bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of crossbreeding indigenous Hair Goat with Saanen on carcass measurements and meat quality of kids under an intensive production system
Authors: YILMAZ Alper , EKIZ Bulent , OZCAN Mustafa , KAPTAN Cuneyt , HANOGLU Hulya , YILDIRIR Mesut
Published: May 2009

The aim of study was to investigate the effect of genotype on carcass measurements and meat quality characteristics of purebred Hair Goat, Saanen × Hair Goat (F1 and B1) kids under an intensive production system. In total, 24 kids were slaughtered at the age of approximately 133 days. Kids were fattened for 56 days immediately after weaning. Hot carcass weights were 6.78, 7.61 and 7.02 kg and dressing percentages were 49.71, 49.27 and 48.78%, respectively (P > 0.05). Differences between genotypes for carcass measurements and indexes were not significant. Effect of genotype on pH measurements, drip loss, water holding capacity, cooking loss and Warner Bratzler shear force values were not significant. Meat lightness values at 0 h, 1 h and 1 day after cutting were higher in crossbred kids than Hair Goat kids (P < 0.05). Redness value was significantly higher in meat samples of Hair goat kids at 0 h, 1 h and 1 day measurements (P < 0.05). Kid genotype had no significant effect on meat sensory characteristics, except tenderness. Panelists gave lower scores for meat tenderness to F1 and B1 crosses compared to purebred Hair Goat kids. In conclusion, higher meat lightness values of crossbred kids, at particularly B1 level, might have a positive effect on the consumer choices.
Novel SNP in 5′ flanking region of EDG1 associated with marbling in Japanese Black beef cattle
Authors: YAMADA Takahisa , SASAKI Seiki , SUKEGAWA Shin , MIYAKE Takeshi , FUJITA Tatsuo , KOSE Hiroyuki , MORITA Mitsuo , TAKAHAGI Youichi , MURAKAMI Hiroshi , MORIMATSU Fumiki , SASAKI Yoshiyuki
Published: May 2009

Marbling, defined by the amount and distribution of intramuscular fat, is an economically important trait of beef cattle in Japan. The endothelial differentiation, sphingolipid G‐protein‐coupled receptor, 1 (EDG1) gene has been considered as a positional functional candidate for the gene responsible for marbling. We have recently reported that 2 single nucleotide polymorphisms (SNPs), c.‐312A>G in the 5′ untranslated region (UTR) and c.*446G>A in the 3′ UTR in EDG1 were associated with marbling in Japanese Black beef cattle, but this was not functional and a causal mutation for marbling. In the present study, we detected 2 novel SNPs, referred to as g.1475435G>A and g.1471620G>T, in the 5′ flanking region of the EDG1 between low‐marbled and high‐marbled steer groups, which were previously shown to have EDG1 expression differences in musculus longissimus muscle. The g.1475435G>A SNP seemed not to segregate in Japanese Black beef cattle. The g.1471620G>T SNP was associated with the predicted breeding value for beef marbling standard number by the analyses using Japanese Black beef cattle population. Based on these findings, we hypothesized that the g.1471620G>T SNP might have an impact on EDG1 expression and also marbling.
Mass spectrometric characterization of the covalent modification of the nitrogenase Fe‐protein in Azoarcus sp. BH72
Authors: Oetjen Janina , Rexroth Sascha , Reinhold‐Hurek Barbara
Published: May 2009

Nitrogenase Fe‐protein modification was analyzed in the endophytic β‐proteobacterium Azoarcus sp. BH72. Application of modern MS techniques localized the modification in the peptide sequence and revealed it to be an ADP‐ribosylation on Arg102 of one subunit of nitrogenase Fe‐protein. A double digest with trypsin and endoproteinase Asp‐N was necessary to obtain an analyzable peptide because the modification blocked the trypsin cleavage site at this residue. Furthermore, a peptide extraction protocol without trifluoroacetic acid was crucial to acquire the modified peptide, indicating an acid lability of the ADP‐ribosylation. This finding was supported by the presence of a truncated version of the original peptide with Arg102 exchanged by ornithine. Site‐directed mutagenesis verified that the ADP‐ribosylation occurred on Arg102. With our approach, we were able to localize a labile modification within a large peptide of 31 amino acid residues. The present study provides a method suitable for the identification of so far unknown protein modifications on nitrogenases or other proteins. It represents a new tool for the MS analysis of protein mono‐ADP‐ribosylations.
Insecticide susceptibility and resistance of larvae of the Anopheles sinensis Group (Diptera: Culicidae) from Paju, Republic of Korea
Authors: CHANG Kyu‐Sik , JUNG Jin‐Sung , PARK Chan , LEE Dong‐Kyu , SHIN E‐Hyun
Published: May 2009

The susceptibility of members of the Anopheles sinensis Group in Korea to insecticides was evaluated under laboratory conditions using 15 insecticides currently used by local public health centers in Korea. The insecticides included eight pyrethroids, six organophosphates and a pyrazol analogue. Based on their LC50 values, the order of susceptibility of An. sinensis larvae to the insecticides was bifenthrin, chlorfenapyr, α‐cypermethrin and λ‐cyhalothrin, with values of 0.009, 0.04, 0.06 and 0.08 p.p.m., respectively. The least susceptibility was obtained with fenitrothion, with an LC50 of 7.7 p.p.m. In the comparative resistance test, the resistance ratios (RR) of 14 insecticides were compared to each other using two strains of members of the An. sinensis Group collected in the locality in 2001 and 2008. Anopheles spp. demonstrated higher RR to organophosphates such as fenthion, and low RR for the pyrethroids. Among the organophosphates, fenthion had the highest RR of 33.3 and 270.0 fold differences for LC50 and LC90 values, respectively. Among the pyrethroids, permethrin was observed to have the highest RR of 3.8 and 1.8 fold differences for LC50 and LC90 values, respectively. However, there were no significant differences in susceptibility to chlorfenapyr, chlorpyrifos, deltamethrin and fenitrothion. An. sinensis s. l. was more susceptible to the six insecticides bifenthrin, λ‐cyhalothrin, α‐cypermethrin, cypermethrin, cyfluthrin and pyridafenthion, showing 0.03, 0.06, 0.3, 0.3, 0.4 and 0.4 fold differences in resistance rates (RR LC50), respectively.
Cultural Industries and the Creative Economy – Vague but Useful Concepts
Authors: Boggs Jeff
Published: May 2009

For those new to it, the literature on cultural industries can be confusing. While some authors refer to cultural industries, others refer to cultural‐products industries or creative industries. Collectively, this heterogeneous group of industries comprises the cultural economy or the creative economy. Four typologies are presented, enabling one to more easily compare and contrast the essential features of commonly used definitions. The paper then discusses how this vague bundle of concepts is still useful as a lens on contemporary trends in industrialized economies.
Prognostic Utility of Right Ventricular Systolic Functions Assessed by Tissue Doppler Imaging in Dilated Cardiomyopathy and Its Correlation With Plasma NT‐pro‐BNP Levels
Authors: Tigen Kursat , Karaahmet Tansu , Cevik Cihan , Gurel Emre , Pala Selcuk , Mutlu Bulent , Basaran Yelda
Published: May 2009

The authors invesitgated the impact of right ventricular systolic function measured by tissue Doppler imaging on clinical end points and its correlation with plasma NT‐pro‐BNP levels in 75 patients with nonischemic dilated cardiomyopathy. Echocardiographic peak systolic velocities of tricuspid lateral annulus by tissue Doppler imaging and plasma pro‐B‐type natriuretic peptide (NT‐pro‐BNP) levels were measured. Forty patients had clinical end points in 29±16 months. They were found to have higher plasma NT‐pro‐BNP levels and lower tricuspid lateral annulus and interventricular septum tissue Doppler peak systolic velocities than patients without clinical end points. Cut‐off level of plasma NT‐pro‐BNP levels for predicting clinical end points was 1700 pg/mL (sensitivity and specificity, 82% and 75%, respectively). Cut‐off level of tricuspid lateral annulus tissue Doppler peak systolic velocities for predicting clinical end points was 6.25 cm/sec (sensitivity and specificity, 80% and 57%, respectively). In conclusion, plasma NT‐pro‐BNP levels and tissue Doppler–derived right ventricular systolic functional parameters are helpful in determining prognosis in dilated cardiomyopathy.
Tyramine biosynthesis in Enterococcus durans is transcriptionally regulated by the extracellular pH and tyrosine concentration
Authors: Linares Daniel M. , Fernández María , Martín M. Cruz , Álvarez Miguel A.
Published: May 2009

The microbial decarboxylation of some amino acids leads to the undesirable presence of biogenic amines in foods. One of the most abundant and frequent biogenic amines found in fermented foods is tyramine, which is produced by the decarboxylation of tyrosine. In the present work, transcriptional analysis of tyramine biosynthesis in Enterococcus durans IPLA655, a strain isolated from cheese, was studied. The gene coding for the tyrosine decarboxylase (tdcA) and that coding for the tyrosine‐tyramine antiporter (tyrP) form an operon transcribed from the promoter PtdcA, the expression of which is regulated by the extracellular pH and tyrosine concentration. Quantification of gene expression during the log phase of growth showed high concentrations of tyrosine and acidic pH conditions to induce tdcA‐tyrP polycistronic messenger transcription.
An Experimental Test of the Theory of Planned Behavior
Authors: Sniehotta Falko
Published: May 2009

The Theory of Planned Behavior (TPB) is one of the leading theories of health behavior, yet supporting evidence is exclusively based on correlational research. This study aims to test the TPB experimentally. N = 579 participants were randomised to receive persuasive messages addressing salient beliefs elicited in a pilot study, following a 2*2*2 factorial design. Participants were randomised to a behavioral‐belief‐intervention (BBI) or not, a normative‐belief‐intervention (NBI) or not, and a control‐belief‐intervention (CBI) or not. The primary outcome was objectively recorded attendance at university sports facilities over 2 months; and the secondary outcomes were post‐intervention TPB measures. Main effects of the BBI on attitudes and of the NBI on subjective norm, PBC, attitudes, and intentions were found. The CBI did not alter post‐intervention cognitions, but was the only intervention to change behavior not mediated by cognitions. While the findings support the TPB's assumptions on intention formation, behavior change results are not in line with the theory and therefore further question the TPB's leading role in behavioral science.
Burning mouth syndrome and psychological disorders
Authors: Abetz LM , Savage NW
Published: May 2009

Burning mouth syndrome (BMS) is an oral dysaesthesia that causes chronic orofacial pain in the absence of a detectable organic cause. The aetiology of BMS is complex and multifactorial, and has been associated in the literature with menopause, trigger events and even genetic polymorphisms. Other studies have found evidence for mechanisms such as central and peripheral nervous system changes, with clinical and laboratory investigations supporting a neuropathologic cause. These physiological explanations notwithstanding, there is still much evidence that BMS aetiology has at least some psychological elements. Somatoform pain disorder has been suggested as a mechanism and factors such as personality, stress, anxiety, depression and other psychological, psychosocial and even psychiatric disorders play a demonstrable role in BMS aetiology and symptomatology. In order to treat BMS patients, both physiological and psychological factors must be managed, but patient acceptance of possible components of psychological disease basis is a major hurdle. Clinical signs of patient stress, anxiety or depression are a useful reinforcement of clinical discussions. The current paper proposes a number of clinical signs that may be useful for both clinical assessment and subsequent patient discussions by providing visible supportive evidence of the diagnosis.
Biomarkers of periodontal inflammation in the Australian adult population
Authors: Fitzsimmons TR , Sanders AE , Slade GD , Bartold PM
Published: May 2009

Background:  Several inflammatory biomarkers are implicated in the pathogenesis of periodontitis including interleukin‐1β (IL‐1β) and C‐reactive protein (CRP). This study investigated the presence of these factors in gingival crevicular fluid (GCF) and their relationship to clinical and social determinants of periodontitis in the Australian population.

Methods:  Equal numbers of periodontitis cases and non‐cases were sampled during oral epidemiologic examination in the National Survey of Adult Oral Health. GCF was sampled from four sites where probing pocket depth (PPD) and recession were recorded. From these, IL‐1β and CRP were quantified by ELISA and the log amount of GCF IL‐1β (pg) per person and the proportion of adults with detectable CRP was computed.

Results:  Periodontitis cases (n = 511) had significantly higher levels of IL‐1β and CRP than non‐cases (n = 562). PPD, clinical attachment loss, plaque and gingivitis indices were positively associated with elevated levels of both biomarkers. Levels of both were positively associated with age, low socio‐economic position and non‐Australian birth.

Conclusions:  The presence of IL‐1β and CRP in GCF are associated with periodontal disease parameters within the Australian population. The levels of both biomarkers are influenced by age, education and eligibility for public dental care.
Public dental service utilization among adults in South Australia
Authors: Luzzi L , Spencer AJ
Published: May 2009

Background:  Longitudinal patterns of public dental service use may reflect access issues to public dental care services. Therefore, patterns of dental service use among South Australian adult public dental patients over a 3½‐year period were examined.

Methods:  Public dental patients (n = 898) initially receiving a course of emergency dental care (EDC) or general dental care (GDC) at baseline were followed for up to 3½ years. Patient clinical records were accessed electronically to obtain information on dental visits and treatment received at those visits.

Results:  Some 70.7 per cent of EDC and 51.3 per cent of GDC patients returned for dental treatment post‐baseline. EDC patients returned within a significantly shorter time period post‐baseline, received significantly more courses of care and were visiting more frequently than GDC patients. A greater proportion of EDC patients received oral surgery, restorative, endodontic and prosthodontic services, but fewer received periodontic services. EDC patients received significantly more oral surgery and fewer preventive services per follow‐up year, on average, than GDC patients. Large proportions of EDC (52.4 per cent) and GDC (63.8 per cent) patients who returned sought emergency care post‐baseline.

Conclusions:  Patients appeared to be cycling through emergency dental care because of lack of access to general care services, highlighting access problems to public dental care.
Response to Comment on “Functional Traits and Niche-Based Tree Community Assembly in an Amazonian Forest”
Authors: Kraft Nathan J. B. , Ackerly David D.
Published: May 2009

Lake and Ostling address several issues that they suggest could influence our analyses of tropical forest community assembly. Some of the issues have already been considered, whereas others appear to arise from misunderstandings. We offer clarification of our analyses and additional discussion of our results.
Deep Tremors and Slow Quakes
Authors: Beroza Gregory C. , Ide Satoshi
Published: May 2009

Detection and monitoring of slow earthquakes may provide a better understanding of ordinary earthquakes.
Problems Well Worth Pondering
Big Questions in Ecology and Evolution

by Thomas N. Sherratt and David M. Wilkinson

Oxford University Press, New York, 2009. 311 pp. $99, £55. ISBN 9780199548606. Paper, $45, £27.50. ISBN 9780199548613.
Authors: Kokko Hanna
Published: May 2009

Sherratt and Wilkinson offer thought-provoking answers to questions about aging, sex, cooperation, species, tropical diversity, chaos, our green world, the blue sea, when humans started to change the world, and possible ends to Earth's biosphere.
A Glucose-to-Gene Link
Authors: Rathmell Jeffrey C. , Newgard Christopher B.
Published: May 2009

A regulatory loop links glucose metabolism to chromatin alterations and the controlled expression of metabolic genes.
Epidemic Science in Real Time
Authors: Fineberg Harvey V. , Wilson Mary Elizabeth
Published: May 2009

Few situations more dramatically illustrate the salience of science to policy than an epidemic. The relevant science takes place rapidly and continually, in the laboratory, clinic, and community. In facing the current swine flu (H1N1 influenza) outbreak, the world has benefited from research investment over many years, as well as from preparedness exercises and planning in many countries. The global public health enterprise has been tempered by the outbreak of severe acute respiratory syndrome (SARS) in 2002–2003, the ongoing threat of highly pathogenic avian flu, and concerns over bioterrorism. Researchers and other experts are now able to make vital contributions in real time. By conducting the right science and communicating expert judgment, scientists can enable policies to be adjusted appropriately as an epidemic scenario unfolds.
Group Calls for Rapid Release of More Genomics Data
Authors: Pennisi Elizabeth
Published: May 2009

In 1996, at a meeting in Bermuda, researchers participating in the Human Genome Project agreed to release DNA sequence data daily into a public database. Now pressure is mounting to extend the Bermuda Principles to a broad range of publicly funded projects that go beyond sequencing.
Repetition Is Not Duplication
Authors: Couzin-Frankel Jennifer
Published: May 2009

In response to concerns about updated reviews of clinical research being flagged in Déjà vu, the plagiarism database's operators created a special category for legitimate duplications—but they refuse to remove the papers entirely.
Stressed Out Over a Stress Hormone
Authors: Pennisi Elizabeth
Published: May 2009

The hormone ABA lets plants handle rough times and holds promise for making drought-resistant crops, if only researchers could nail down its molecular partners.
Specific Antibodies Elicited by a Novel DNA Vaccine Targeting Gastrin-Releasing Peptide Inhibit Murine Melanoma Growth In Vivo
Authors: Fang Jing , Lu Yong , Ouyang Kedong , Wu Guojun , Zhang Huiyong , Liu Yanhua , Chen Yingying , Lin Ming , Wang Huaqian , Jin Liang , Cao Rongyue , Roque Rouel S. , Zong Li , Liu Jingjing , Li Taiming
Published: May 2009

The elevated expression and receptor binding of gastrin-releasing peptide (GRP) in various types of cancer, especially in malignant melanoma of the skin, suggest that GRP might be a putative target for immunotherapy in neoplastic diseases. We have therefore constructed a novel DNA vaccine coding for six tandem repeats of a fragment of GRP from amino acids 18 to 27 (GRP6) flanked by helper T-cell epitopes for increased immunogenicity, including HSP65, a tetanus toxoid fragment from amino acids 830 to 844 (T), pan-HLA-DR-binding epitope (PADRE) (P), and two repeats of a mycobacterial HSP70 fragment from amino acids 407 to 426 (M). The anti-GRP DNA vaccine (pCR3.1-VS-HSP65-TP-GRP6-M2) was constructed on a backbone of a pCR3.1 plasmid vector with eight 5′-GACGTT-3′ CpG motifs and the VEGF183 signal peptide (VS). Intramuscular (IM) injections of anti-GRP vaccine in mice stimulated the production of high titers of specific antibodies against GRP and suppressed the growth of subcutaneous tumors of B16-F10 melanoma cells. Parallel results were obtained in vitro, showing inhibition of B16-F10 cell proliferation by GRP antisera. IM injections of the DNA vaccine also significantly attenuated tumor-induced angiogenesis associated with intradermal tumors of B16-F10 cells. In addition, lung invasion of intravenously injected cells was highly diminished, suggesting potent antimetastatic activity of the DNA vaccine. These findings support the highly immunogenic and potent antitumorigenic activity of specific anti-GRP antibodies elicited by the anti-GRP DNA vaccine.
Development of a Murine Mycobacterial Growth Inhibition Assay for Evaluating Vaccines againstMycobacterium tuberculosis
Authors: Parra Marcela , Yang Amy L. , Lim JaeHyun , Kolibab Kristopher , Derrick Steven , Cadieux Nathalie , Perera Liyanage P. , Jacobs William R. , Brennan Michael , Morris Sheldon L.
Published: May 2009

The development and characterization of new tuberculosis (TB) vaccines has been impeded by the lack of reproducible and reliable in vitro assays for measuring vaccine activity. In this study, we developed a murine in vitro mycobacterial growth inhibition assay for evaluating TB vaccines that directly assesses the capacity of immune splenocytes to control the growth ofMycobacterium tuberculosiswithin infected macrophages. Using this in vitro assay, protective immune responses induced by immunization with five different types of TB vaccine preparations (Mycobacterium bovis BCG, an attenuatedM. tuberculosismutant strain, a DNA vaccine, a modified vaccinia virus strain Ankara [MVA] construct expressing four TB antigens, and a TB fusion protein formulated in adjuvant) can be detected. Importantly, the levels of vaccine-induced mycobacterial growth-inhibitory responses seen in vitro after 1 week of coculture correlated with the protective immune responses detected in vivo at 28 days postchallenge in a mouse model of pulmonary tuberculosis. In addition, similar patterns of cytokine expression were evoked at day 7 of the in vitro culture by immune splenocytes taken from animals immunized with the different TB vaccines. Among the consistently upregulated cytokines detected in the immune cocultures are gamma interferon, growth differentiation factor 15, interleukin-21 (IL-21), IL-27, and tumor necrosis factor alpha. Overall, we have developed an in vitro functional assay that may be useful for screening and comparing new TB vaccine preparations, investigating vaccine-induced protective mechanisms, and assessing manufacturing issues, including product potency and stability.
Denaturing Gradient Gel Electrophoresis of PCR-Amplified
gki
Genes: a New Technique for Tracking Streptococci
Authors: van Vliet M. J. , Tissing W. J. E. , de Bont E. S. J. M. , Meessen N. E. L. , Kamps W. A. , Harmsen H. J. M.
Published: May 2009

Viridans group streptococci (VGS) are a well-known cause of infections in immunocompromised patients, accounting for severe morbidity and mortality.
Streptococcus
mitis
group species (
Streptococcus mitis
,
Streptococcus pneumoniae
,
Streptococcus oralis
) are among the VGS most often encountered in clinical practice. Identifying the portal of entry for
S. mitis
group strains is crucial for interventions preventing bacterial translocation. Unfortunately, tracking the source of
S. mitis
group strains is dependent on a combination of extremely laborious and time-consuming cultivation and molecular techniques (enterobacterial repetitive intergenic consensus-PCR [ERIC-PCR]). To simplify this procedure, a PCR analysis with newly designed primers targeting the household gene glucose kinase (
gki
) was used in combination with denaturing gradient gel electrophoresis (DGGE). This
gki
-PCR-DGGE technique proved to be specific for
S. mitis
group strains. Moreover, these strains could be detected in samples comprised of highly diverse microbiota, without prior cultivation. To study the feasibility of this new approach, a pilot study was performed. This confirmed that the source of
S. mitis
group bacteremia in pediatric patients with acute myeloid leukemia could be tracked back to the throat in five out of six episodes of bacteremia, despite the fact that throat samples are polymicrobial samples containing multiple
S. mitis
group strains. In contrast, using the classical combination of cultivation techniques and ERIC-PCR, we could detect these strains in only two out of six cases, showing the superiority of the newly developed technique. The new
gki
-PCR-DGGE technique can track the source of
S. mitis
group strains in polymicrobial samples without prior cultivation. Therefore, it is a valuable tool in future epidemiological studies.
Pseudo-Outbreak of
Rhizobium radiobacter
Infection Resulting from Laboratory Contamination of Saline Solution
Authors: Pereira Lynette A. , Chan Douglas Su Gin , Ng Toon Mae , Lin Raymond , Jureen Roland , Fisher Dale A. , Tambyah Paul A.
Published: May 2009

We report a pseudo-outbreak of
Rhizobium radiobacter
infections resulting from contamination by a saline dispenser in the microbiology laboratory. Isolates from clinical specimens had identical antimicrobial susceptibilities and electrophoretic fingerprints. The episode resolved with autoclaving of the dispenser. This demonstrates the importance of timely, thorough investigation of unusual organisms, particularly when they appear as a cluster.
The Nucleocapsid Region of Human Immunodeficiency Virus Type 1 Gag Assists in the Coordination of Assembly and Gag Processing: Role for RNA-Gag Binding in the Early Stages of Assembly
Authors: Ott David E. , Coren Lori V. , Shatzer Teresa
Published: May 2009

Human immunodeficiency virus type 1 (HIV-1) Gag-RNA interactions are required for virus assembly. However, our prior study found that a defect in particle production exhibited by an HIV-1 proviral mutant with a severe deletion in the RNA-binding nucleocapsid (NC) region of Gag, NX, could be reversed by eliminating its protease activity. While our follow-up study indicated that a secondary RNA-binding site in Gag can also provide the required RNA-binding function, how protease activity inhibits NX virion production is still unclear. Therefore, we tested three possible mechanisms: NX virions are unstable and fall apart after budding; NX Gag assembly is slowed, allowing protease processing to start before particle formation; or the protease region within NX Gag-Pol becomes activated prematurely and processes the assembling Gag. We found that NX particles were as stable as wild-type virions. Furthermore, even a modest slowing of protease activity could rescue NX. Pulse-chase analysis revealed that the initial particle production by NC-deleted Gag was delayed compared to that of wild type Gag, but once started, the rate of production was similar, revealing a defect in the initiation of assembly. Wild-type Gag particle production was not eliminated or decreased in the presence of excess NX Gag-Pol, inconsistent with a premature activation of protease. Overall, these results indicate that the particle formation defect of NX is due to delayed initiation of assembly caused by the absence of NC in Gag, making it vulnerable to protease processing before budding can occur. Therefore, NC plays an important initiating role in Gag assembly.
Human Immunodeficiency Virus Type 1-Specific CD8+T-Cell Responses during Primary Infection Are Major Determinants of the Viral Set Point and Loss of CD4+T Cells
Authors: Streeck Hendrik , Jolin Jonathan S. , Qi Ying , Yassine-Diab Bader , Johnson Randall C. , Kwon Douglas S. , Addo Marylyn M. , Brumme Chanson , Routy Jean-Pierre , Little Susan , Jessen Heiko K. , Kelleher Anthony D. , Hecht Frederick M. , Sekaly Rafick-Pierre , Rosenberg Eric S. , Walker Bruce D. , Carrington Mary , Altfeld Marcus
Published: May 2009

Primary HIV-1 infection (PHI) is marked by a flu-like syndrome and high levels of viremia that decrease to a viral set point with the first emergence of virus-specific CD8+T-cell responses. Here, we investigated in a large cohort of 527 subjects the immunodominance pattern of the first virus-specific cytotoxic T-lymphocyte (CTL) responses developed during PHI in comparison to CTL responses in chronic infection and demonstrated a distinct relationship between the early virus-specific CTL responses and the viral set point, as well as the slope of CD4+T-cell decline. CTL responses during PHI followed clear hierarchical immunodominance patterns that were lost during the transition to chronic infection. Importantly, the immunodominance patterns of human immunodeficiency virus type 1 (HIV-1)-specific CTL responses detected in primary, but not in chronic, HIV-1 infection were significantly associated with the subsequent set point of viral replication. Moreover, the preservation of the initial CD8+T-cell immunodominance patterns from the acute into the chronic phase of infection was significantly associated with slower CD4+T-cell decline. Taken together, these data show that the specificity of the initial CTL response to HIV is critical for the subsequent control of viremia and have important implications for the rational selection of antigens for future HIV-1 vaccines.
Evaluation of Vaccines for H5N1 Influenza Virus in Ferrets Reveals the Potential for Protective Single-Shot Immunization
Authors: Middleton Deborah , Rockman Steven , Pearse Martin , Barr Ian , Lowther Sue , Klippel Jessica , Ryan David , Brown Lorena
Published: May 2009

As part of influenza pandemic preparedness, policy decisions need to be made about how best to utilize vaccines once they are manufactured. Since H5N1 avian influenza virus has the potential to initiate the next human pandemic, isolates of this subtype have been used for the production and testing of prepandemic vaccines. Clinical trials of such vaccines indicate that two injections of preparations containing adjuvant will be required to induce protective immunity. However, this is a working assumption based on classical serological measures only. Examined here are the dose of viral hemagglutinin (HA) and the number of inoculations required for two different H5N1 vaccines to achieve protection in ferrets after lethal H5N1 challenge. Ferrets inoculated twice with 30 μg of A/Vietnam/1194/2004 HA vaccine with AlPO
4
, or with doses as low as 3.8 μg of HA with Iscomatrix (ISCOMATRIX, referred to as Iscomatrix herein, is a registered trademark of CSL Limited) adjuvant, were completely protected against death and disease after H5N1 challenge, and the protection lasted at least 15 months. Cross-clade protection was also observed with both vaccines. Significantly, complete protection against death could be achieved with only a single inoculation of H5N1 vaccine containing as little as 15 μg of HA with AlPO
4
or 3.8 μg of HA with Iscomatrix adjuvant. Ferrets vaccinated with the single-injection Iscomatrix vaccines showed fewer clinical manifestations of infection than those given AlPO
4
vaccines and remained highly active. Our data provide the first indication that in the event of a future influenza pandemic, effective mass vaccination may be achievable with a low-dose “single-shot” vaccine and provide not only increased survival but also significant reduction in disease severity.
Upstream Regulatory Region Alterations Found in Human Papillomavirus Type 16 (HPV-16) Isolates from Cervical Carcinomas Increase Transcription,
ori
Function, and HPV Immortalization Capacity in Culture
Authors: Lace Michael J. , Isacson Christina , Anson James R. , Lörincz Attila T. , Wilczynski Sharon P. , Haugen Thomas H. , Turek Lubomír P.
Published: May 2009

Human papillomavirus (HPV) DNAs isolated from cervical and head and neck carcinomas frequently contain nucleotide sequence alterations in the viral upstream regulatory region (URR). Our study has addressed the role such sequence changes may play in the efficiency of establishing HPV persistence and altered keratinocyte growth. Genomic mapping of integrated HPV type 16 (HPV-16) genomes from 32 cervical cancers revealed that the viral E6 and E7 oncogenes, as well as the L1 region/URR, were intact in all of them. The URR sequences from integrated and unintegrated viral DNA were found to harbor distinct sets of nucleotide substitutions. A subset of the altered URRs increased the potential of HPV-16 to establish persistent, cell growth-altering viral-genome replication in the cell. This aggressive phenotype in culture was not solely due to increased viral early gene transcription, but also to augmented initial amplification of the viral genome. As revealed in a novel
ori
-dependent HPV-16 plasmid amplification assay, the altered motifs that led to increased viral transcription from the intact genome also greatly augmented HPV-16
ori
function. The nucleotide sequence changes correlate with those previously described in the distinct geographical North American type 1 and Asian-American variants that are associated with more aggressive disease in epidemiologic studies and encompass, but are not limited to, alterations in previously characterized sites for the negative regulatory protein YY1. Our results thus provide evidence that nucleotide alterations in HPV regulatory sequences could serve as potential prognostic markers of HPV-associated carcinogenesis.
Murine Cytomegalovirus Capsid Assembly Is Dependent on US22 Family Gene M140 in Infected Macrophages
Authors: Hanson Laura K. , Slater Jacquelyn S. , Cavanaugh Victoria J. , Newcomb William W. , Bolin Lisa L. , Nelson Christine N. , Fetters Lisa D. , Tang Qiyi , Brown Jay C. , Maul Gerd G. , Campbell Ann E.
Published: May 2009

Macrophages are an important target cell for infection with cytomegalovirus (CMV). A number of viral genes that either are expressed specifically in this cell type or function to optimize CMV replication in this host cell have now been identified. Among these is the murine CMV (MCMV) US22 gene family member M140, a nonessential early gene whose deletion (RVΔ140) leads to significant impairment in virus replication in differentiated macrophages. We have now determined that the defect in replication is at the stage of viral DNA encapsidation. Although the rate of RVΔ140 genome replication and extent of DNA cleavage were comparable to those for revertant virus, deletion of M140 resulted in a significant reduction in the number of viral capsids in the nucleus, and the viral DNA remained sensitive to DNase treatment. These data are indicative of incomplete virion assembly. Steady-state levels of both the major capsid protein (M86) and tegument protein M25 were reduced in the absence of the M140 protein (pM140). This effect may be related to the localization of pM140 to an aggresome-like, microtubule organizing center-associated structure that is known to target misfolded and overexpressed proteins for degradation. It appears, therefore, that pM140 indirectly influences MCMV capsid formation in differentiated macrophages by regulating the stability of viral structural proteins.
Reassessing the Human Immunodeficiency Virus Type 1 Life Cycle through Age-Structured Modeling: Life Span of Infected Cells, Viral Generation Time, and Basic Reproductive Number,R0
Authors: Althaus Christian L. , De Vos Anneke S. , De Boer Rob J.
Published: May 2009

The rapid decay of the viral load after drug treatment in patients infected with human immunodeficiency virus type 1 (HIV-1) has been shown to result from the rapid loss of infected cells due to their high turnover, with a generation time of around 1 to 2 days. Traditionally, viral decay dynamics after drug treatment is investigated using models of differential equations in which both the death rate of infected cells and the viral production rate are assumed to be constant. Here, we describe age-structured models of the viral decay dynamics in which viral production rates and death rates depend on the age of the infected cells. In order to investigate the effects of age-dependent rates, we compared these models with earlier descriptions of the viral load decay and fitted them to previously published data. We have found no supporting evidence that infected-cell death rates increase, but cannot reject the possibility that viral production rates increase, with the age of the cells. In particular, we demonstrate that an exponential increase in viral production with infected-cell age is perfectly consistent with the data. Since an exponential increase in virus production can compensate for the exponential loss of infected cells, the death rates of HIV-1-infected cells may be higher than previously anticipated. We discuss the implications of these findings for the life span of infected cells, the viral generation time, and the basic reproductive number,R0.
LARGE DEVIATION GENERATING FUNCTION FOR CURRENTS IN THE PAULI–FIERZ MODEL
Authors: DE ROECK WOJCIECH
Published: May 2009

We consider a finite quantum system coupled to quasifree thermal reservoirs at different temperatures. We construct the statistics of energy transport between the reservoirs and we show that the corresponding large deviation generating function exists and it is analytic on a compact set. This result is valid for small coupling and exponentially decaying reservoir correlation functions. Our technique consists of a diagrammatic expansion that uses the Markovian limit of the system as a reference. As a corollary, we derive the Gallavotti–Cohen fluctuation relation for the entropy production.
Agriculture for Development: Toward a New Paradigm
Authors: Byerlee Derek , de Janvry Alain , Sadoulet Elisabeth
Published: May 2009

The fundamental role that agriculture plays in development has long been recognized. In the seminal work on the subject, agriculture was seen as a source of contributions that helped induce industrial growth and a structural transformation of the economy. However, globalization, integrated value chains, rapid technological and institutional innovations, and environmental constraints have deeply changed the context for agriculture's role. We argue that a new paradigm is needed that recognizes agriculture's multiple functions for development in that emerging context: triggering economic growth, reducing poverty, narrowing income disparities, providing food security, and delivering environmental services. Yet, governments and donors have neglected these functions of agriculture with the result that agriculture growth has been reduced, 75% of world poverty is rural, sectoral income disparities have exploded, food insecurity has returned, and environmental degradation is widespread, compromising sustainability. Mobilizing these functions requires shifting the political economy to overcome antiagriculture policy biases, strengthening governance for agriculture, and tailoring priorities to country conditions.
Recent Developments in Renewable Technologies: R&D Investment in Advanced Biofuels
Authors: Rajagopal Deepak , Sexton Steve , Hochman Gal , Zilberman David
Published: May 2009

Investment in renewable energy, both in research and development and in commercial production, has risen significantly during the current decade. Although a variety of different renewable sources have been targeted for expansion, biomass technologies, especially those for converting biomass to liquid biofuels for transportation, have cornered a large share of the new investments. Cutting-edge knowledge in genomics and biotechnology, process chemistry, and engineering is being applied to produce new types of energy feedstock and process them into novel biofuels. If these investments bear fruit, liquid biofuels have the potential to displace a substantial amount of oil over the next few decades, with limited negative impact on food supply and the natural habitat. Energy-security and food-security constraints and environmental considerations will determine which technologies emerge as winners. The search for new transportation fuels is also giving rise to the development of new paradigms in innovation, commercialization, and regulation.
Cerebral microvascular endothelial cell Na/H exchange: evidence for the presence of NHE1 and NHE2 isoforms and regulation by arginine vasopressin
Authors: Lam Tina I. , Wise Phyllis M. , O'Donnell Martha E.
Published: May 2009

Blood-brain barrier (BBB) Na transporters are essential for brain water and electrolyte homeostasis. However, they also contribute to edema formation during the early hours of ischemic stroke by increased transport of Na from blood into brain across an intact BBB. We previously showed that a luminal BBB Na-K-Cl cotransporter is stimulated by hypoxia, aglycemia, and AVP and that inhibition of the cotransporter by intravenous bumetanide significantly reduces edema and infarct in the rat middle cerebral artery occlusion (MCAO) model of stroke. More recently, we found evidence that intravenous cariporide (HOE-642), a highly potent Na/H exchange inhibitor, also reduces brain edema after MCAO. The present study was conducted to investigate which Na/H exchange protein isoforms are present in BBB endothelial cells and to evaluate the effects of ischemic factors on BBB Na/H exchange activity. Western blot analysis of bovine cerebral microvascular endothelial cells (CMEC) and immunoelectron microscopy of perfusion-fixed rat brain revealed that Na/H exchanger isoforms 1 and 2 (NHE1 and NHE2) are present in BBB endothelial cells. Using microspectrofluorometry and the pH-sensitive dye BCECF, we found that hypoxia (2% O2, 30 min), aglycemia (30 min), and AVP (1–200 nM, 5 min) significantly increased CMEC Na/H exchange activity, assessed as Na-dependent, HOE-642-sensitive H+ flux. We found that AVP stimulation of CMEC Na/H exchange activity is dependent on intracellular Ca concentration and is blocked by V1, but not V2, vasopressin receptor antagonists. Our findings support the hypothesis that a BBB Na/H exchanger, possibly NHE1 and/or NHE2, is stimulated during ischemia to participate in cerebral edema formation.
The molecular effects of skeletal muscle myosin regulatory light chain phosphorylation
Authors: Greenberg Michael J. , Mealy Tanya R. , Watt James D. , Jones Michelle , Szczesna-Cordary Danuta , Moore Jeffrey R.
Published: May 2009

Phosphorylation of the myosin regulatory light chain (RLC) in skeletal muscle has been proposed to act as a molecular memory of recent activation by increasing the rate of force development, ATPase activity, and isometric force at submaximal activation in fibers. It has been proposed that these effects stem from phosphorylation-induced movement of myosin heads away from the thick filament backbone. In this study, we examined the molecular effects of skeletal muscle myosin RLC phosphorylation using in vitro motility assays. We showed that, independently of the thick filament backbone, the velocity of skeletal muscle myosin is decreased upon phosphorylation due to an increase in the myosin duty cycle. Furthermore, we did not observe a phosphorylation-dependent shift in calcium sensitivity in the absence of the myosin thick filament. These data suggest that phosphorylation-induced movement of myosin heads away from the thick filament backbone explains only part of the observed phosphorylation-induced changes in myosin mechanics. Last, we showed that the duty cycle of skeletal muscle myosin is strain dependent, consistent with the notion that strain slows the rate of ADP release in striated muscle.
Individual variation in macronutrient regulation measured by proton magnetic resonance spectroscopy of human plasma
Authors: Park Youngja , Kim Seoung Bum , Wang Bing , Blanco Roberto A. , Le Ngoc-Anh , Wu Shaoxiong , Accardi Carolyn J. , Alexander R. Wayne , Ziegler Thomas R. , Jones Dean P.
Published: May 2009

Proton nuclear magnetic resonance (1H-NMR) spectroscopy of plasma provides a global metabolic profiling method that shows promise for clinical diagnostics. However, cross-sectional studies are complicated by a lack of understanding of intraindividual variation, and this limits experimental design and interpretation of data. The present study determined the diurnal variation detected by1H NMR spectroscopy of human plasma. Data reduction methods revealed three time-of-day metabolic patterns, which were associated with morning, afternoon, and night. Major discriminatory regions for these time-of-day patterns included the various kinds of lipid signals (-CH2- and -CH2OCOR), and the region between 3 and 4 ppm heavily overlapped with amino acids that had α-CH and α-CH2. The phasing and duration of time-of-day patterns were variable among individuals, apparently because of individual difference in food processing/digestion and absorption and clearance of macronutrient energy sources (fat, protein, carbohydrate). The times of day that were most consistent among individuals, and therefore most useful for cross-sectional studies, were fasting morning (0830–0930), postprandial afternoon (1430–1630), and nighttime samples (0430–0530). Importantly, the integrated picture of metabolism provided by1H-NMR spectroscopy of plasma suggests that this approach is suitable to study complex regulatory processes, including eating patterns/eating disorders, upper gastrointestinal functions (gastric emptying, pancreatic, biliary functions), and absorption/clearance of macronutrients. Hence,1H-NMR spectroscopy of plasma could provide a global metabolic tolerance test to assess complex processes involved in disease, including eating disorders and the range of physiological processes causing dysregulation of energy homeostasis.
Role of BKβ1 in Na+ reabsorption by cortical collecting ducts of Na+-deprived mice
Authors: Grimm P. Richard , Irsik Debra L. , Liu Liping , Holtzclaw J. David , Sansom Steven C.
Published: May 2009

On a low-Na+ diet (LNa+), urinary Na+ loss is prevented by aldosterone-induced Na+ reabsorption through epithelial Na+ channels (ENaC) in the connecting tubules (CNT) and cortical collecting ducts (CCD). However, the mechanism whereby K+ loss is minimized and Na+ reabsorption is maximized in the face of a reduced lumen-to-bath Na+ gradient is not fully understood. The large-conductance calcium-activated potassium channel (BK)β1 subunit (gene: Kcnmb1), which has a role in K+ secretion in the CNT, is absent in the CCD in mice on a control diet. We hypothesized that BKα/β1 helps to maximize Na+ reabsorption during Na+ deficiency. With LNa+, the Na+ clearance of Kcnmb1-mutant mice ( Kcnmb1−/−) was 45% greater and the plasma Na+ concentration and osmolality were significantly reduced compared with wild-type mouse (WT) controls. On LNa+, Kcnmb1−/− exhibited exacerbated volume depletion (higher Hct and weight loss) compared with WT. LNa+, which did not affect the mean arterial blood pressure (MAP) of WT, significantly reduced MAP of Kcnmb1−/−. The plasma aldosterone concentration of Kcnmb1−/− on LNa+ was significantly elevated compared with Kcnmb1−/− on a control diet but was not different from WT on LNa+. Immunohistochemical staining revealed that BKα and BKβ1, which were absent in the principal cells (PCs) of the CCD, were localized on the basolateral membrane (BSM) of PCs of WT on LNa+. Moreover, BKα was absent from the BSM of PCs of Na+-deficient Kcnmb1−/−. We conclude that part of the mechanism to maximize Na+ reabsorption during Na+ deficiency is the placement of BKα/β1 channels in the BSM of CCD PCs.