bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural and Biological Diversity of Lipopolysaccharides from
Burkholderia pseudomallei
and
Burkholderia thailandensis
Authors: Novem Vidhya , Shui Guanghou , Wang Dongling , Bendt Anne K. , Sim Siew Hoon , Liu Yichun , Thong Tuck Weng , Sivalingam Suppiah Paramalingam , Ooi Eng Eong , Wenk Markus R. , Tan Gladys
Published: August 2009

Burkholderia pseudomallei
, the etiological agent of melioidosis, is a facultative intracellular pathogen. As
B. pseudomallei
is a gram-negative bacterium, its outer membrane contains lipopolysaccharide (LPS) molecules, which have been shown to have low-level immunological activities in vitro. In this study, the biological activities of
B. pseudomallei
LPS were compared to those of
Burkholderia thailandensis
LPS, and it was found that both murine and human macrophages produced levels of tumor necrosis factor alpha, interleukin-6 (IL-6), and IL-10 in response to
B. pseudomallei
LPS that were lower than those in response to
B. thailandensis
LPS in vitro. In order to elucidate the molecular mechanisms underlying the low-level immunological activities of
B. pseudomallei
LPS, its lipid A moiety was characterized using mass spectrometry. The major lipid A species identified in
B. pseudomallei
consists of a biphosphorylated disaccharide backbone, which is modified with 4-amino-4-deoxy-arabinose (Ara4N) at both phosphates and penta-acylated with fatty acids (FA) C
14:0
(3-OH), C
16:0
(3-OH), and either C
14:0
or C
14:0
(2-OH). In contrast, the major lipid A species identified in
B. thailandensis
was a mixture of tetra- and penta-acylated structures with differing amounts of Ara4N and FA C
14:0
(3-OH). Lipid A species acylated with FA C
14:0
(2-OH) were unique to
B. pseudomallei
and not found in
B. thailandensis
. Our data thus indicate that
B. pseudomallei
synthesizes lipid A species with long-chain FA C
14:0
(2-OH) and Ara4N-modified phosphate groups, allowing it to evade innate immune recognition.
Proficiency Program for Real-Time PCR Diagnosis of
Bordetella pertussis
Infections in French Hospital Laboratories and at the French National Reference Center for Whooping Cough and other Bordetelloses
Authors: Caro Valérie , Guiso Nicole , Alberti Corinne , Liguori Sandrine , Burucoa Christophe , Couetdic Gérard , Doucet-Populaire Florence , Ferroni Agnès , Papin-Gibaud Sophie , Grattard Florence , Réglier-Poupet Hélène , Raymond Josette , Soler Catherine , Bouchet Sylvie , Charreau Sandrine , Couzon Brigitte , Leymarie Isabelle , Tavares Nicole , Choux Mathilde , Bingen Edouard , Bonacorsi Stéphane
Published: August 2009

With the support of a ministerial program for innovative and expensive technologies, dedicated to the economic evaluation of laboratory diagnosis of pertussis by real-time PCR, external quality assessment for real-time IS
481
PCR was carried out. Coordinated by the National Centre of Reference of Pertussis and other Bordetelloses (NCR), this study aimed to harmonize and to assess the performances of eight participating microbiology hospital laboratories throughout the French territory. Between January 2006 and February 2007, 10 proficiency panels were sent by the NCR (ascending proficiency program), representing a total of 49 samples and including eight panels to analyze and evaluate the global sensitivity and specificity of real-time PCR, one to assess the limit of detection, and one to evaluate nucleic acid extraction methods. As part of the descending proficiency program, extracted DNA from clinical samples was sent by the eight participating laboratories in different panels and analyzed by the NCR. In the ascending proficiency analysis, the sensitivity and specificity of the real-time PCR methods were 92.2% and 94.3%, respectively. The limit of detection of the different methods ranged between 0.1 and 1 fg/μl (0.2 to 2 CFU/μl). The nucleic acid extraction methods showed similar performances. During the descending proficiency analysis, performed with 126 samples, the result of the NCR for 15 samples (11.9%) was discordant with the result obtained by the source laboratory. Despite several initial differences, harmonization was easy and performances were homogeneous. However, the risk of false-positive results remains quite high, and we strongly recommend establishment of uniform quality control procedures performed regularly.
Patterns of Susceptibility of
Aspergillus
Isolates Recovered from Patients Enrolled in the Transplant-Associated Infection Surveillance Network
Authors: Baddley John W. , Marr Kieren A. , Andes David R. , Walsh Thomas J. , Kauffman Carol A. , Kontoyiannis Dimitrios P. , Ito James I. , Balajee S. Arunmozhi , Pappas Peter G. , Moser Stephen A.
Published: August 2009

We analyzed antifungal susceptibilities of 274 clinical
Aspergillus
isolates from transplant recipients with proven or probable invasive aspergillosis collected as part of the Transplant-Associated Infection Surveillance Network (TRANSNET) and examined the relationship between MIC and mortality at 6 or 12 weeks. Antifungal susceptibility testing was performed by the Clinical and Laboratory Standards Institute (CLSI) M38-A2 broth dilution method for amphotericin B (AMB), itraconazole (ITR), voriconazole (VOR), posaconazole (POS), and ravuconazole (RAV). The isolate collection included 181
Aspergillus fumigatus
, 28
Aspergillus niger
, 27
Aspergillus flavus
, 22
Aspergillus terreus
, seven
Aspergillus versicolor
, five
Aspergillus calidoustus
, and two
Aspergillus nidulans
isolates and two isolates identified as
Aspergillus
spp. Triazole susceptibilities were ≤4 μg/ml for most isolates (POS, 97.6%; ITR, 96.3%; VOR, 95.9%; RAV, 93.5%). The triazoles were not active against the five
A. calidoustus
isolates, for which MICs were ≥4 μg/ml. AMB inhibited 93.3% of isolates at an MIC of ≤1 μg/ml. The exception was
A. terreus
, for which 15 (68%) of 22 isolates had MICs of >1 μg/ml. One of 181 isolates of
A. fumigatus
showed resistance (MIC ≥ 4 μg/ml) to two of three azoles tested. Although there appeared to be a correlation of higher VOR MICs with increased mortality at 6 weeks, the relationship was not statistically significant (
R
2
= 0.61;
P
= 0.065). Significant relationships of in vitro MIC to all-cause mortality at 6 and 12 weeks for VOR or AMB were not found.
Recurrent
Klebsiella pneumoniae
Liver Abscess: Clinical and Microbiological Characteristics
Authors: Yang Ya-Sung , Siu L. K. , Yeh Kuo-Ming , Fung Chang-Phong , Huang Shenq-Jie , Hung Han-Chang , Lin Jung-Chung , Chang Feng-Yee
Published: August 2009

Recurrent
Klebsiella pneumoniae
liver abscesses (KLAs) are rarely reported. Six cases of recurrent KLAs are characterized. Most of the patients had diabetes and K1 serotype KLAs. All of the isolates were uniformly susceptible to cefazolin. Distinct molecular fingerprints were found for the strains isolated from both primary and recurrent KLAs.
Rapid Human Immunodeficiency Virus Test Quality Assurance Practices and Outcomes among Testing Sites Affiliated with 17 Public Health Departments
Authors: Wesolowski Laura G. , Ethridge Steven F. , Martin Eugene G. , Cadoff Evan M. , MacKellar Duncan A.
Published: August 2009

Rapid human immunodeficiency virus testing is often conducted in nonclinical settings by staff with limited training, so quality assurance (QA) monitoring is critical to ensure accuracy of test results. Rapid tests (
n
= 86,749) were generally conducted according to manufacturers' instructions, but ongoing testing competency assessments and on-site QA monitoring were not uniformly conducted.
Occurrence of OXA-107 and IS
Aba
1 in Carbapenem-Resistant Isolates of
Acinetobacter baumannii
from Croatia
Authors: Goic-Barisic Ivana , Bedenic Branka , Tonkic Marija , Novak Anita , Katic Stjepan , Kalenic Smilja , Punda-Polic Volga , Towner Kevin J.
Published: August 2009

Carbapenem-resistant isolates of
Acinetobacter baumannii
from intensive care units at Split University Hospital, Split, Croatia, were studied. Most (100 of 106) had IS
Aba
1 inserted upstream of a
bla
OXA-107
gene, encoding an unusual OXA-51-type oxacillinase. Pulsed-field gel electrophoresis revealed that the isolates formed three clusters belonging to the sequence group 2 (European clone 1) lineage.
X4 Human Immunodeficiency Virus Type 1 gp120 Down-Modulates Expression and Immunogenicity of Codelivered Antigens
Authors: Hovav Avi-Hai , Santosuosso Michael , Bivas-Benita Maytal , Plair Andre , Cheng Alex , Elnekave Mazal , Righi Elda , Chen Tao , Kashiwagi Satoshi , Panas Michael W. , Xiang Shi-Hua , Furmanov Karina , Letvin Norman L. , Poznansky Mark C.
Published: August 2009

In order to increase the immune breadth of human immunodeficiency virus (HIV) vaccines, strategies such as immunization with several HIV antigens or centralized immunogens have been examined. HIV-1 gp120 protein is a major immunogen of HIV and has been routinely considered for inclusion in both present and future AIDS vaccines. However, recent studies proposed that gp120 interferes with the generation of immune response to codelivered antigens. Here, we investigate whether coimmunization with plasmid-encoded gp120 alters the immune response to other coadministered plasmid encoded antigens such as luciferase or ovalbumin in a mouse model. We found that the presence of gp120 leads to a significant reduction in the expression level of the codelivered antigen in vivo. Antigen presentation by antigen-presenting cells was also reduced and resulted in the induction of weak antigen-specific cellular and humoral immune responses. Importantly, gp120-mediated immune interference was observed after administration of the plasmids at the same or at distinct locations. To characterize the region in gp120 mediating these effects, we used plasmid constructs encoding gp120 that lacks the V1V2 loops (ΔV1V2) or the V3 loop (ΔV3). After immunization, the ΔV1V2, but not the ΔV3 construct, was able to reduce antigen expression, antigen presentation, and subsequently the immunogenicity of the codelivered antigen. The V3 loop dependence of this phenomenon seems to be limited to V3 loops known to interact with the CXCR4 molecule but not with CCR5. Our study presents a novel mechanism by which HIV-1 gp120 interferes with the immune response against coadministered antigen in a polyvalent vaccine preparation.
Characterization of a Mumps Virus Nucleocapsidlike Particle
Authors: Cox Robert , Green Todd J. , Qiu Shihong , Kang Jungsoon , Tsao Jun , Prevelige Peter E. , He Biao , Luo Ming
Published: August 2009

The nucleocapsid protein (NP) of mumps virus (MuV), a paramyxovirus, was coexpressed with the phosphoprotein (P) in
Escherichia coli
. The NP and P proteins form a soluble complex containing RNA. Under a transmission electron microscope, the NP-RNA complex appears as a nucleocapsidlike ring that has a diameter of approximately 20 nm with 13 subunits. There is a piece of single-stranded RNA with a length of 78 nucleotides in the NP-RNA ring. Shorter RNA pieces are also visible. The MuV NP protein may provide weaker protection of the RNA than the NP protein of some other negative-strand RNA viruses, reflecting the degree of NP protein association.
Human Uterine Natural Killer Cells but Not Blood Natural Killer Cells Inhibit Human Immunodeficiency Virus Type 1 Infection by Secretion of CXCL12
Authors: Mselle Teddy F. , Howell Alexandra L. , Ghosh Mimi , Wira Charles R. , Sentman Charles L.
Published: August 2009

Natural killer (NK) cells derived from the human female reproductive tract (FRT) are phenotypically and functionally distinct from those obtained from peripheral blood. Because the FRT is a primary site of human immunodeficiency virus type 1 (HIV-1) infection in women, we determined whether soluble factors secreted by uterine-derived NK (uNK) cells inhibit HIV-1 infection. Clonal populations of uNK cells were activated with interleukin-12 (IL-12) and IL-15, and conditioned media (CM) from these cultures evaluated for their ability to inhibit infection of cells by HIV-1IIIB, HIV-1NL4.3, and HIV-1HC4(X4-tropic) or HIV-1BaL(R5-tropic) viruses. We found that soluble factors secreted by activated uNK cells significantly inhibited X4-tropic virus infection of TZM-bl cells, peripheral blood mononuclear cells, and primary human endometrial cells, but not infection by HIV-1BaL. In contrast, CM from peripheral blood NK (bNK) cells did not inhibit HIV-1 infection of cells. Analysis of factors secreted from uNK clones with anti-HIV-1 activity demonstrated significantly higher levels of CXCL12 compared to uNK clones without this activity, and the HIV inhibitory activity was neutralized by antibodies to CXCL12. Collectively, these data demonstrate that human uNK cells release chemokines with anti-HIV-1 activity for X4-tropic strains and this suggest that these chemokines may contribute to the inhibition of X4-tropic strain transmission across mucosal tissues.
Virion-Associated Vpr of Human Immunodeficiency Virus Type 1 Triggers Activation of Apoptotic Events and Enhances Fas-Induced Apoptosis in Human T Cells
Authors: Arokium Hubert , Kamata Masakazu , Chen Irvin
Published: August 2009

Human immunodeficiency virus type 1 (HIV-1) Vpr protein exists in three different forms: soluble, intracellular, and virion associated. Previous studies showed that virion-associated Vpr induces apoptosis in activated peripheral blood mononuclear cells (PBMCs) and Jurkat T cells, but these studies were conducted in the presence of other de novo-expressed HIV proteins that may have had additive proapoptotic effects. In this report, we show that virion-associated Vpr triggers apoptosis through caspases 3/7 and 9 in human T cells independently of other HIV de novo-expressed proteins. In contrast to a previous study, we also detected the activation of caspase 8, the initiator caspase of the death receptor pathway. However, activation of all caspases by virion-associated Vpr was independent of the Fas death receptor pathway. Further analyses showed that virion-associated Vpr enhanced caspase activation in Fas-mediated apoptosis in Jurkat T cells and human activated PBMCs. Thus, our results indicate for the first time that viral particles that contain virion-associated Vpr can cause apoptosis in the absence of other de novo-expressed viral factors and can act in synergy with the Fas receptor pathway, thereby enhancing the apoptotic process in T cells. These findings suggest that virion-associated Vpr can contribute to the depletion of CD4+lymphocytes either directly or by enhancing Fas-mediated apoptosis during acute HIV-1 infection and in AIDS.
A Single-Amino-Acid Substitution in a Polymerase Protein of an H5N1 Influenza Virus Is Associated with Systemic Infection and Impaired T-Cell Activation in Mice
Authors: Fornek Jamie L. , Gillim-Ross Laura , Santos Celia , Carter Victoria , Ward Jerrold M. , Cheng Lily I. , Proll Sean , Katze Michael G. , Subbarao Kanta
Published: August 2009

The transmission of H5N1 influenza viruses from birds to humans poses a significant public health threat. A substitution of glutamic acid for lysine at position 627 of the PB2 protein of H5N1 viruses has been identified as a virulence determinant. We utilized the BALB/c mouse model of H5N1 infection to examine how this substitution affects virus-host interactions and leads to systemic infection. Mice infected with H5N1 viruses containing lysine at amino acid 627 in the PB2 protein exhibited an increased severity of lesions in the lung parenchyma and the spleen, increased apoptosis in the lungs, and a decrease in oxygen saturation. Gene expression profiling revealed that T-cell receptor activation was impaired at 2 days postinfection (dpi) in the lungs of mice infected with these viruses. The inflammatory response was highly activated in the lungs of mice infected with these viruses and was sustained at 4 dpi. In the spleen, immune-related processes including NK cell cytotoxicity and antigen presentation were highly activated by 2 dpi. These differences are not attributable solely to differences in viral replication in the lungs but to an inefficient immune response early in infection as well. The timing and magnitude of the immune response to highly pathogenic influenza viruses is critical in determining the outcome of infection. The disruption of these factors by a single-amino-acid substitution in a polymerase protein of an influenza virus is associated with severe disease and correlates with the spread of the virus to extrapulmonary sites.
An Amphipathic α-Helix at the C Terminus of Hepatitis C Virus Nonstructural Protein 4B Mediates Membrane Association
Authors: Gouttenoire Jérôme , Montserret Roland , Kennel Audrey , Penin François , Moradpour Darius
Published: August 2009

Nonstructural protein 4B (NS4B) plays an essential role in the formation of the hepatitis C virus (HCV) replication complex. It is an integral membrane protein that has been only poorly characterized to date. It is believed to comprise a cytosolic N-terminal part, a central part harboring four transmembrane passages, and a cytosolic C-terminal part. Here, we describe an amphipathic α-helix at the C terminus of NS4B (amino acid residues 229 to 253) that mediates membrane association and is involved in the formation of a functional HCV replication complex.
Mechanism of Human Immunodeficiency Virus Type 1 Resistance to Monoclonal Antibody b12 That Effectively Targets the Site of CD4 Attachment
Authors: Wu Xueling , Zhou Tongqing , O'Dell Sijy , Wyatt Richard T. , Kwong Peter D. , Mascola John R.
Published: August 2009

The region of the human immunodeficiency virus type 1 (HIV-1) envelope glycoprotein gp120 that engages its primary cellular receptor CD4 forms a site of vulnerability to neutralizing antibodies. The monoclonal antibody b12 exploits the conservation and accessibility of the CD4-binding site to neutralize many, though not all, HIV-1 isolates. To understand the basis of viral resistance to b12, we used the atomic-level definition of b12-gp120 contact sites to study a panel of diverse circulating viruses. A combination of sequence analysis, computational modeling, and site-directed mutagenesis was used to determine the influence of amino acid variants on binding and neutralization by b12. We found that several substitutions within the dominant b12 contact surface, called the CD4-binding loop, mediated b12 resistance, and that these substitutions resided just proximal to the known CD4 contact surface. Hence, viruses varied in key b12 contact residues that are proximal to, but not part of, the CD4 contact surface. This explained how viral isolates were able to evade b12 neutralization while maintaining functional binding to CD4. In addition, some viruses were resistant to b12 despite minimal sequence variation at b12 contact sites. Such neutralization resistance usually could be reversed by alterations at residues thought to influence the quaternary configuration of the viral envelope spike. To design immunogens that elicit neutralizing antibodies directed to the CD4-binding site, researchers need to address the antigenic variation within this region of gp120 and the restricted access to the CD4-binding site imposed by the native configuration of the trimeric viral envelope spike.
Race between Retroviral Spread and CD4+T-Cell Response Determines the Outcome of Acute Friend Virus Infection
Authors: Pike Rebecca , Filby Andrew , Ploquin Mickaël J.-Y. , Eksmond Urszula , Marques Rute , Antunes Inês , Hasenkrug Kim , Kassiotis George
Published: August 2009

Retroviruses can establish persistent infection despite induction of a multipartite antiviral immune response. Whether collective failure of all parts of the immune response or selective deficiency in one crucial part underlies the inability of the host to clear retroviral infections is currently uncertain. We examine here the contribution of virus-specific CD4+T cells in resistance against Friend virus (FV) infection in the murine host. We show that the magnitude and duration of the FV-specific CD4+T-cell response is directly proportional to resistance against acute FV infection and subsequent disease. Notably, significant protection against FV-induced disease is afforded by FV-specific CD4+T cells in the absence of a virus-specific CD8+T-cell or B-cell response. Enhanced spread of FV infection in hosts with increased genetic susceptibility or coinfection with Lactate dehydrogenase-elevating virus (LDV) causes a proportional increase in the number of FV-specific CD4+T cells required to control FV-induced disease. Furthermore, ultimate failure of FV/LDV coinfected hosts to control FV-induced disease is accompanied by accelerated contraction of the FV-specific CD4+T-cell response. Conversely, an increased frequency or continuous supply of FV-specific CD4+T cells is both necessary and sufficient to effectively contain acute infection and prevent disease, even in the presence of coinfection. Thus, these results suggest that FV-specific CD4+T cells provide significant direct protection against acute FV infection, the extent of which critically depends on the ratio of FV-infected cells to FV-specific CD4+T cells.
Adaptive Mutations in a Human Immunodeficiency Virus Type 1 Envelope Protein with a Truncated V3 Loop Restore Function by Improving Interactions with CD4
Authors: Agrawal-Gamse Caroline , Lee Fang-Hua , Haggarty Beth , Jordan Andrea P. O. , Yi Yanjie , Lee Benhur , Collman Ronald G. , Hoxie James A. , Doms Robert W. , Laakso Meg M.
Published: August 2009

We previously reported that a human immunodeficiency virus type 1 (HIV-1) clade B envelope protein with a severely truncated V3 loop regained function after passage in tissue culture. The adapted virus, termed TA1, retained the V3 truncation, was exquisitely sensitive to neutralization by the CD4 binding site monoclonal antibody b12 and by HIV-positive human sera, used CCR5 to enter cells, and was completely resistant to small molecule CCR5 antagonists. To examine the mechanistic basis for these properties, we singly and in combination introduced each of the 5 mutations from the adapted clone TA1 into the unadapted envelope. We found that single amino acid changes in the C3 region, the V3 loop, and in the fusion peptide were responsible for imparting near-normal levels of envelope function to TA1. T342A, which resulted in the loss of a highly conserved glycosylation site in C3, played the primary role. The adaptive amino acid changes had no impact on CCR5 antagonist resistance but made virus more sensitive to neutralization by antibodies to the CD4 binding site, modestly enhanced affinity for CD4, and made TA1 more responsive to CD4 binding. Specifically, TA1 was triggered by soluble CD4 more readily than the parental Env and, unlike the parental Env, could mediate entry on cells that express low levels of CD4. In contrast, TA1 interacted with CCR5 less efficiently and was highly sensitive to antibodies that bind to the CCR5 N terminus and ECL2. Therefore, enhanced utilization of CD4 is one mechanism by which HIV-1 can overcome mutations in the V3 region that negatively affect CCR5 interactions.
A Quantitative Affinity-Profiling System That Reveals Distinct CD4/CCR5 Usage Patterns among Human Immunodeficiency Virus Type 1 and Simian Immunodeficiency Virus Strains
Authors: Johnston Samantha. H. , Lobritz Michael A. , Nguyen Sandra , Lassen Kara , Delair Shirley , Posta Filippo , Bryson Yvonne J. , Arts Eric J. , Chou Tom , Lee Benhur
Published: August 2009

The affinity of human immunodeficiency virus (HIV) envelope for CD4 and CCR5 appears to be associated with aspects of R5 virus (virus using the CCR5 coreceptor) pathogenicity. However, entry efficiency results from complex interactions between the viral envelope glycoprotein and both CD4 and CCR5, which limits attempts to correlate viral pathogenicity with surrogate measures of envelope CD4 and CCR5 affinities. Here, we present a system that provides a quantitative and comprehensive characterization of viral entry efficiency as a direct interdependent function of both CD4 and CCR5 levels. This receptor affinity profiling system also revealed heretofore unappreciated complexities underlying CD4/CCR5 usage. We first developed a dually inducible cell line in which CD4 and CCR5 could be simultaneously and independently regulated within a physiologic range of surface expression. Infection by multiple HIV type 1 (HIV-1) and simian immunodeficiency virus isolates could be examined simultaneously for up to 48 different combinations of CD4/CCR5 expression levels, resulting in a distinct usage pattern for each virus. Thus, each virus generated a unique three-dimensional surface plot in which viral infectivity varied as a function of both CD4 and CCR5 expression. From this functional form, we obtained a sensitivity vector along with corresponding metrics that quantified an isolate's overall efficiency of CD4/CCR5 usage. When applied to viral isolates with well-characterized sensitivities to entry/fusion inhibitors, the vector metrics were able to encapsulate their known biological phenotypes. The application of the vector metrics also indicated that envelopes derived from elite suppressors had overall-reduced entry efficiencies compared to those of envelopes derived from chronically infected viremic progressors. Our affinity-profiling system may help to refine studies of R5 virus tropism and pathogenesis.
Broad Neutralization of Human Immunodeficiency Virus Type 1 Mediated by Plasma Antibodies against the gp41 Membrane Proximal External Region
Authors: Gray Elin S. , Madiga Maphuti C. , Moore Penny L. , Mlisana Koleka , Abdool Karim Salim S. , Binley James M. , Shaw George M. , Mascola John R. , Morris Lynn
Published: August 2009

We identified three cross-neutralizing plasma samples with high-titer anti-membrane proximal external region (MPER) peptide binding antibodies from among 156 chronically human immunodeficiency virus type 1-infected individuals. In order to establish if these antibodies were directly responsible for the observed neutralization breadth, we used MPER-coated magnetic beads to deplete plasmas of these specific antibodies. Depletion of anti-MPER antibodies from BB34, CAP206, and SAC21 resulted in 77%, 68%, and 46% decreases, respectively, in the number of viruses neutralized. Antibodies eluted from the beads showed neutralization profiles similar to those of the original plasmas, with potencies comparable to those of the known anti-MPER monoclonal antibodies (MAbs), 4E10, 2F5, and Z13e1. The anti-MPER neutralizing antibodies in BB34 were present in the immunoglobulin G3 subclass-enriched fraction. Alanine scanning of the MPER showed that the antibodies from these three plasmas had specificities distinct from those of the known MAbs, requiring one to three crucial residues at positions 670, 673, and 674. These data demonstrate the existence of MPER-specific cross-neutralizing antibodies in plasma, although the ability to elicit such potent antiviral antibodies during natural infection appears to be rare. Nevertheless, the identification of three novel antibody specificities within the MPER supports its further study as a promising target for vaccine design.
Équilibre électrostatique de deux conducteurs sphériques concentriques dont l'un est muni d'une ouverture circulaire
Authors: Boridy Elie
Published: August 2009

The Laplace equation for two electrostatic configurations is solved using the method of serial dual equations. These configurations consist of two concentric conducting spherical shells with a circular aperture in one of them. The equations of electrostatic equilibrium are obtained as well as the capacitances, the coefficients of influence, and the effective capacitance. The variation of effective capacitance with the size of the aperture is also discussed.[Journal translation]
The B2Σ+–A2Πr system of MgCl
Authors: Singh M. , Saksena M. D. , Ghodgaonkar G. S.
Published: August 2009

The 0–0 band of the B2Σ+–A2Πr system of MgCl near 4730 Å has been photographed at high resolution and analyzed for its rotational structure for the first time. Rotational constants have been determined for the B state, which is shown to be 2Σ+. Rotational perturbations have been observed in the F2 sublevels for J < 42.5 and in the F1 sublevels for J ≤ 16.5 of the B2Σ+ state.
On a sphere performing linear and torsional oscillations in a viscous fluid
Authors: Karahalios G. T. , Sfetsos C.
Published: August 2009

A sphere executes small-amplitude linear and torsional oscillations in a fluid at rest. The equations of motion of the fluid are solved by the method of successive approximations. Outside the boundary layer, a steady secondary flow is induced in addition to the time-varying motion.
A new perturbative derivation of the axial anomaly
Authors: McKeon D. G. C. , Sherry T. N.
Published: August 2009

We examine the anomalous VVA and AAA three-point functions by using a perturbative expansion due to Schwinger in place of the usual Feynman diagramatic expansion. Using dimensional regularization, we show that the usual anomaly in the divergence of the axial current is automatically obtained if γ5 is treated naively (i.e., γ5 anticommutes with all γμ in n dimensions); no extra contributions occur even if γ5 is defined according to the ′t Hooft–Veltman prescription. Furthermore, no explicit divergences occur in our computation of VVA and AAA.
Theoretical energies for the n = 1 and 2 states of the helium isoelectronic sequence up to Z = 100
Authors: Drake G. W.
Published: August 2009

The unified method described previously for combining high-precision nonrelativistic variational calculations with relativistic and quantum electrodynamic corrections is applied to the 1s2 1S0, 1s2s 1S0, 1s2s 3S1, 1s2p 1P1, and 1s2p 3P0,1,2 staters of helium-like ions. Detailed tabulations are presented for all ions in the range 2 ≤ Z ≤ 100 and are compared with a wide range of experimental data up to 34Kr+. The results for 90U+ significantly alter the recent Lamb shift measurement of Munger and Gould from 70.4 ± 8.3 to 71.0 ± 8.3 eV, in comparison with a revised theoretical value of 74.3 ± 0.4 eV. The improved agreement is due to the inclusion of higher order two-electron corrections in the present work.
Growing stock estimation for alpine forests in Austria: a robust lidar-based approach
Authors: Hollaus M. , Wagner W. , Schadauer K. , Maier B. , Gabler K.
Published: August 2009

The overall goal of this study was to describe a novel area-based semiempirical model for estimating growing stock from small-footprint light detection and ranging (lidar) data. The model assumes a linear relationship between growing stock and lidar-derived canopy volume that is stratified according to several canopy height classes to account for height dependent differences in canopy structure and nonlinear tree size-shape relationships. It was applied over a 128 km2 alpine area in Austria where operational forest inventory data and lidar data acquired in winter and summer were available. The analysis showed that the semiempirical model was quite robust against changes in laser point density and acquisition time. Further, it was found that the model performed as well as a widely used iterative regression method based on a multiplicative model. Both models reached a high coefficient of determination (R2 = 0.76–0.86) and a standard deviation of the residuals in the order of 20.4%–29.1%. Although it is less flexible than the multiplicative model, the advantages of the semiempirical model are its simplicity and the fact that its coefficients can be physically interpreted. These traits can be expected to enhance the applicability of the model in regions where high-quality inventory data are lacking.
Mountain pine beetle, global markets, and the British Columbia forest economy
Authors: Abbott Brant , Stennes Brad , Cornelis van Kooten G.
Published: August 2009

A number of near-term timber supply shocks are projected to impact global forest product markets, particularly mountain pine beetle induced timber reductions, a Russian log export tax, and timber supply increases from plantation forests in the Southern Hemisphere and Sweden. We examined their effect on a number of global jurisdictions using a dynamic global forest products trade model that separates British Columbia (BC) into coastal and interior forest sectors. The results suggest that global increases in plantation timber would have negligible effects on BC log and lumber markets, that the Russian tax would have minor effects on this market, and that the beetle-induced timber supply drop would moderately increase BC prices (primarily log prices). In the United States South, lumber and log prices could rise as a result of the mountain pine beetle, while other shocks will have a negligible impact on prices. Yet, lumber production will fall because log prices will increase substantially more than lumber prices. Japan could be impacted much more than other regions by the Russian tax on log exports. In the absence of export taxes, a beetle-induced timber shortage would cause lumber production in Japan to rise (as Japan can access nearby Russian logs), while the export tax would reduce lumber production because log prices rise disproportionately more than in other regions.
Effects of tree species and clear-cut forestry on forest-floor characteristics in adjacent temperate forests in northern Spain
Authors: Gartzia-Bengoetxea Nahia , González-Arias Ander , Martínez de Arano Inazio
Published: August 2009

The litter layer (L) and fermented humified layer (FH) in forest floor under European beech ( Fagus sylvatica L.), pedunculate oak ( Quercus robur L.), and radiata pine ( Pinus radiata D. Don) were studied in northern Spain. Recovery from heavy mechanization was also assessed in a chronosequence from two adjacent pine plantations (3 and 16 years old). Interspecific differences in forest-floor mass and mass distribution were related to litter quality and decomposition rates. In the L layer, acid-insoluble residue/N, C/N, and C/P ratios were lower, and pH and Ca contents higher in the deciduous stands than in the pine stand. The microbial respiration rate was higher and functional diversity lower in the pine stand than in the deciduous stands, without differences in microbial biomass. Cross-polarization, magic angle spinning 13C nuclear magnetic resonance and proximate analysis revealed similar C functional groups in beech and pine stands. Forest floor was still absent 3 years after heavy mechanization, and after 16 years, it was 50% less abundant than in the mature stand. Microbial respiration rate, biomass, and diversity were similar in the L layer in 16-year-old and mature pine stands, but in the FH layer, microbial-community diversity remained low after 16 years. The results underline the effects of forest management on C transformations in the forest-floor layers. These effects may be evident even after 16 years of heavy mechanization.
A rules-based approach for predicting the eastern hemlock component of forests in the northeastern United States
Authors: Doucette Jarrod S. , Stiteler William M. , Quackenbush Lindi J. , Walton Jeffrey T.
Published: August 2009

The expanding threat of hemlock woolly adelgid (Adelges tsugae Annand) infestation has generated interest in locating eastern hemlock ( Tsuga canadensis (L.) Carr.). Prior studies have incorporated remotely sensed imagery to detect eastern hemlock presence or absence. The goal of this study was to develop methodology to quantify hemlock abundance using software and data accessible to forest managers. Three seasons of Landsat ETM+ scenes served as the imagery basis, whereas simple (slope, aspect, and curvature) and detailed (heat and wetness) environmental indices were extracted from a digital elevation model. Three hundred and forty-nine forest plots representing the typical forest cover found in the Catskill Mountain Region, New York, served as ground reference; model input used the percentage of hemlock basal area for each plot. The models generally underpredicted in plots with substantial hemlock composition, whereas overpredictions mainly occurred in mixed forests that lacked hemlock. Underpredictions negated overpredictions in mixed hemlock deciduous forests resulting in a neutral model. Correlation coefficients ranged from a high of 0.67 for the model created from three Landsat images to a low of 0.01 for the heat and wetness indices model. Although the models were typically within 10% of field measurements, there was no overall benefit in including topographic indices for mapping hemlock abundance.
Controlling Kalmia and reestablishing conifer dominance enhances soil fertility indicators in central Newfoundland, Canada
Authors: Moroni Martin T. , Thiffault Nelson , Titus Brian D. , Mante Christina , Makeschin Franz
Published: August 2009

Growth rates of young conifers can be poor on disturbed sites dominated by Kalmia angustifolia L. Hence, a conifer revegetation trial was established on a Kalmia -dominated site to evaluate the effects of various silvicultural options and planted species on selected soil organic layer characteristics. Larix laricina (Du Roi) K. Koch, Pinus banksiana Lamb., and Picea mariana (Mill.) BSP seedlings were planted in plots with or without Kalmia control with herbicides. The effect of fertilizer amendment was also assessed. Seventeen years postplanting, organic layer fertility indicators suggest that soil fertility improved after Kalmia control and conifer reestablishment, especially if nitrogen (N) – phosphorus – potassium fertilizer was also applied. When Kalmia was controlled, aerobically mineralizable N and exchangeable sodium concentrations were increased; fertilizer addition to herbicided plots also increased exchangeable potassium and calcium concentrations, and cation exchange capacity compared with untreated control plots. Conifer height, diameter, and canopy closure were Larix > Pinus > Picea. Kalmia cover in control plots was 87%; Kalmia reinvasion in herbicided plots achieved 40%–43% cover but did not differ among the conifer species. Principal component analysis indicated that aerobically mineralizable N and total N were positively correlated with canopy closure. Our results suggest that increases in organic-layer fertility were related to increased conifer size resulting from Kalmia control.
Relationships between acoustic variables and different measures of stiffness in standing Pinus taeda trees
Authors: Mora Christian R. , Schimleck Laurence R. , Isik Fikret , Mahon Jerry M. , Clark Alexander , Daniels Richard F.
Published: August 2009

Acoustic tools are increasingly used to estimate standing-tree (dynamic) stiffness; however, such techniques overestimate static stiffness, the standard measurement for determining modulus of elasticity (MOE) of wood. This study aimed to identify correction methods for standing-tree estimates making dynamic and static stiffness comparable. Sixty Pinus taeda L. trees, ranging from 14 to 19 years old, obtained from genetic tests established in the southeastern United States, were analyzed. Standing-tree acoustic velocities were measured using the TreeSonic tool. Acoustic velocities were also recorded in butt logs cut from the same trees using the Director HM200. A strong but biased relationship between tree and log velocities was observed, with tree velocities 32% higher (on average) than the corresponding log velocities. Two correction methods, one for calibrating tree velocities and one for accounting for differences in wood moisture content, were used to determine an adjusted MOE. After correction, adjusted MOE estimates were in good agreement with static longitudinal MOE values measured on clearwood specimens obtained from the trees, and no systematic bias was observed. The results of this study show that acoustic estimates of MOE on standing trees largely depend on how the data are processed and the reference method used.
Death and Taxus: the high cost of palatability for a declining evergreen shrub, Taxus canadensis
Authors: Holmes Stacie A. , Webster Christopher R. , Flaspohler David J. , Froese Robert E.
Published: August 2009

Taxus canadensis Marsh., a shade-tolerant evergreen shrub, is in decline as a result of past anthropogenic disturbances and increased cervid browsing. To identify factors that may be influencing establishment for this species, we planted 1080 T. canadensis cuttings in a hemlock–hardwood forest in the spring of 2004. Cuttings were planted across a gradient of light environments, consisting of artificial canopy gaps (61–441 m2) and closed-canopy conditions, and half were protected with deer exclosures. Following four growing seasons, T. canadensis survival in exclosures was 92% compared with 75% in controls. A mixed-effects binary logistic regression analysis revealed that deer exclusion had the most influence on the probability of survival; all else being equal an individual was nearly seven times more likely to survive if planted inside an exclosure (P < 0.001). Increasing light intensity had a counterbalancing effect on growth and survival; light increased leader growth (P = 0.019) but reduced an individual’s probability of survival (P < 0.001), possibly owing to enhanced herbivory and elevated moisture stress. Consequently, enhancing resource availability and growth may not decrease the impact of biomass loss to herbivory. These results suggest that even with relatively low herbivore densities, exclosures are required for the recovery of highly palatable species.
Postfire seed rain of black spruce, a semiserotinous conifer, in forests of interior Alaska
Authors: Johnstone Jill , Boby Leslie , Tissier Emily , Mack Michelle , Verbyla Dave , Walker Xanthe
Published: August 2009

The availability of viable seed can act as an important constraint on plant regeneration following disturbance. This study presents data on seed quantity and quality for black spruce ( Picea mariana (Mill.) B.S.P.), a semiserotinous conifer that dominates large areas of North American boreal forest. We sampled seed rain and viability for 2 years after fire (2005–2007) in 39 sites across interior Alaska that burned in 2004. All sites were dominated by black spruce before they burned. Structural equation modeling was used to assess the relative importance of prefire spruce abundance, topography effects, canopy fire severity, and distance to unburned stands in explaining variations in black spruce seed rain. Prefire basal area of spruce that remained standing after fire was a significant predictor of total seed rain, but seed viability was more strongly related to site elevation, canopy fire severity, and distances to unburned stands. Although positive relations between tree basal area and the size of the aerial seed bank may place a first constraint on seed availability, accurate prediction of postfire viable seed rain for serotinous conifers also requires consideration of the effects of abiotic stress and canopy fire severity on seed viability.
Carbon sequestration in a chronosequence of Scots pine stands in a reclaimed opencast oil shale mine
Authors: Karu Helen , Szava-Kovats Robert , Pensa Margus , Kull Olevi
Published: August 2009

Ecosystems that develop on mine spoil can serve as significant sinks for CO2. The aim of this study was to estimate the rate of carbon accumulation and its distribution along forest ecosystem partitions in young Scots pine ( Pinus sylvestris L.) plantations in the Narva oil shale opencast, Estonia. The tree layer was measured in 2004 in 13 stands afforested with 2-year-old seedlings during 1968 to 1994. Three stands (afforested in 1990, 1983, and 1968) were selected for detailed analysis of the carbon sequestration. Soil profiles were sampled in these stands in 2005. Radiocarbon analysis combined with a simple model of litter production was used to differentiate between plant-derived recent carbon and carbon stemming from fragments of oil shale. Total carbon accumulated since afforestation in vegetation, forest floor, and A horizon was 7.8 t·ha–1in the stand established in 1990, 34.5 t·ha–1in that established in 1983, and 133.4 t·ha–1in that established in 1968. Most of the sequestered carbon was allocated to tree stems; their portion increasing with age from 28% to 51%. The portion of recent soil organic carbon increased from 5% to 23%, which shows that soils contribute significantly to carbon accumulation during early forest succession on degraded land.
Influences of climate, fire, and topography on contemporary age structure patterns of Douglas-fir at 205 old forest sites in western Oregon
Authors: Poage Nathan J. , Weisberg Peter J. , Impara Peter C. , Tappeiner John C. , Sensenig Thomas S.
Published: August 2009

Knowledge of forest development is basic to understanding the ecology, dynamics, and management of forest ecosystems. We hypothesized that the age structure patterns of Douglas-fir at 205 old forest sites in western Oregon are extremely variable with long and (or) multiple establishment periods common, and that these patterns reflect variation in regional-scale climate, landscape-scale topography, and landscape-scale fire history. We used establishment dates for 5892 individual Douglas-firs from these sites to test these hypotheses. We identified four groups of old forest sites with fundamentally different Douglas-fir age structure patterns. Long and (or) multiple establishment periods were common to all groups. One group described old forests characterized by substantial establishment from the early 1500s to the mid-1600s, with decreasing establishment thereafter. Another group was characterized by peaks of establishment in the middle to late 1600s and in the late 1800s and early 1900s. A third group was characterized by a small peak of establishment in the mid-1500s and a larger peak in the middle to late 1800s. Characteristic of the fourth group was the extended period of Douglas-fir establishment from the late 1600s to the late 1800s. Group membership was explained moderately well by contemporary, regional climatic variables and landscape-scale fire history, but only weakly by landscape-scale topography.
Climate and intraannual density fluctuations in Pinus pinaster subsp. mesogeensis in Spanish woodlands
Authors: Bogino Stella , Bravo Felipe
Published: August 2009

Intraannual features or anomalies in the tree rings of woody species may provided useful information for ecological and climatological studies. The frequency of intraannual density fluctuations (IADFs), differences in IADFs according to the cambial age, changes in IADFs in the last century, and relationships of IADFs to radial growth and climate were analyzed in five stands of Pinus pinaster subsp. mesogeensis (Fieschi & Gaussen) Silba in east-central Spain. Standard dendrochronological techniques were used. Two cores were extracted 1.30 m above ground level from 15 dominant and codominant trees at each sampling site. The data were analyzed by analysis of variance, Pearson’s correlation, and logistic regression. Results showed that (i) the mean frequency of IADFs was higher in younger than older trees; (ii) the frequency of IADFs increased from the 1940s to the present; (iii) radial growth was negatively correlated with the presence of IADFs; and (iv) density fluctuations may be predicted by using a logistic model, with monthly rainfall and temperature as independent variables. Studies of intraannual features or anomalies in radial growth may be useful for ecological and climatological applications under forecasted climate change scenarios.