antibody Targeting a Novel Conserved Epitope on the Influenza Virus H5N1 Hemagglutinin
Authors: Du Lanying , Jin Lei , Zhao Guangyu , Sun Shihui , Li Junfeng , Yu Hong , Li Ye , Zheng Bo-Jian , Liddington Robert C. , Zhou Yusen , Jiang Shibo
Published: December 2012

The unabated circulation of the highly pathogenic avian influenza A virus/H5N1 continues to be a serious threat to public health worldwide. Because of the high frequency of naturally occurring mutations, the emergence of H5N1 variants with high virulence has raised great concerns about the potential transmissibility of the virus in humans. Recent studies have shown that laboratory-mutated or reassortant H5N1 viruses could be efficiently transmitted among mammals, particularly ferrets, the best animal model for humans. Thus, it is critical to establish effective strategies to combat future H5N1 pandemics. In this study, we identified a broadly neutralizing monoclonal antibody (MAb), HA-7, that potently neutralized all tested strains of H5N1 covering clades 0, 1, 2.2, 2.3.4, and 2.3.2.1 and completely protected mice against lethal challenges of H5N1 viruses from clades 1 and 2.3.4. HA-7 specifically targeted the globular head of the H5N1 virus hemagglutinin (HA). Using electron microscopy technology with three-dimensional reconstruction (3D-EM), we discovered that HA-7 bound to a novel and highly conserved conformational epitope that was centered on residues 81 to 83 and 117 to 122 of HA1 (H5 numbering). We further demonstrated that HA-7 inhibited viral entry during postattachment events but not at the receptor-binding step, which is fully consistent with the 3D-EM result. Taken together, we propose that HA-7 could be humanized as an effective passive immunotherapeutic agent for antiviral stockpiling for future influenza pandemics caused by emerging unpredictable H5N1 strains. Our study also provides a sound foundation for the rational design of vaccines capable of inducing broad-spectrum immunity against H5N1.
Attenuation of the Adaptive Immune Response in Rhesus Macaques Infected with Simian Varicella Virus Lacking Open Reading Frame 61
Authors: Meyer Christine , Kerns Amelia , Haberthur Kristen , Dewane Jesse , Walker Joshua , Gray Wayne , Messaoudi Ilhem
Published: December 2012

Varicella zoster virus (VZV) is a neurotropic alphaherpesvirus that causes chickenpox during primary infection and establishes latency in sensory ganglia. Infection of rhesus macaques (RM) with the homologous simian varicella virus (SVV) recapitulates hallmarks of VZV infection. We have shown that an antisense transcript of SVV open reading frame 61 (ORF61), a viral transactivator, was detected most frequently in latently infected RM sensory ganglia. In this study, we compared disease progression, viral replication, immune response, and the establishment of latency following intrabronchial infection with a recombinant SVV lacking ORF61 (SVVΔORF61) to those following infection with wild-type (WT) SVV. Varicella severity and viral latency within sensory ganglia were comparable in RMs infected with SVVΔORF61 and WT SVV. In contrast, viral loads, B and T cell responses, and plasma inflammatory cytokine levels were decreased in RMs infected with SVVΔORF61. To investigate the mechanisms underlying the reduced adaptive immune response, we compared acute SVV gene expression, frequency and proliferation of dendritic cell (DC) subsets, and the expression of innate antiviral genes in bronchoalveolar lavage (BAL) samples. The abundance of SVV transcripts in all kinetic classes was significantly decreased in RMs infected with SVVΔORF61. In addition, we detected a higher frequency and proliferation of plasmacytoid dendritic cells in BAL fluid at 3 days postinfection in RMs infected with SVVΔORF61, which was accompanied by a slight increase in type I interferon gene expression. Taken together, our data suggest that ORF61 plays an important role in orchestrating viral gene expressionin vivoand interferes with the host antiviral interferon response.
Frequent Cross-Species Transmission of Parvoviruses among Diverse Carnivore Hosts
Authors: Allison Andrew B. , Kohler Dennis J. , Fox Karen A. , Brown Justin D. , Gerhold Richard W. , Shearn-Bochsler Valerie I. , Dubovi Edward J. , Parrish Colin R. , Holmes Edward C.
Published: December 2012

Although parvoviruses are commonly described in domestic carnivores, little is known about their biodiversity in nondomestic species. A phylogenetic analysis of VP2 gene sequences from puma, coyote, gray wolf, bobcat, raccoon, and striped skunk revealed two major groups related to either feline panleukopenia virus (“FPV-like”) or canine parvovirus (“CPV-like”). Cross-species transmission was commonplace, with multiple introductions into each host species but, with the exception of raccoons, relatively little evidence for onward transmission in nondomestic species.
The Kaposi's Sarcoma-Associated Herpesvirus ORF34 Protein Binds to HIF-1α and Causes Its Degradation via the Proteasome Pathway
Authors: Haque Muzammel , Kousoulas Konstantin G.
Published: December 2012

Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent for Kaposi's sarcoma (KS) and two other lymphoproliferative disorders, primary effusion lymphoma (PEL) and multicentric Castleman's disease (MCD). Kaposi's sarcoma is a highly vascular tumor, and recently both hypoxia-inducible factor 1α (HIF-1α) and HIF-2α were detected in KS samples, indicating a role of HIFs in the KSHV life cycle. Previously, we showed that ORF34, a lytic gene of unassigned function, was activated by hypoxia and that ORF34 transcription was upregulated by both HIFs (M. Haque, D. A. Davis, V. Wang, I. Widmer, and R. Yarchoan, J Virol.
77:
6761–6768, 2003). In the present study, we show that coexpression of ORF34 with HIF-1αm (degradation-resistant HIF-1α) caused substantial reduction in HIF-1α-dependent transcription, as evidenced by reporter assays. Two-way immunoprecipitation experiments revealed that ORF34 physically interacted with HIF-1αm in transient expression experiments. Deletion analysis revealed that three different ORF34 domains interacted with the amino-terminal domain of HIF-1α. Also, purified HIF-1α and ORF34 proteins interacted with each other. The observed transcriptional inhibition of HIF-1α-dependent promoters was attributed to degradation of HIF-1α after binding with ORF34, since the overall amount of wild-type HIF-1α but not the degradation-resistant one (HIF-1αm) was reduced in the presence of ORF34. Moreover, ORF34 caused degradation of HIF-1α in a dose-dependent manner. Inhibition of the ubiquitin-dependent pathway by the chemical proteasome inhibitor MG132 prevented HIF-1α degradation in the presence of ORF34. These results show that ORF34 binds to HIF-1α, leading to its degradation via the proteasome-dependent pathway.
Design Requirements for Interfering Particles To Maintain Coadaptive Stability with HIV-1
Authors: Rouzine Igor M. , Weinberger Leor S.
Published: December 2012

Defective interfering particles (DIPs) are viral deletion mutants lacking essential transacting or packaging elements and must be complemented by wild-type virus to propagate. DIPs transmit through human populations, replicating at the expense of the wild-type virus and acting as molecular parasites of viruses. Consequently, engineered DIPs have been proposed as therapies for a number of diseases, including human immunodeficiency virus (HIV). However, it is not clear if DIP-based therapies would face evolutionary blocks given the high mutation rates and high within-host diversity of lentiviruses. Divergent evolution of HIV and DIPs appears likely since natural DIPs have not been detected for lentiviruses, despite extensive sequencing of HIVs and simian immunodeficiency viruses (SIVs). Here, we tested if the apparent lack of lentiviral DIPs is due to natural selection and analyzed which molecular characteristics a DIP or DIP-based therapy would need to maintain coadaptive stability with HIV-1. Using a well-established mathematical model of HIV-1 in a host extended to include its replication in a single cell and interference from DIP, we calculated evolutionary selection coefficients. The analysis predicts that interference by codimerization between DIPs and HIV-1 genomes is evolutionarily unstable, indicating that recombination between DIPs and HIV-1 would be selected against. In contrast, DIPs that interfere via competition for capsids have the potential to be evolutionarily stable if the capsid-to-genome production ratio of HIV-1 is >1. Thus, HIV-1 variants that attempt to “starve” DIPs to escape interference would be selected against. In summary, the analysis suggests specific experimental measurements that could address the apparent lack of naturally occurring lentiviral DIPs and specifies how therapeutic approaches based on engineered DIPs could be evolutionarily robust and avoid recombination.
Hypervariable Domains of nsP3 Proteins of New World and Old World Alphaviruses Mediate Formation of Distinct, Virus-Specific Protein Complexes
Authors: Foy Niall J. , Akhrymuk Maryna , Akhrymuk Ivan , Atasheva Svetlana , Bopda-Waffo Alain , Frolov Ilya , Frolova Elena I.
Published: December 2012

Alphaviruses are a group of single-stranded RNA viruses with genomes of positive polarity. They are divided into two geographically isolated groups: the Old World and the New World alphaviruses. Despite their similar genome organizations and virion structures, they differ in many aspects of pathogenesis and interaction with the host cell. Here we present new data highlighting previously unknown differences between these two groups. We found that nsP3 proteins of Sindbis virus (SINV) and Venezuelan equine encephalitis virus (VEEV) form cytoplasmic complexes with different morphologies and protein compositions. Unlike the amorphous aggregates formed by SINV nsP3 and other Old World alphavirus-specific nsP3s, VEEV nsP3 forms unique, large spherical structures with striking symmetry. Moreover, VEEV nsP3 does not interact with proteins previously identified as major components of SINV nsP3 complexes, such as G3BP1 and G3BP2. Importantly, the morphology of the complexes and the specificity of the interaction with cellular proteins are largely determined by the hypervariable domain (HVD) of nsP3. Replacement of the VEEV nsP3 HVD with the corresponding domain of SINV nsP3 rendered this protein capable of interaction with G3BPs. Conversely, replacement of the SINV nsP3 HVD with that of VEEV abolished SINV nsP3's interaction with G3BPs. The replacement of natural HVDs with those from heterologous viruses did not abrogate virus replication, despite these fragments demonstrating very low levels of sequence identity. Our data suggest that in spite of the differences in morphology and composition of the SINV- and VEEV-specific nsP3 complexes, it is likely that they have similar functions in virus replication and modification of the cellular environment.
Helicobacter pylori Peptidoglycan Modifications Confer Lysozyme Resistance and Contribute to Survival in the Host
Authors: Wang Ge , Lo Leja F. , Forsberg Lennart S. , Maier Robert J.
Published: December 2012

The prominent host muramidase lysozyme cleaves bacterial peptidoglycan (PG), and the enzyme is abundant in mucosal secretions. The lytic enzyme susceptibility of Gram-negative bacteria and mechanisms they use to thwart lytic enzyme activity are poorly studied. We previously characterized a
Helicobacter pylori
PG modification enzyme, an N-deacetylase (PgdA) involved in lysozyme resistance. In this study, another PG modification enzyme, a putative PG O-acetyltransferase (PatA), was identified. Mass spectral analysis of the purified PG demonstrated that a
patA
strain contained a greatly reduced amount of acetylated muropeptides, indicating a role for PatA in
H. pylori
PG O-acetylation. The PG modification mutant strains (
pgdA
,
patA
, or
pgdA patA
) were more susceptible to lysozyme killing than the parent, but this assay required high lysozyme levels (up to 50 mg/ml). However, addition of host lactoferrin conferred lysozyme sensitivity to
H. pylori
, at physiologically relevant concentrations of both host components (3 mg/ml lactoferrin plus 0.3 mg/ml lysozyme). The
pgdA patA
double mutant strain was far more susceptible to lysozyme/lactoferrin killing than the parent. Peptidoglycan purified from a
pgdA patA
mutant was five times more sensitive to lysozyme than PG from the parent strain, while PG from both single mutants displayed intermediate sensitivity. Both sensitivity assays for whole cells and for purified PGs indicated that the modifications mediated by PgdA and PatA have a synergistic effect, conferring lysozyme tolerance. In a mouse infection model, significant colonization deficiency was observed for the double mutant at 3 weeks postinoculation. The results show that PG modifications affect the survival of a Gram-negative pathogen.

IMPORTANCE
Pathogenic bacteria evade host antibacterial enzymes by a variety of mechanisms, which include resisting lytic enzymes abundant in the host. Enzymatic modifications to peptidoglycan (PG, the site of action of lysozyme) are a known mechanism used by Gram-positive bacteria to protect against host lysozyme attack. However, Gram-negative bacteria contain a thin layer of PG and a recalcitrant outer membrane permeability barrier to resist lysis, so molecular modifications to cell wall structure in order to combat lysis remain largely unstudied. Here we show that two
Helicobacter pylori
PG modification enzymes (PgdA and PatA) confer a clear protective advantage to a Gram-negative bacterium. They protect the bacterium from lytic enzyme degradation, albeit via different PG modification activities. Many pathogens are Gram negative, so some would be expected to have a similar cell wall-modifying strategy. Understanding such strategies may be useful for combating pathogen growth.
Experimental Infections of the Reservoir Species Peromyscus leucopus with Diverse Strains of Borrelia burgdorferi, a Lyme Disease Agent
Authors: Baum Elisabeth , Hue Fong , Barbour Alan G.
Published: December 2012

The rodentPeromyscus leucopusis a major natural reservoir for the Lyme disease agentBorrelia burgdorferiand a host for its vectorIxodes scapularis. At various locations in northeastern United States 10 to 15 B. burgdorferistrains coexist at different prevalences in tick populations. We asked whether representative strains of high or low prevalence differed in their infections ofP. leucopus. After 5 weeks of experimental infection of groups with each of 6 isolates, distributions and burdens of bacteria in tissues were measured by quantitative PCR, and antibodies toB. burgdorferiwere evaluated by immunoblotting and protein microarray. All groups of animals were infected in their joints, ears, tails, and hearts, but overall spirochete burdens were lower in animals infected with low-prevalence strains. Animals were similar regardless of the infecting isolate in their levels of antibodies to whole cells, FlaB, BmpA, and DbpB proteins, and the conserved N-terminal region of the serotype-defining OspC proteins. But there were strain-specific antibody responses to full-length OspC and to plasmid-encoded VlsE, BBK07, and BBK12 proteins. Sequencing of additional VlsE genes revealed substantial diversity within some pairs of strains but near-identical sequences within other pairs, which otherwise differed in theirospCalleles. The presence or absence of full-length bbk07 and bbk12 genes accounted for the differences in antibody responses. We propose that forB. burgdorferi, there is selection in reservoir species for (i) sequence diversity, as for OspC and VlsE, and (ii) the presence or absence of polymorphisms, as for BBK07 and BBK12.

IMPORTANCEHumans are dead-end hosts forBorreliaagents of Lyme disease (LD), and, thus, irrelevant for the pathogens’ maintenance. Many reports of human cases and laboratory mouse infections exist, but less is known about infection and immunity in natural reservoirs, such as the rodentPeromyscus leucopus. We observed that high- and low-prevalence strains ofBorrelia burgdorferiwere capable of infectingP. leucopusbut elicited different patterns of antibody responses. Antibody reactivities to the VlsE protein were as type-specific as previously characterized reactivities to serotype-defining OspC proteins. In addition, the low-prevalence strains lacked full-length genes for two proteins that (i) are encoded by a virulence-associated plasmid in some high-prevalence strains and (ii) LD patients and field-captured rodents commonly have antibodies to. Immune selection against these genes may have led to null phenotype lineages that can infect otherwise immune hosts but at the cost of reduced fitness and lower prevalence.
Sparganosis of liver: a rare entity and review of literature
Authors: Khurana Sumeeta , Appannanavar Suma , Bhatti Harinder Singh , Verma Sanjay
Published: December 2012

Humans are known to serve as the secondary intermediate host for some larval forms of canine or feline tapeworms. Sparganosis is caused by plerocercoid larva ofSpirometraof which there are three main species;Spirometra mansoni(orSpirometra erinaceieuropaei),Spirometra mansonoidesandSpirometra proliferum. A one-and-half-year-old patient presenting with febrile illness was diagnosed radiologically as a case of liver abscess. The aspirate from the abscess cavity had a thin thread-like worm which was identified as a larval stage of Pseudophyllidea that was further confirmed as belonging to genusSpirometra. Aspiration of the worm and antiparasitic therapy with metronidazole led to complete recovery. Reports of sparganosis from Indian subcontinent are scanty and these cases had involvement of brain, kidney and eye. To the best of our knowledge this is the first case of hepatic sparganosis from India.
Wrist clonus mimicking as action-induced tremors: an important clinical lesson
Authors: Sharma Bhawna , Sannegowda Raghavendra Bakki , Nagpal Kadam , Jain Rahul
Published: December 2012

We report a 35-year-old man who presented with abnormal movement of hand upon extension at wrist joint in an outstretched arm. He was diagnosed and treated elsewhere as having action-induced tremors. On examination, he had action-induced clonus at wrist joint with bilateral corticospinal tract features in the form of weakness, spasticity and extensor plantars. Evaluation also revealed cervical compressive myelopathy. The purpose of presenting this case report is to highlight this rare clinical sign which can be mistaken for action-induced tremors.
Exercise-induced myalgia and rhabdomyolysis in a patient with the rare m.3243A>T mtDNA mutation
Authors: Czell David , Abicht Angela , Hench Jürgen , Weber Markus
Published: December 2012

Mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes comprises a number of mitochondrial disorders with a wide range of clinical presentations. We present the case of a 32-year-old patient with an m.3243A>T mitochondrial DNA mutation who presented with rhabdomyolysis after 2 days of excessive physical work. The case presented here demonstrates a new clinical phenotype associated with this pathogenic mtDNA mutation.
Brachial amyotrophic diplegia in the setting of complete HIV viral load suppression
Authors: Cachia David , Izzy Saef , Ionete Carolina , Salameh Johnny
Published: December 2012

Brachial amyotrophic diplegia (BAD) is a rare segmental form of motor neuron disease which presents with asymmetric lower motor neuron weakness largely confined to the upper extremities (UE). In the case being reported, a 62-year-old gentleman on antiretroviral treatment since 1993, presented with left-arm weakness in 2007 that quickly progressed to involve the right arm. Complete HIV-viral load suppression had been achieved since 2003. Examination revealed lower motor neuron weakness in both UEs, worse proximally than distally and normal strength in the lower extremities (LEs). Nerve conduction studies showed reduced amplitudes of bilateral median and ulnar nerves’ motor responses. Needle electromyography of bilateral UE showed active and chronic denervation/reinnervation changes with normal findings in both LEs. MRI of the cervical spine showed cord atrophy. This is the first case report describing a patient who presented with BAD in the setting of complete HIV-viral load suppression for many years.
De-differentiation of papillary thyroid carcinoma into squamous cell carcinoma. A case of coexistence within an excised neck lesion
Authors: Evans William David George
Published: December 2012

An 80-year-old man with papillary thyroid carcinoma of the neck underwent surgery and radioiodide therapy. He presented 11 years later with a lesion adjudged from fine needle aspiration to be a squamous cell carcinoma (SCC). Histological analysis of the excised mass revealed a lymph node overwhelmed with papillary thyroid carcinoma and moderately differentiated SCC thought to have transformed from papillary cells. A very small number of similar transformations specifically involving the ‘tall cell variant’  of papillary carcinoma transforming to spindle cell carcinoma have been reported previously. This case report demonstrates clear images of this rare occurrence and briefly considers factors leading to de-differentiation. The clinician should consider possible transformation from papillary thyroid cancer in cases of SCC of the head and neck as this variation may be more aggressive.
Evaluation of the filter paper IP-10 tests in school children after exposure to tuberculosis: a prospective cohort study with a 4-year follow-up
Authors: Tuuminen Tamara , Salo Eeva , Kotilainen Hannele , Ruhwald Morten
Published: December 2012

Objectives

The prevalence of active tuberculosis (TB) is low in Finland, but outbreaks do occur. Following exposure national guidelines recommend either tuberculosis skin test or interferon-γ-release assay-testing of asymptomatic children. The aim of this study was to compare QuantiFERON-TB Gold In-Tube test (QFT) and interferon-γ-inducible protein (IP-10) release assay for detection ofMycobacterium tuberculosisinfection following exposure to TB in a primary school.

Design

A prospective cohort study.

Setting

School children in Helsinki, Finland.

Participants

Two siblings of the index case and 58 classmates exposed toM tuberculosis.

Intervention

All the children were screened using the QFT, which was used to guide preventive treatment. All those exposed were followed up through the national TB registry.

Outcome measures

IP-10 was measured in plasma supernatants from the QFT test supernatants and in plasma dried and stored for 1 year on filter paper. IP-10 test results were calculated using preset algorithms for positive and indeterminate tests. The negative predictive values of the tests were assessed.

Results

At an initial screening 2 months after the debut of symptoms in the index case, QFT was positive in two children; 56 tests were negative; one was indeterminate and one was borderline. IP-10 showed a perfect concordance between the dried plasma spot and plasma method; two children were IP-10 positive and two were IP-10 indeterminate. There were two (3%) discordant results between the QFT and IP-10 tests. Four children converted to positive QFT at a 1–3 month follow-up. None of the QFT negative/borderline children developed TB in the 4-year period since exposure.

Conclusions

We demonstrated that IP-10 and QFT perform comparably as screening tools for infection withM tuberculosisin a contact investigation. IP-10 determined in dried plasma spots was at par with IP-10 determined in plasma, which further supports the usefulness of this alternative approach.
Antioxidant effect of organic purple grape juice on exhaustive exercise
Authors: Dalla Corte Cristiane L. , de Carvalho Nélson R. , Amaral Guilherme P. , Puntel Gustavo O. , Silva Luiz Fernando A. , Retamoso Leandro T. , Royes Luiz Fernando F. , Bresciani Guilherme B. , da Cruz Ivana B.M. , Rocha João B.T. , Barrio Lera Juan Pablo , Soares Félix A.A.
Published: December 2012

This study aimed to assess the potential protective effect of organic purple grape juice (PGJ) on oxidative stress produced by an exhaustive exercise bout in rats. To test this hypothesis, rats were acutely treated with organic PGJ (Vitis labrusca) and subsequently submitted to an exhaustive exercise bout. Parameters of oxidative stress, such as thiobarbituric acid reactive species (TBARS) levels, 2′,7′,-dichlorofluorescein diacetate (DCFH-DA) oxidation, and nonprotein sulfhydryl levels (NP-SH) in the brain, skeletal muscle, and blood, were evaluated. Enzyme activity of Na+,K+-ATPase, Ca2+-ATPase, and δ-aminolevulinate dehydratase (δ-ALA-D) in the brain, skeletal muscle, and blood were also assayed. Statistical analysis showed that the exhaustive exercise bout increased TBARS levels and DCFH-DA oxidation, and decreased NP-SH levels in rat tissue. Ca2+-ATPase activity was increased in groups exposed to both exercise and PGJ treatment. The results indicate that organic PGJ intake was able to protect against the oxidative damage caused by an exhaustive exercise bout in different rat tissues.
Geographical parthenogenesis in Pacific Northwest hawthorns (Crataegus; Rosaceae)
Authors: Lo E.Y.Y. , Stefanović S. , Dickinson T.A.
Published: December 2012

We have demonstrated geographical parthenogenesis in Crataegus series Douglasianae, an agamic complex comprising exclusively tetraploid Crataegus douglasii sensu lato and the morphologically distinct Crataegus suksdorfii complex that comprises diploids and polyploids. Here we characterize ploidy level and breeding system by detailed flow cytometric measurements of the 2C nuclear DNA content of leaf, embryo, and endosperm tissues from 282 black-fruited hawthorns (Crataegus series Douglasianae) representing 33 localities in the Pacific Northwest, one in the Cypress Hills, and three more in the upper Great Lakes basin. We use existing climate and molecular data to place our flow cytometry results in an environmental and evolutionary context. Crataegus douglasii occupies more widely distributed sites that experience more extreme temperature and moisture regimes than do the sites occupied by diploid C. suksdorfii.
Relationships between Arabidopsis genotype-specific biomass accumulation and associated soil microbial communities
Authors: Sugiyama Akifumi , Bakker Matthew G. , Badri Dayakar V. , Manter Daniel K. , Vivanco Jorge M.
Published: December 2012

Rhizosphere microbial communities are impacted by resident plant species and have reciprocal effects on their host plants. We collected resident soil from five wild populations of Arabidopsis in the United States and Europe in an effort to characterize the impacts of natural soil microbiomes on Arabidopsis growth performance. The microbial communities present in these soils showed differences in community structure as assessed by 454 sequencing and in metabolic activity. While pathogens associated with the Brassica family were rare, diverse genera of potential plant growth promoting rhizobacteria were detected. Seed corresponding to the five Arabidopsis genotypes was grown in resident and nonresident soils to determine relationships among plant growth performance and soil microbial community and edaphic characteristics. Arabidopsis genotypes demonstrated different patterns of relationship between biomass accumulation and microbial community characteristics. This work sheds light on the bacterial populations naturally associated with Arabidopsis and suggests implications of the rhizosphere microbiome for plant growth performance.
Isolation and characterization of the grain mold fungiCochliobolusandAlternariaspp. from sorghum using semiselective media and DNA sequence analyses
Authors: Funnell-Harris Deanna L. , Prom Louis K. , Pedersen Jeffrey F.
Published: December 2012

Mold diseases, caused by fungal complexes including Alternaria, Cochliobolus, and Fusarium species, limit sorghum grain production. Media were tested by plating Fusarium thapsinum, Alternaria sp., and Curvularia lunata, individually and competitively. Dichloran chloramphenicol rose bengal (DRBC) and modified V8 juice (ModV8) agars, found to be useful, were compared with commonly used agar media, dichloran chloramphenicol peptone (DCPA) and pentachloronitrobenzene (PCNB). Radial growth, starting with mycelia or single-conidia and hyphal tips, demonstrated an effect of media. For isolation of grain fungi, DRBC and ModV8 were similar or superior to DCPA and PCNB. When seedlings were inoculated with conidia of C. lunata, Alternaria sp., F. thapsinum, or mixtures, the percentage of root infection ranged from 28% to 77%. For mixed inoculations, shoot weights, lesion lengths, and percentage of root infections were similar to F. thapsinum inoculations; most colonies recovered from roots were F. thapsinum. For Alternaria grain isolates, 5 morphological types, including Alternaria alternata, were distinguished by colony morphologies and conidial dimensions. Sequence analysis using a portion of the endo-polygalacturonase gene was able to further distinguish isolates. Cochliobolus isolates were identified morphologically as C. lunata, Curvularia sorghina, and Bipolaris sorghicola. Multiple molecular genotypes were apparent from rRNA internal transcribed spacer region sequences from Cochliobolus grain isolates.
COUNTING AND COMPUTING THE EIGENVALUES OF A COMPLEX TRIDIAGONAL MATRIX, LYING IN A GIVEN REGION OF THE COMPLEX PLANE
Authors: VALVI F. N. , GEROYANNIS V. S.
Published: December 2012

We present a numerical technique for counting and computing the eigenvalues of a complex tridiagonal matrix, lying in a given region of the complex plane. First, we evaluate the integral of the logarithmic derivative p′(λ)/p(λ), where p(λ) is the characteristic polynomial of the tridiagonal matrix, on a simple closed contour, being the closure of that region. The problem of evaluating this integral is transformed into the equivalent problem of numerically solving a complex initial value problem defined on an ordinary first-order differential equation, integrated along this contour, and solved by the Fortran package dcrkf54.f95 (developed recently by the authors). In accordance with the "argument principle," the value of the contour integral, divided by 2πi, counts the eigenvalues lying in the region. Second, a Newton–Raphson (NR) method, fed by random guesses lying in the region, computes the roots one by one. If, however, NR signals that |p′(λ)| converges to zero, i.e. a multiple root probably exists at the current value λ, then counting the roots within an elementary square centered at λ reveals the multiplicity of this root.
ELECTROMAGNETICALLY INDUCED TRANSPARENCY (EIT)-LIKE TRANSMISSION IN ORTHOGONAL-COUPLED SLOT CAVITIES
Authors: GUO YINGHUI , YAN LIANSHAN , PAN WEI , LUO BIN , WEN KUNHUA , GUO ZHEN , LUO XIANGANG
Published: December 2012

The transmission characteristics and electromagnetic responses of orthogonal-coupled slot cavities system are investigated with finite difference time domain (FDTD) method. Results show the electromagnetically induced transparency (EIT)-like transmission can be realized in the proposed structure due to the destructive interference between the horizontal cavity (bright mode) and the vertical cavity (dark mode). Moreover, trapped resonance modes in the horizontal cavity can be selective whether to be induced in vertical cavity or not depending on their relative position. Consequently, EIT-like transmission can be obtained in visible and near-infrared range, simultaneously or individually. The corresponding physical mechanisms are discussed in terms of counter profiles of fields | Hz | and coupled mode theory. Influences of the geometrical parameters on EIT-like transmission are also investigated to generate transparency windows with different shape.
NEW OPTIMAL ASYMMETRIC QUANTUM CODES
Authors: QIAN JIANFA , ZHANG LINA
Published: December 2012

By using q2-ary cyclotomic cosets, we construct new asymmetric quantum codes with parameters [[q2+1, q2+1-2(k+i-2), (2k+3)/(2i+3)]]q2, where k and i are positive integers, and [Formula: see text]. The constructed asymmetric quantum codes are not covered by the codes available in the literature. Moreover, the constructed asymmetric quantum codes are optimal.