bluuebunny/crossref_metadata_2025 huggingface dataset:
Circulating Human Antibody-Secreting Cells during Vaccinations and Respiratory Viral Infections Are Characterized by High Specificity and Lack of Bystander Effect
Authors: Lee F. Eun-Hyung , Halliley Jessica L. , Walsh Edward E. , Moscatiello Andrew P. , Kmush Brittany L. , Falsey Ann R. , Randall Troy D. , Kaminiski Denise A. , Miller Richard K. , Sanz Iñaki
Published: March 2011

Surges of serum Abs after immunization and infection are highly specific for the offending Ag, and recent studies demonstrate that vaccines induce transient increases in circulating Ab-secreting cells (ASCs). These ASCs are highly enriched but not universally specific for the immunizing Ag, suggesting that a fraction of these ASCs could arise from polyclonal bystander stimulation of preexisting memory cells to unrelated Ags. This model is proposed to explain maintenance of long-lived serological memory in the absence of Ag exposure. To test this model, we measure the ability of respiratory syncytial virus and influenza virus infection or immunizations to influenza virus, tetanus toxoid, hepatitis B Ag, and human papillomavirus to stimulate bystander memory cells specific for other major environmental Ags that represent a large fraction of the preexisting memory B compartment. Bystander or nonspecific ASC responses to respiratory syncytial virus and tetanus could not be detected above the background levels in healthy adults, despite the presence of circulating memory B cells specific for the corresponding Ags. Nonspecific ASC responses in the healthy subjects and cord blood samples were similar. In contrast, both vaccination and infection induce massive expansion of circulating Ag-specific ASCs without significant increases in the frequencies of ASCs against unrelated Ags. Hence, nonspecific stimulation of memory B cells is unlikely to contribute to the mechanisms of long-term serological memory against major human pathogens. Additionally, high specificity of circulating ASCs after antigenic challenge highlights the diagnostic value of interrogating ASCs as an ideal single-time-point diagnostic immune surrogate for serology during acute infection.
A Novel Leukocyte Adhesion Deficiency III Variant: Kindlin-3 Deficiency Results in Integrin- and Nonintegrin-Related Defects in Different Steps of Leukocyte Adhesion
Authors: Robert Philippe , Canault Matthias , Farnarier Catherine , Nurden Alan , Grosdidier Charlotte , Barlogis Vincent , Bongrand Pierre , Pierres Anne , Chambost Hervé , Alessi Marie-Christine
Published: March 2011

Leukocyte adhesion deficiency type III is a recently described condition involving a Glanzmann-type bleeding syndrome and leukocyte adhesion deficiency. This was ascribed to a defect of the FERMT3 gene resulting in abnormal expression of kindlin-3, a protein expressed in hematopoietic cells with a major role in the regulation of integrin activation. In this article, we describe a patient with a new mutation of FERMT3 and lack of kindlin-3 expression in platelets and leukocytes. We assayed quantitatively the first steps of kindlin-3–defective leukocyte adhesion, namely, initial bond formation, bond strengthening, and early spreading. Initial bond formation was readily stimulated with neutrophils stimulated by fMLF, and neutrophils and lymphocytes stimulated by a phorbol ester or Mn2+. In contrast, attachment strengthening was defective in the patient’s lymphocytes treated with PMA or Mn2+, or fMLF-stimulated neutrophils. However, attachment strengthening was normal in patient’s neutrophils treated with phorbol ester or Mn2+. In addition, the patient’s T lymphocytes displayed defective integrin-mediated spreading and a moderate but significant decrease of spreading on anti-CD3–coated surfaces. Patient’s neutrophils displayed a drastic alteration of integrin-mediated spreading after fMLF or PMA stimulation, whereas signaling-independent Mn2+ allowed significant spreading. In conclusion, the consequences of kindlin-3 deficiency on β2 integrin function depend on both cell type and the stimulus used for integrin activation. Our results suggest looking for a possible kindlin-3 involvement in membrane dynamical event independent of integrin-mediated adhesion.
IL-21 Promotes Skin Recruitment of CD4+ Cells and Drives IFN-γ–Dependent Epidermal Hyperplasia
Authors: Sarra Massimiliano , Caruso Roberta , Cupi Maria Laura , Monteleone Ivan , Stolfi Carmine , Campione Elena , Diluvio Laura , Mazzotta Annamaria , Botti Elisabetta , Chimenti Sergio , Costanzo Antonio , MacDonald Thomas T. , Pallone Francesco , Monteleone Giovanni
Published: March 2011

Psoriasis is a chronic inflammatory disorder of the skin characterized by epidermal hyperplasia and infiltration of leukocytes into the dermis and epidermis. T cell-derived cytokines, such as IFN-γ and IL-17A, play a major role in the psoriasis-associated epidermal hyperplasia, even though factors/mechanisms that regulate the production of these cytokines are not fully understood. We have recently shown that IL-21 is synthesized in excess in psoriatic skin lesions and causes epidermal hyperplasia when injected intradermally in mice. Moreover, in the human psoriasis SCID mouse model, neutralization of IL-21 reduces both skin thickening and expression of inflammatory molecules, thus supporting the pathogenic role of IL-21 in psoriasis. However, the basic mechanism by which IL-21 promotes skin pathology remains unknown. In this study, we show that CD4+ cells accumulate early in the dermis of IL-21–treated mice and mediate the development of epidermal hyperplasia. Indeed, IL-21 fails to induce skin damage in RAG1-deficient mice and CD4+ cell-depleted wild-type mice. The majority of CD4+ cells infiltrating the dermis of IL-21–treated mice express IFN-γ and, to a lesser extent, IL-17A. Studies in cytokine knockout mice show that IFN-γ, but not IL-17A, is necessary for IL-21–induced epidermal hyperplasia. Finally, we demonstrate that IFN-γ–producing CD4+ cells infiltrating the human psoriatic plaque express IL-21R, and abrogation of IL-21 signals reduces IFN-γ expression in cultures of psoriatic CD4+ cells. Data indicate that IL-21 induces an IFN-γ–dependent pathogenic response in vivo, thus contributing to elucidate a mechanism by which IL-21 sustains skin-damaging inflammation.
Chronic Exposure to a TLR Ligand Injures Hematopoietic Stem Cells
Authors: Esplin Brandt L. , Shimazu Tomoyuki , Welner Robert S. , Garrett Karla P. , Nie Lei , Zhang Qingzhao , Humphrey Mary Beth , Yang Qi , Borghesi Lisa A. , Kincade Paul W.
Published: March 2011

Hematopoietic stem cells (HSC) can be harmed by disease, chemotherapy, radiation, and normal aging. We show in this study that damage also occurs in mice repeatedly treated with very low doses of LPS. Overall health of the animals was good, and there were relatively minor changes in marrow hematopoietic progenitors. However, HSC were unable to maintain quiescence, and transplantation revealed them to be myeloid skewed. Moreover, HSC from treated mice were not sustained in serial transplants and produced lymphoid progenitors with low levels of the E47 transcription factor. This phenomenon was previously seen in normal aging. Screening identified mAbs that resolve HSC subsets, and relative proportions of these HSC changed with age and/or chronic LPS treatment. For example, minor CD150HiCD48− populations lacking CD86 or CD18 expanded. Simultaneous loss of CD150Lo/−CD48− HSC and gain of the normally rare subsets, in parallel with diminished transplantation potential, would be consistent with age- or TLR-related injury. In contrast, HSC in old mice differed from those in LPS-treated animals with respect to VCAM-1 or CD41 expression and lacked proliferation abnormalities. HSC can be exposed to endogenous and pathogen-derived TLR ligands during persistent low-grade infections. This stimulation might contribute in part to HSC senescence and ultimately compromise immunity.
Lymphotoxin Signal Promotes Thymic Organogenesis by Eliciting RANK Expression in the Embryonic Thymic Stroma
Authors: Mouri Yasuhiro , Yano Masashi , Shinzawa Miho , Shimo Yusuke , Hirota Fumiko , Nishikawa Yumiko , Nii Takuro , Kiyonari Hiroshi , Abe Takaya , Uehara Hisanori , Izumi Keisuke , Tamada Koji , Chen Lieping , Penninger Josef M. , Inoue Jun-ichiro , Akiyama Taishin , Matsumoto Mitsuru
Published: March 2011

It has recently become clear that signals mediated by members of the TNFR superfamily, including lymphotoxin-β receptor (LTβR), receptor activator for NF-κB (RANK), and CD40, play essential roles in organizing the integrity of medullary thymic epithelial cells (mTECs) required for the establishment of self-tolerance. However, details of the mechanism responsible for the unique and cooperative action of individual and multiple TNFR superfamily members during mTEC differentiation still remain enigmatic. In this study, we show that the LTβR signal upregulates expression of RANK in the thymic stroma, thereby promoting accessibility to the RANK ligand necessary for mTEC differentiation. Cooperation between the LTβR and RANK signals for optimal mTEC differentiation was underscored by the exaggerated defect of thymic organogenesis observed in mice doubly deficient for these signals. In contrast, we observed little cooperation between the LTβR and CD40 signals. Thus, the LTβR signal exhibits a novel and unique function in promoting RANK activity for mTEC organization, indicating a link between thymic organogenesis mediated by multiple cytokine signals and the control of autoimmunity.
CXCR3 Deficiency Exacerbates Liver Disease and Abrogates Tolerance in a Mouse Model of Immune-Mediated Hepatitis
Authors: Erhardt Annette , Wegscheid Claudia , Claass Benjamin , Carambia Antonella , Herkel Johannes , Mittrücker Hans-Willi , Panzer Ulf , Tiegs Gisa
Published: March 2011

The chemokine receptor CXCR3 is preferentially expressed by Th1 cells and critically involved in their recruitment to inflamed tissue. In a mouse model of immune-mediated liver injury inducible by Con A, we investigated the role of CXCR3 in acute IFN-γ–mediated hepatitis as well as in tolerance induction, which has been shown to depend on IL-10–producing CD4+CD25+Foxp3+ regulatory T cells (Tregs). Induction of Con A hepatitis resulted in increased intrahepatic expression of the CXCR3 ligands CXCL9, CXCL10, and CXCL11. CXCR3−/− mice developed a more severe liver injury with higher plasma transaminase activities and a more pronounced Th1/Th17 response compared with wild-type (wt) animals upon Con A injection. Moreover, CXCR3−/− mice did not establish tolerance upon Con A restimulation, although Tregs from CXCR3−/− mice were still suppressive in an in vitro suppression assay. Instead, Tregs failed to accumulate in livers of CXCR3−/− mice upon Con A restimulation in contrast to those from wt animals. Con A-tolerant wt mice harbored significantly increased numbers of intrahepatic CXCR3+T-bet+ Tregs that produced IL-10 compared with nontolerant animals. IFN-γ deficiency or anti–IFN-γ Ab treatment demonstrated that conversion to CXCR3+T-bet+ Tregs depended on a Th1 response. Accordingly, in an immunotherapeutic approach, CD4+CD25+Foxp3+ Tregs from Con A-pretreated CXCR3-deficient mice failed to protect against Con A-induced hepatitis, whereas Tregs from Con A-tolerant wt mice allowed CXCR3-deficient mice to recover from Con A hepatitis. In summary, CXCR3+T-bet+IL-10+ Tregs are generated in the liver in dependence of IFN-γ, then disseminated into the organism and specifically migrate into the liver, where they limit immune-mediated liver damage.
A Multifunctional Element in the Mouse Igκ Locus That Specifies Repertoire and Ig Loci Subnuclear Location
Authors: Xiang Yougui , Zhou Xiaorong , Hewitt Susannah L. , Skok Jane A. , Garrard William T.
Published: March 2011

Nonbiased V gene usage for V(D)J joining is essential for providing an optimal immune system, but no cis-acting sequence with this function has been uncovered. We previously identified a recombination silencer and heterochromatin targeting element in the Vκ-Jκ intervening sequence of germline Igκ transgenes, which we termed Sis. We now have generated Sis knockout mice in the endogenous locus. Intriguingly, Sis−/− mice exhibit a skewed Igκ repertoire with markedly decreased distal and enhanced proximal Vκ gene usage for primary rearrangement, which is associated with reduced occupancy of Ikaros and CCCTC-binding factor in the Vκ-Jκ intervening sequence in pre-B cells, proteins believed to be responsible for dampening the recombination of nearby Vκ genes and altering higher-order chromatin looping. Furthermore, monoallelic heterochromatin localization is significantly reduced in Sis−/− mice for Igκ in cis and IgH loci in trans in pre-B cells. Because Sis−/− mice still allelically excluded Igκ and IgH loci and still exhibited IgL isotype exclusion, we concluded that stable localization at pericentromeric heterochromatin is neither necessary nor sufficient for the establishment or maintenance of allelic exclusion. Hence, Sis is a novel multifunctional element that specifies repertoire and heterochromatin localization to Ig genes.
Early Induction of Polyfunctional Simian Immunodeficiency Virus (SIV)-Specific T Lymphocytes and Rapid Disappearance of SIV from Lymph Nodes of Sooty Mangabeys during Primary Infection
Authors: Meythaler Mareike , Wang Zichun , Martinot Amanda , Pryputniewicz Sarah , Kasheta Melissa , McClure Harold M. , O’Neil Shawn P. , Kaur Amitinder
Published: March 2011

Although the cellular immune response is essential for controlling SIV replication in Asian macaques, its role in maintaining nonpathogenic SIV infection in natural hosts such as sooty mangabeys (SM) remains to be defined. We have previously shown that similar to rhesus macaques (RM), SM are able to mount a T lymphocyte response against SIV infection. To investigate early control of SIV replication in natural hosts, we performed a detailed characterization of SIV-specific cellular immunity and viral control in the first 6 mo following SIV infection in SM. Detection of the initial SIV-specific IFN-γ ELISPOT response in SIVsmE041-infected SM coincided temporally with a decline in peak plasma viremia and was similar in magnitude, specificity, and breadth to SIVsmE041-infected and SIVmac239-infected RM. Despite these similarities, SM showed a greater reduction in postpeak plasma viremia and a more rapid disappearance of productively SIV-infected cells from the lymph node compared with SIVmac239-infected RM. The early Gag-specific CD8+ T lymphocyte response was significantly more polyfunctional in SM compared with RM, and granzyme B-positive CD8+ T lymphocytes were present at significantly higher frequencies in SM even prior to SIV infection. These findings suggest that the early SIV-specific T cell response may be an important determinant of lymphoid tissue viral clearance and absence of lymph node immunopathology in natural hosts of SIV infection.
Type I IFNs Control Antigen Retention and Survival of CD8α+ Dendritic Cells after Uptake of Tumor Apoptotic Cells Leading to Cross-Priming
Authors: Lorenzi Silvia , Mattei Fabrizio , Sistigu Antonella , Bracci Laura , Spadaro Francesca , Sanchez Massimo , Spada Massimo , Belardelli Filippo , Gabriele Lucia , Schiavoni Giovanna
Published: March 2011

Cross-presentation is a crucial mechanism for generating CD8 T cell responses against exogenous Ags, such as dead cell-derived Ag, and is mainly fulfilled by CD8α+ dendritic cells (DC). Apoptotic cell death occurring in steady-state conditions is largely tolerogenic, thus hampering the onset of effector CD8 T cell responses. Type I IFNs (IFN-I) have been shown to promote cross-priming of CD8 T cells against soluble or viral Ags, partly through stimulation of DC. By using UV-irradiated OVA-expressing mouse EG7 thymoma cells, we show that IFN-I promote intracellular Ag persistence in CD8α+ DC that have engulfed apoptotic EG7 cells, regulating intracellular pH, thus enhancing cross-presentation of apoptotic EG7-derived OVA Ag by CD8α+ DC. Notably, IFN-I also sustain the survival of Ag-bearing CD8α+ DC by selective upmodulation of antiapoptotic genes and stimulate the activation of cross-presenting DC. The ensemble of these effects results in the induction of CD8 T cell effector response in vitro and in vivo. Overall, our data indicate that IFN-I cross-prime CD8 T cells against apoptotic cell-derived Ag both by licensing DC and by enhancing cross-presentation.
B Cell-Specific Expression of B7-2 Is Required for Follicular Th Cell Function in Response to Vaccinia Virus
Authors: Salek-Ardakani Samira , Choi Youn Soo , Rafii-El-Idrissi Benhnia Mohammed , Flynn Rachel , Arens Ramon , Shoenberger Stephen , Crotty Shane , Croft Michael , Salek-Ardakani Shahram
Published: March 2011

Follicular Th (TFH) cells are specialized in provision of help to B cells that is essential for promoting protective Ab responses. CD28/B7 (B7-1 and B7-2) interactions are required for germinal center (GC) formation, but it is not clear if they simply support activation of naive CD4 T cells during initiation of responses by dendritic cells or if they directly control TFH cells and/or directly influence follicular B cell differentiation. Using a model of vaccinia virus infection, we show that B7-2 but not B7-1 deficiency profoundly impaired TFH cell development but did not affect CD4 T cell priming and Th1 differentiation. Consistent with this, B7-2 but not B7-1 was required for acquisition of GC B cell phenotype, plasma cell generation, and virus-specific neutralizing Ab responses. Mixed adoptive transfer experiments indicated that bidirectional interactions between CD28 expressed on activated T cells and B7-2 expressed on follicular B cells were essential for maintenance of the TFH phenotype and GC B cell development. Our data provide new insight into the source and nature of molecules required for TFH cells to direct GC B cell responses.
Molecular Characteristics of Pancreatic Ductal Adenocarcinoma
Authors: Ottenhof Niki A. , de Wilde Roeland F. , Maitra Anirban , Hruban Ralph H. , Offerhaus G. Johan A.
Published: March 2011

Pancreatic cancer is an almost universally lethal disease and despite extensive research over the last decades, this has not changed significantly. Nevertheless, much progress has been made in understanding the pathogenesis of pancreatic ductal adenocarcinoma (PDAC) suggesting that different therapeutic strategies based on these new insights are forthcoming. Increasing focus exists on designing the so-called targeted treatment strategies in which the genetic characteristics of a tumor guide therapy. In the past, the focus of research was on identifying the most frequently affected genes in PDAC, but with the complete sequencing of the pancreatic cancer genome the focus has shifted to defining the biological function that the altered genes play. In this paper we aimed to put the genetic alterations present in pancreatic cancer in the context of their role in signaling pathways. In addition, this paper provides an update of the recent advances made in the development of the targeted treatment approach in PDAC.
Do PPAR-Gamma Agonists Have a Future in Parkinson's Disease Therapy?
Authors: Carta Anna R. , Pisanu Augusta , Carboni Ezio
Published: March 2011

Thiazolidinediones (TZDs) are peroxisome proliferator-activated receptor (PPAR)-γagonists commonly used as insulin-sensitizing drugs for the treatment of type 2 diabetes. In the last decade, PPAR-γagonists have received increasing attention for their neuroprotective properties displayed in a variety of neurodegenerative diseases, including Parkinson's disease (PD), likely related to the anti-infammatory activity of these compounds. Recent studies indicate that neuroinflammation, specifically reactive microglia, plays important roles in PD pathogenesis. Moreover, after the discovery of infiltrating activated Limphocytes in the substantia nigra (SN) of PD patients, most recent research supports a role of immune-mediated mechanisms in the pathological process leading to chronic neuroinflammation and dopaminergic degeneration. PPAR-γare highly expressed in cells of both central and peripheral immune systems, playing a pivotal role in microglial activation as well as in monocytes and T cells differentiation, in which they act as key regulators of immune responses. Here, we review preclinical evidences of PPAR-γ-induced neuroprotection in experimental PD models and highlight relative anti-inflammatory mechanisms involving either central or peripheral immunomodulatory activity. Specific targeting of immune functions contributing to neuroinflammation either directly (central) or indirectly (peripheral) may represent a novel therapeutic approach for disease modifying therapies in PD.
An ethics model to develop an ethical organisation
Authors: Lloyd Hendrik R. , Mey Michelle R.
Published: March 2011

Orientation: As background to the study it can be stated that the ethical conduct of employees in an organisation is of paramount importance to the successful operations of an organisation, both real and perceived. In recent times the ethical conduct of employees has received extensive publicity and, as such, has emphasised the impact of organisational ethics on the global competitiveness of organisations.Research purpose: The main aim of the paper is to analyse the impact of business ethics in the Eastern Cape Motor Industry Cluster (ECMIC) and the different perceptions regarding such ethics. This is based on the main research question, namely, whether a business ethics model should be developed to assist in creating an ethical organisation.Motivation of the study: The motivation for this study is based on the question of whether there is a dedicated drive within the motor industry to establish an ethical organisation and, if such is the case, what benefits would accrue to the organisations in ECMIC.Research design, approach and method: An empirical study was conducted within ECMIC to test the proposed ethics intervention model. A questionnaire, as the main measuring instrument, was developed and 150 questionnaires were distributed. Statistical hypothesis testing was used, with a significance level set at 5%. The aim of the hypothesis testing was to test whether the percentage responses in certain categories were significantly higher than a pre-determined test-value.Main findings: The research results substantiate the fact that the majority of the surveyed organisations do not implement specific ethics interventions. Nevertheless, the majority of respondents acknowledge the importance of ethical behaviour in the organisation, especially with regard to their financial positions.Practical/managerial implications: From this study it became clear that the implementation of a code of ethics would create a platform for ethical behaviour in organisations. It is also concluded from this study that all organisations must strive towards creating an ethical organisation which would have long-term rewards for the organisation, especially from a financial perspective.Contribution/value-add: This study highlights the fact that although ethics and ethical behaviour in organisations are emphasised and receive wide-spread media coverage, not enough action is linked to this task at hand. The results of this research clearly indicate where the shortcomings are, in the process of establishing ethical organisations and who should be seen as the custodians of such activities.
Krill (Meganyctiphanes norvegica) swim faster at night
Authors: Klevjer Thor A. , Kaartvedt Stein
Published: March 2011

Krill are key members in marine food webs, and measurement of swimming speed is vital to assess their bioenergetic budgets, feeding, and encounters with predators. We document a consistent and marked diel signal in swimming speed of krill in their natural habitat that is not related to diel vertical migration. The results were obtained using a bottom‐mounted, upward‐looking echo sounder at 150‐m depth in the Oslofjord, Norway, spanning 5 months from late autumn to spring at a temporal resolution of ~1–2 records s−1. Swimming speed was assessed using acoustic target tracking of individual krill. At the start of the registration period, both daytime and nocturnal average swimming speeds of Meganyctiphanes norvegica were ~ 3.5 cm s−1 (~ 1 body lengths ([bl] s−1) in waters with oxygen concentrations of ~ 15–20% O2 saturation. Following intrusion of more oxygenated water, nocturnal average swimming speeds increased to ~ 10 cm s−1 (~ 3 bl s−1), i.e., more than double that of daytime swimming speeds in the same period. We hypothesize that krill activity during the first period was limited by oxygen, and the enhanced swimming at night subsequent to the water renewal is due to increased feeding activity under lessened danger of predation in darkness.
Observed variability of Lake Superior pCO2
Authors: Atilla Nazan , McKinley Galen A. , Bennington Val , Baehr Matthew , Urban Noel , DeGrandpre Michael , Desai Ankur R. , Wu Chin
Published: March 2011

We present and compare direct and indirect pCO2 observations taken in Lake Superior in the last decade and use them to understand temporal and spatial variability in lake carbon cycle processes. In situ observations from 2001 and biannual survey data for 1996–2006 indicate that Lake Superior was, on average, supersaturated (annual mean = 46.7 ± 17.3 Pa [461 ± 171 μatm]) with respect to atmospheric pCO2 (mean = 38.3 ± 0.6 Pa) in April and close to equilibrium (mean = 37.5 ± 6.7 Pa) with respect to atmospheric pCO2 (mean = 36.4 ± 0.7 Pa) in August. Both data sets indicate that temporal variability in surface lake pCO2 from weekly to interannual timescales was predominantly controlled by changing dissolved inorganic carbon and associated changes in pH. An unstratified water column appears to have limited pCO2 fluctuations in spring. Through summer and into early fall, pCO2 variability on a daily timescale at 12 m increased with time to a maximum amplitude of 19 Pa, likely as a result of internal waves on the thermocline. Year‐to‐year changes in mean surface lake pCO2 and temperature were of the same sign and approximate magnitude at all observed points, consistent with the lake's small size relative to the synoptic‐scale meteorological systems that force it. Variability in pCO2 was not correlated with major climate indices. While these data provide a first large‐scale overview of Lake Superior's pCO2 and its temporal variability, their time–space resolution and accuracy are not sufficient to further refine previously imbalanced lake‐wide carbon budgets.
Physical and biological processes underlying the sudden surface appearance of a red tide in the nearshore
Authors: Omand Melissa M. , Leichter James J. , Franks Peter J. S. , Guza R. T. , Lucas Andrew J. , Feddersen Falk
Published: March 2011

The sudden appearance at the surface of an alongshore‐parallel band of red tide near Huntington Beach, California, is described in high spatial and temporal resolution using novel instrumentation including a global positioning system–tracked jet‐ski. The scale of the surface chlorophyll a (Chl a) band was small (~ 200 m cross‐shore) and ephemeral (3 h) compared with the subsurface extent of the red tide (~ 2 km, > 7 d). The red tide was dominated by the regionally common dinoflagellate Lingulodinium polyedrum (F. Stein) and had developed as a subsurface Chl a layer during the 7 d prior to the surface appearance. A few hours before the surface appearance, a subsurface patch of elevated Chl a (Chl a > 30 μg L−1) was observed in 13‐m total depth in the trough of a shoreward‐propagating internal wave, consistent with dinoflagellate vertical swimming interacting with the internal wave‐driven convergence. Internal wave‐breaking–induced vertical mixing in ~ 8‐m water depth vertically spread the Chl a patch to the surface, creating the alongshore surface band ~ 500 m from shore. Both the subsurface Chl a patch and the surface Chl a band were prevented from entering the surf‐zone by a density barrier of warm water adjacent to the beach. These high‐resolution observations emphasize the role of nearshore physical dynamics in controlling the duration and intensity of red tide exposure to coastal habitats.
Inter‐annual changes in prey fields trigger different foraging tactics in a large marine predator
Authors: Garthe Stefan , Montevecchi William A. , Davoren Gail K.
Published: March 2011

We report on inter‐annual comparisons of the foraging behavior of Global Positioning System–equipped chick‐rearing northern gannets (Morus bassanus) in the western Atlantic during years with contrasting oceanographic and prey conditions. We hypothesized that the predators would modify their foraging tactics when small fishes (capelin [Mallotus villosus]) and large pelagic fishes (mackerel, saury) varied in inter‐annual abundances. We predicted differences in (1) diving behavior, (2) spatial, and (3) temporal patterning of foraging behavior. Predictions 1 and 2 were supported, prediction 3 rejected. Dives were significantly deeper (4.3 ± 0.4 vs. 2.7 ± 0.3 m) and longer (10.1 ± 1.0 vs. 5.0 ± 0.2 s), and more U‐shaped dives (dives where birds stayed at more or less one depth) were performed (52% ± 7% vs. 7% ± 2%) in the year with higher abundance of forage fishes. Flight patterns exhibited remarkable spatial and geographic differences: gannets flew significantly (17%) more and foraging ranges were about twice as long when they pursued large pelagic fishes (mean = 122 ± 81 km vs. 62 ± 12 km). The 95% kernel feeding range was 34 times larger when large pelagic fishes were available. Yet foraging trip durations were not different between years. Inter‐annual variation in foraging tactics by the same species at the same colony in successive years was strongly related to prey availability, showing that spatial foraging parameters can be determined largely by ocean and prey conditions.
Responses to iron limitation in two colonies of Stylophora pistillata exposed to high temperature: Implications for coral bleaching
Authors: Shick J. Malcolm , Iglic Katrina , Wells Mark L. , Trick Charles G. , Doyle Jason , Dunlap Walter C.
Published: March 2011

Exposing the coral Stylophora pistillata to seawater depleted in available iron by complexation with the strong chelator desferrioxamine B reduces the photosynthetic efficiency and alters the pigment composition in its symbiotic algae at high temperatures. Similar effects of iron limitation are known for free‐living algae, but this is the first demonstration of low‐iron stress in a dinoflagellate living endosymbiotically. Maintaining corals at elevated temperature (30°C and 31°C) under diminished iron availability leads to reduced maximum quantum yields (Fv:Fm) of photosystem II (PSII), specifically on brightly illuminated surfaces of the coral. This reduction in maximum quantum yield is due in part to increased photoprotection, indicated by an increase in the photoprotective xanthophyll diatoxanthin, which promotes nonphotochemical quenching of excess light energy to restrict oxidative damage under conditions that impair photosynthetic electron transfer. However, photophysiological changes associated with the lowered maximum quantum yield did not prevent photodamage to PSII under the combined effects of elevated temperature and low iron availability, as shown by the decrease in maximum (Fm) that was not accompanied by significant change in the minimum (Fo) fluorescence yield. All of the foregoing is consistent with the potential of iron limitation to contribute to the underlying conditions by which thermal stress evokes the physiological response by corals that culminates in the symbiotic dysfunction of natural bleaching.
Effects of changing pCO2 and phosphate availability on domoic acid production and physiology of the marine harmful bloom diatom Pseudo‐nitzschia multiseries
Authors: Sun Jun , Hutchins David A. , Feng Yuanyuan , Seubert Erica L. , Caron David A. , Fu Fei-Xue
Published: March 2011

Some members of the diatom genus Pseudo‐nitzschia produce the toxin domoic acid (DA), which through trophic transfer causes mass mortalities of wildlife, shellfish harvesting closures, and risks to human health. Nutrient and micronutrient limitation have been shown to regulate DA production. This study tested the hypothesis that changing partial pressure of CO2 (pCO2) can interact with nutrient limitation to help determine cellular DA levels, an environmentally relevant issue in light of current increases in atmospheric pCO2. Cultures of the toxic species Pseudo‐nitzschia multiseries were incubated using semicontinuous methods under a matrix of three pCO2 conditions: ∼ 22 Pa (220 ppm), ∼ 41 Pa (400 ppm), and ~ 74 Pa (730 ppm), and two phosphate concentrations: 20 μmol L−1, P‐replete; and 0.5 μmol L−1, P‐limited. DA production was regulated by both pCO2 and phosphate availability. DA concentrations were 30–50 times higher in P‐limited cultures compared to P‐replete ones, at the same pCO2 levels. Increasing CO2 levels stimulated DA production under both nutrient conditions, but especially in P‐limited cultures, where DA levels increased approximately four times over the pCO2 range examined. Growth rates, primary productivity, photosynthesis vs. irradiance parameters, and cellular elemental ratios also responded interactively to the availability of both CO2 and phosphate. Our results raise the possibility that growth rates and toxicity of the diatom Pseudo‐nitzschia multiseries could increase substantially in the future high‐CO2 ocean, suggesting a potentially escalating negative effect of this harmful algal bloom species on the future marine environment.
Spatial variation in basal resources supporting benthic food webs revealed for the inner continental shelf
Authors: Grippo Mark A. , Fleeger John W. , Dubois Stanislas F. , Condrey Richard
Published: March 2011

We used stable isotopes to examine the relative importance of phytodetritus and microphytobenthos (MPB) in supporting benthic food webs on the Louisiana continental shelf. Primary producers and macroinfauna were collected from Ship Shoal (SS), a submerged, sandy, barrier island where sediment‐associated algae are primarily MPB and from silty, off‐shoal areas where sediment‐associated algae are primarily phytodetritus or a mixture of the two resources. Macroinfauna, as individual taxa and trophic guilds, were significantly more enriched in 13C on SS indicating greater dependence on MPB, which is enriched in 13C compared to phytoplankton. Using δ13C in a two‐source mixing model, the estimated MPB dietary contribution for SS macroinfauna averaged across trophic guilds, ranged from 53.4% to 83.0%, depending on the mixing‐model end‐members used, and 5 of 14 taxa had lower 95% confidence intervals (CI) > 20%, indicating that MPB was a primary resource for most SS macroinfauna. Off‐shoal, the dietary contribution of MPB ranged from14.5% to 47.7% and most taxa had a lower CI near 0%. Settled phytoplankton are the primary microalgal food source in muddy sediments, but the importance of MPB increases in more sandy sediments where MPB are the predominant microalgal resource. Sandy shoals play a unique food‐web role in deltaic shelf systems and support benthic food webs on the continental shelf.
Spatial variability of emergence, splash, surge, and submergence in wave‐exposed rocky‐shore ecosystems
Authors: Mislan K. A. S. , Blanchette Carol A. , Broitman Bernardo R. , Washburn Libe
Published: March 2011

To distinguish the intertidal states of emergence, splash, surge, and submergence and record their relative durations, we deployed a water‐level logger paired with a temperature logger in the mid‐intertidal zone at each of 10 wave‐exposed sites during the summer in the northeast Pacific. Relative durations of intertidal states were different among the different sites, even at sites close together. Splash was temporally variable, being recorded by the loggers on 50% or fewer days at most sites. Daily surge durations tended to be longer at sites in northern and central California compared with sites in Oregon and Washington. Return times to surge and submergence showed the opposite trend with longer return times in Oregon and Washington compared with California. We estimated the effect of interannual changes in tides on intertidal states by applying the logger data to tidal predictions and comparing duration and return time over the 18.6‐yr tidal epoch. Over long time periods, compared with the logger deployments, daily durations of surge increased, return times to the surge state became more uniform, and return times to submergence lengthened.
Radiocarbon and stable carbon isotopic insights into provenance and cycling of carbon in Lake Superior
Authors: Zigah Prosper K. , Minor Elizabeth C. , Werne Josef P. , McCallister S. Leigh
Published: March 2011

This study applies radiocarbon and stable carbon isotopic distributions to investigate carbon sources and cycling within Lake Superior. We report the radiocarbon (Δ14C) and stable carbon isotope (δ13C) values and the carbon concentrations within dissolved organic carbon (DOC), particulate organic carbon (POC), and dissolved inorganic carbon (DIC) in the lake's western basin water column. Samples were taken during spring mixing and late‐summer thermal stratification over a 2‐yr period (2007–2009). Distinct processes operating in the surface (photosynthesis) and deep waters (sediment resuspension and pore‐water intrusion) control the relative contribution of modern and ancient DOC and POC in the water column. The terrigenous carbon input to the open lake POC varied from 13% ± 4% during late summer stratification to 9% ± 3% during spring mixing, with most of the terrestrial carbon being 14C‐enriched (modern). The DIC reservoir cycles rapidly, with a bulk Δ14CDIC value that records atmospheric radiocarbon levels from 3 yr prior to sampling. The DOC pool recycles on a longer time scale than does the DIC, with a DOC residence time of ≤ 60 yr. The suspended POC was in most cases older than co‐occurring DOC, most likely as a result of resuspension of lake sediments.
Patterns of macroinvertebrate production, trophic structure, and energy flow along a tallgrass prairie stream continuum
Authors: Whiting Daniel P. , Whiles Matt R. , Stone Mandy L.
Published: March 2011

We estimated benthic organic matter standing stocks, macroinvertebrate production, food‐web structure, and stream metabolism along a longitudinal continuum of Kings Creek at Konza Prairie Biological Station in Kansas. Benthic macroinvertebrates were sampled for 1 yr from three stream reaches (grass, shrub, gallery forest). Total habitat‐weighted production ranged from 9.1 g to 31.9 g ash‐free dry weight m−2 yr−1 with the grass headwaters accounting for the highest production. Functional group contributions to production were similar along the continuum, with collector–gatherers (40–56% of total) and predators (23–38%) dominating all reaches. Detrital pathways appeared to account for most energy flow in all reaches, and all reaches were net heterotrophic on all dates when metabolism was measured, except for the grass headwater reach in spring. Predators were well‐represented and consumed 65–107% of total macroinvertebrate production, whereas scrapers (11–15%), shredders (2–4%), and filterers (< 1%) consumed relatively small percentages of available resources. Dominance of predators suggested top‐down controls are important in this system. However, changes in energy flow through other groups reflected longitudinal variation in resource availability. This prairie stream continuum conforms to some predictions of conceptual stream continua models, but biotic interactions, which are often not considered, may override some predicted responses to changes in the physical template.
Phytoplankton allelochemical interactions change microbial food web dynamics
Authors: Weissbach Astrid , Rudström Maria , Olofsson Martin , Béchemin Christian , Icely John , Newton Alice , Tillmann Urban , Legrand Catherine
Published: March 2011

This study investigates the effect of filtrates from an allelopathic dinoflagellate, Alexandrium tamarense, on four microbial food webs that have been manipulated experimentally from natural seawater by modifying the availability of resources in the form of dissolved organic carbon with additions of peptone, and by altering the grazing pressure with size fractionation. Bacterial production was generally not affected by allelochemicals, but bacteria showed higher net growth in all food webs when allelochemicals were added, whereas heterotrophic nanoflagellates > 7 μm and ciliates were constrained in all food webs. Allelochemicals had the largest negative effects on microbial communities with low grazing pressure. In food webs with high grazing pressure and additional resources, phytoplankton and small nanoflagellates were positively affected by the addition of allelochemicals, suggesting that those were interfering with trophic interactions in the microbial communities. By the lysis of organisms sensitive towards allelochemicals, resources are made available and grazing pressure on certain microorganisms is reduced. However, the intensity of these interactions is modulated by both the availability of resources and the biomass of grazers in the initial food web.
Differential cooling drives large‐scale convective circulation in Lake Tanganyika
Authors: Verburg Piet , Antenucci Jason P. , Hecky Robert E.
Published: March 2011

Field data, scaling analysis, and three‐dimensional numerical experiments demonstrate that the dominant large‐scale circulation pattern during the southeast trade winds in Lake Tanganyika (East Africa) is a downwind flow in the metalimnion, with a returning southward upwind flow in the upper region of the epilimnion. This is in the opposite direction to all prior literature available on the lake, which has assumed that the southeast trade winds must drive a northward surface flow due to momentum induced by the wind. The gradient in wind speed and humidity along the length of the lake and the resulting gradient in heat exchange with the atmosphere result in warm water accumulating at the northern end of the lake. The north basin of Lake Tanganyika, thus, acts as a heat sink while the south basin is a net source of heat to the atmosphere. The resulting variation in buoyancy flux is strong enough to drive a convective flow in the upper layer in the opposite direction to the wind. A large‐scale convective circulation results in an annual exchange of 6.2 × 1012 m3 of water and an annual net transport of heat (averaging 0.2 terawatt) from the northern to the southern region of the lake. Currents in the upper 100‐m layer, with a mean flow of 0.2 Sverdrup and flow speed of 0.08 m s−1, can be described by the superposition of a parallel convective flow with the internal seiche motion.
Differential effects of ocean acidification on growth and photosynthesis among phylotypes of Symbiodinium (Dinophyceae)
Authors: Brading Patrick , Warner Mark E. , Davey Phillip , Smith David J. , Achterberg Eric P. , Suggett David J.
Published: March 2011

We investigated the effect of elevated partial pressure of CO2 (pCO2) on the photosynthesis and growth of four phylotypes (ITS2 types A1, A13, A2, and B1) from the genus Symbiodinium, a diverse dinoflagellate group that is important, both free‐living and in symbiosis, for the viability of cnidarians and is thus a potentially important model dinoflagellate group. The response of Symbiodinium to an elevated pCO2 was phylotype‐specific. Phylotypes A1 and B1 were largely unaffected by a doubling in pCO2; in contrast, the growth rate of A13 and the photosynthetic capacity of A2 both increased by ~ 60%. In no case was there an effect of ocean acidification (OA) upon respiration (dark‐ or light‐dependent) for any of the phylotypes examined. Our observations suggest that OA might preferentially select among free‐living populations of Symbiodinium, with implications for future symbioses that rely on algal acquisition from the environment (i.e., horizontal transmission). Furthermore, the carbon environment within the host could differentially affect the physiology of different Symbiodinium phylotypes. The range of responses we observed also highlights that the choice of species is an important consideration in OA research and that further investigation across phylogenetic diversity, for both the direction of effect and the underlying mechanism(s) involved, is warranted.
Dynamics of cyclone evacuation behavior among southwestern coastal residents in Bangladesh: A case study of cyclone Sidr
Authors: Uddin, MSS Jalal
Published: March 2011

Cyclone Sidr struck the southwestern coast of Bangladesh on November 15, 2007, resulting in 3,406 deaths and damaged properties of about US $1.7 billion. Despite the government’s sincere efforts, thousands of coastal residents did not comply with the evacuation orders. This article attempts to identify the sociodemographic factors affecting evacuation choices during the cyclone. Following systematic random sampling technique, a total of 384 heads of household was surveyed in the southwestern coast of Bangladesh. The bivariate results indicate that single women, older residents, people with small possessions, and people with higher level of education and occupation are more likely to evacuate. Moreover, level of education, household’s status of food security, trust in cyclone warning, and perceived severity of cyclone are also found as significant predictors of evacuation choice. Trust in cyclone warning has been found as the single best predictor. This article recommends improvement in the cyclone warning system, establishment of more public cyclone shelters, and implementation of different campaigns in coastal areas to increase the use of public shelters.
A cognitive task analysis of a visual analytic workflow: Exploring molecular interaction networks in systems biology
Authors: Mirel Barbara , Eichinger Felix , Keller Benjamin J , Kretzler Matthias
Published: March 2011

Background: Bioinformatics visualization tools are often not robust enough to support biomedical specialists’ complex exploratory analyses. Tools need to accommodate the workflows that scientists actually perform for specific translational research questions. To understand and model one of these workflows, we conducted a case-based, cognitive task analysis of a biomedical specialist’s exploratory workflow for the question: What functional interactions among gene products of high throughput expression data suggest previously unknown mechanisms of a disease?

Results: From our cognitive task analysis four complementary representations of the targeted workflow were developed. They include: usage scenarios, flow diagrams, a cognitive task taxonomy, and a mapping between cognitive tasks and user-centered visualization requirements. The representations capture the flows of cognitive tasks that led a biomedical specialist to inferences critical to hypothesizing. We created representations at levels of detail that could strategically guide visualization development, and we confirmed this by making a trial prototype based on user requirements for a small portion of the workflow.

Conclusions: Our results imply that visualizations should make available to scientific users “bundles of features” consonant with the compositional cognitive tasks purposefully enacted at specific points in the workflow. We also highlight certain aspects of visualizations that: (a) need more built-in flexibility; (b) are critical for negotiating meaning; and (c) are necessary for essential metacognitive support.