bluuebunny/crossref_metadata_2025 huggingface dataset:
i AK692: A genome-scale metabolic model of Spirulina platensis C1
Authors: Klanchui Amornpan , Khannapho Chiraphan , Phodee Atchara , Cheevadhanarak Supapon , Meechai Asawin
Published: June 2012

Background

Spirulina (Arthrospira) platensis is a well-known filamentous cyanobacterium used in the production of many industrial products, including high value compounds, healthy food supplements, animal feeds, pharmaceuticals and cosmetics, for example. It has been increasingly studied around the world for scientific purposes, especially for its genome, biology, physiology, and also for the analysis of its small-scale metabolic network. However, the overall description of the metabolic and biotechnological capabilities of S. platensis requires the development of a whole cellular metabolism model. Recently, the S. platensis C1 (Arthrospira sp. PCC9438) genome sequence has become available, allowing systems-level studies of this commercial cyanobacterium.

Results

In this work, we present the genome-scale metabolic network analysis of S. platensis C1, i AK692, its topological properties, and its metabolic capabilities and functions. The network was reconstructed from the S. platensis C1 annotated genomic sequence using Pathway Tools software to generate a preliminary network. Then, manual curation was performed based on a collective knowledge base and a combination of genomic, biochemical, and physiological information. The genome-scale metabolic model consists of 692 genes, 837 metabolites, and 875 reactions. We validated i AK692 by conducting fermentation experiments and simulating the model under autotrophic, heterotrophic, and mixotrophic growth conditions using COBRA toolbox. The model predictions under these growth conditions were consistent with the experimental results. The i AK692 model was further used to predict the unique active reactions and essential genes for each growth condition. Additionally, the metabolic states of i AK692 during autotrophic and mixotrophic growths were described by phenotypic phase plane (PhPP) analysis.

Conclusions

This study proposes the first genome-scale model of S. platensis C1, i AK692, which is a predictive metabolic platform for a global understanding of physiological behaviors and metabolic engineering. This platform could accelerate the integrative analysis of various “-omics” data, leading to strain improvement towards a diverse range of desired industrial products from Spirulina.
A quantitative model of the initiation of DNA replication in Saccharomyces cerevisiae predicts the effects of system perturbations
Authors: Gidvani Rohan D , Sudmant Peter , Li Grace , DaSilva Lance F , McConkey Brendan J , Duncker Bernard P , Ingalls Brian P
Published: June 2012

Background

Eukaryotic cell proliferation involves DNA replication, a tightly regulated process mediated by a multitude of protein factors. In budding yeast, the initiation of replication is facilitated by the heterohexameric origin recognition complex (ORC). ORC binds to specific origins of replication and then serves as a scaffold for the recruitment of other factors such as Cdt1, Cdc6, the Mcm2-7 complex, Cdc45 and the Dbf4-Cdc7 kinase complex. While many of the mechanisms controlling these associations are well documented, mathematical models are needed to explore the network’s dynamic behaviour. We have developed an ordinary differential equation-based model of the protein-protein interaction network describing replication initiation.

Results

The model was validated against quantified levels of protein factors over a range of cell cycle timepoints. Using chromatin extracts from synchronized Saccharomyces cerevisiae cell cultures, we were able to monitor the in vivo fluctuations of several of the aforementioned proteins, with additional data obtained from the literature. The model behaviour conforms to perturbation trials previously reported in the literature, and accurately predicts the results of our own knockdown experiments. Furthermore, we successfully incorporated our replication initiation model into an established model of the entire yeast cell cycle, thus providing a comprehensive description of these processes.

Conclusions

This study establishes a robust model of the processes driving DNA replication initiation. The model was validated against observed cell concentrations of the driving factors, and characterizes the interactions between factors implicated in eukaryotic DNA replication. Finally, this model can serve as a guide in efforts to generate a comprehensive model of the mammalian cell cycle in order to explore cancer-related phenotypes.
Bioaccumulative and conchological assessment of heavy metal transfer in a soil-plant-snail food chain
Authors: Nica Dragos V , Bura Marian , Gergen Iosif , Harmanescu Monica , Bordean Despina-Maria
Published: June 2012

Background

Copper (Cu), zinc (Zn), cadmium (Cd), and lead (Pb) can pose serious threats to environmental health because they tend to bioaccumulate in terrestrial ecosystems. We investigated under field conditions the transfer of these heavy metals in a soil-plant-snail food chain in Banat area, Romania. The main goal of this paper was to assess the Roman snail (Helix pomatia) usefulness in environmental monitoring as bioindicator of heavy metal accumulation. Eight sampling sites, selected by different history of heavy metal (HM) exposure, were chosen to be sampled for soil, nettle leaves, and newly matured snails. This study also aimed to identify the putative effects of HM accumulation in the environment on phenotypic variability in selected shell features, which included shell height (SH), relative shell height (RSH), and whorl number (WN).

Results

Significantly higher amounts of HMs were accumulated in snail hepatopancreas and not in foot. Cu, Zn, and Cd have biomagnified in the snail body, particularly in the hepatopancreas. In contrast, Pb decreased when going up into the food chain. Zn, Cd, and Pb correlated highly with each other at all levels of the investigated food chain. Zn and Pb exhibited an effective soil–plant transfer, whereas in the snail body only foot Cu concentration was correlated with that in soil. There were significant differences among sampling sites for WN, SH, and RSH when compared with reference snails. WN was strongly correlated with Cd and Pb concentrations in nettle leaves but not with Cu and Zn. SH was independent of HM concentrations in soil, snail hepatopancreas, and foot. However, SH correlated negatively with nettle leaves concentrations for each HM except Cu. In contrast, RSH correlated significantly only with Pb concentration in hepatopancreas.

Conclusions

The snail hepatopancreas accumulates high amounts of HMs, and therefore, this organ can function as a reliable biomarker for tracking HM bioavailability in soil. Long-term exposure to HMs via contaminated food might influence the variability of shell traits in snail populations. Therefore, our results highlight the Roman snail (Helix pomatia) potential to be used in environmental monitoring studies as bioindicator of HM pollution.
Prevalence of Pulmonary tuberculosis and immunological profile of HIV co-infected patients in Northwest Ethiopia
Authors: Wondimeneh Yitayih , Muluye Dagnachew , Belyhun Yeshambel
Published: June 2012

Background

In sub-Saharan Africa, as high as 2/3 of tuberculosis patients are HIV/AIDS co-infected and tuberculosis is the most common cause of death among HIV/AIDS patients worldwide. Tuberculosis and HIV co-infections are associated with special diagnostic and therapeutic challenges and constitute an immense burden on healthcare systems of heavily infected countries like Ethiopia. The aim of the study was to determine the prevalence of pulmonary tuberculosis and their immunologic profiles among HIV positive patients.

Methods

A cross sectional study was conducted among adult HIV-positive patients attending HIV/AIDS clinic of Gondar University Hospital. Clinical and laboratory investigations including chest x-ray and acid fast staining were used to identify tuberculosis cases. Blood samples were collected to determine CD4+ lymphocyte count. A structured questionnaire was used to collect socio-demographic characteristics of study subjects. The data was entered and analyzed using SPSS version 16 software.

Results

A total of 400 HIV positive study participants were enrolled. Thirty (7.5%, 95%CI: 5.2-10.6%) of the study participants were found to have pulmonary tuberculosis. In multivariate analysis, only CD4+ lymphocyte count (AOR = 2.9; 95% CI: 1.002-8.368) was found to be independently associated with tuberculosis-HIV co-infection. Individuals who had advanced WHO clinical stage were also statistically significant for co-infection. The mean CD4+ lymphocyte count of HIV mono-infected participants were 296 ± 192 Cells/mm3 and tuberculosis-HIV co-infected patients had mean CD4+ lymphocyte count of 199 ± 149 Cells/mm3 with p value of 0.007.

Conclusions

We found high prevalence of tuberculosis-HIV co-infection. Lower CD4+ lymphocyte count was found to be the only predicting factor for co-infection. Early detection of co-infection is very necessary to prolong their ART initiation time and by then strengthening their immune status.
Tongue nodules in canine leishmaniosis — a case report
Authors: Viegas Carlos , Requicha João , Albuquerque Carlos , Sargo Teresa , Machado João , Dias Isabel , Pires Maria A , Campino Lenea , Cardoso Luís
Published: June 2012

Background

Canine leishmaniosis (CanL) caused by Leishmania infantum is an endemic zoonosis in southern European countries. Infected dogs can present rare or atypical forms of the disease and diagnosis can be challenging. The present report describes a case of tongue nodules in a 3-year-old neutered female Labrador Retriever dog with leishmaniosis.

Findings

A fine needle aspiration of the lingual nodules revealed amastigote forms of Leishmania inside macrophages. Differential diagnosis ruled out neoplasia, calcinosis circumscripta, solar glossitis, vasculitis, amyloidosis, eosinophilic granulomas, chemical and electrical burns, uremic glossitis and autoimmune diseases. Combined therapy with antimoniate meglumine and allopurinol for 30 days resulted in the normalization of hematological and biochemical parameters. Two months after diagnosis and the beginning of treatment, a mild inflammatory infiltrate was observed by histopathology, but an anti-Leishmania immunofluorescence antibody test (IFAT) was negative as well as a PCR on both tongue lesions and a bone marrow aspirate. Seven months after diagnosis, the dog’s general condition appeared good, there were no tongue lesions and a new IFAT was negative. Fifteen months after diagnosis this clinically favourable outcome continued.

Conclusions

The dog could have suffered a relapsing episode of CanL, but a new systemic or local infection cannot be excluded. Regular clinical re-evaluation should be maintained, as a future relapse can potentially occur. In conclusion, CanL should be considered in the differential diagnosis of nodular glossitis in dogs.
Initial Emergency Department Diagnosis and Management of Adult Patients with Severe Sepsis and Septic Shock
Authors: Perman Sarah M , Goyal Munish , Gaieski David F
Published: June 2012

Severe sepsis is a medical emergency affecting up to 18 million individuals world wide, with an annual incidence of 750,000 in North America alone. Mortality ranges between 28-50% of those individuals stricken by severe sepsis. Sepsis is a time critical illness, requiring early identification and prompt intervention in order to improve outcomes. This observation has led to increased awareness and education in the field of Emergency Medicine; it has also led to the implementation of critical interventions early in the course of patient management, specifically Early-Goal Directed Therapy, and rapid administration of appropriate antimicrobials. This review begins with a brief summary of the pathophysiology of sepsis, and then addresses the fundamental clinical aspects of ED identification and resuscitation of the septic patient.
Spinal metastasis in head and neck cancer
Authors: Trilling Gregory M , Cho Hyongyu , Ugas Mohamed A , Saeed Samerah , Katunda Asia , Jerjes Waseem , Giannoudis Peter
Published: June 2012

Background

The incidence of head and neck cancer is relatively low in developed countries and highest in South East Asia. Notwithstanding advances in surgery and radiotherapy over the past several decades, the 5-year survival rate for head and neck cancer has stagnated and remains at 50–55%. This is due, in large part, to both regional and distant disease spread, including spinal metastasis. Spinal metastasis from head and neck cancer is rare, has a poor prognosis and can significantly impede end-stage quality of life; normally only palliative care is given.

This study aims to conduct a systematic review of the evidence available on management of spinal metastasis from head and neck cancer and to use such evidence to draw up guiding principles in the management of the distant spread.

Methods

Systematic review of the electronic literature was conducted regarding the management of spinal metastasis of head and neck malignancies.

Results

Due to the exceptional rarity of head and neck cancers metastasizing to the spine, there is a paucity of good randomized controlled trials into the management of spinal metastasis. This review produced only 12 case studies/reports and 2 small retrospective cohort studies that lacked appropriate controls.

Conclusion

Management should aim to improve end-stage quality of life and maintain neurological function. This review has found that radiotherapy +/− medical adjuvant is considered the principle treatment of spinal metastasis of head and neck cancers.

There is an absence of a definitive treatment protocol for head and neck cancer spinal metastasis. Our failure to find and cite high-quality scientific evidence only serves to stress the need for good quality research in this area.
Peptidomic profiles of post myocardial infarction rats affinity depleted plasma using matrix‐assisted laser desorption/ionization time of flight (MALDI‐ToF) mass spectrometry
Authors: Wang Bing Hui , Reisman Simone , Bailey Mark , Kompa Andrew , Ayhan Mustafa , Krum Henry , Rice Gregory
Published: June 2012

Background

Despite major advances in drug development, effective cardiovascular therapies and suitable cardiovascular biomarkers remain limited. The aim of this study was to leverage mass spectrometry (MS) based peptide profiling strategies to identify changes that occur in peptidomic profiles of rat plasma following coronary artery ligation generated myocardial infarction (MI).

Methods

One week after MI, rats were randomized to receive either an ACE inhibitor (ramipril, Ram‐1 mg/kg/day), or vehicle (Veh) for 12 weeks. Echocardiography and hemodynamic measurements were made before sacrifice and plasma collection. High abundance proteins were depleted with affinity capture before MS profiling. Differentially expressed peptide ions were identified using proprietary software (ClinProtTools).

Results

MI increased heart/body weight (18%), lung/body weight (56%), and left ventricular (LV) end diastolic pressure (LVEDP, 247%); and significantly reduced percentage fractional shortening (FS, 75%) and rate of pressure rise in the LV (dP/dtmax, 20%). Ram treatment significantly attenuated the changes in LVEDP (61%) and FS (27%). Analysis of MALDI‐ToF generated mass spectra demonstrated that peptide ions 1271, 1878, 1955, 2041 and 2254 m/z were consistently decreased by Ram treatment (p < 0.001) and thus may be associated with the agent's therapeutic effects. Among peptides that were significantly changed, synapsin‐2, adenomatous polyposis coli protein and transcription factor jun‐D were identified as significantly reduced by Ram treatment.

Conclusions

This approach allows us to screen for potential biomarkers in a window of the blood proteome that previously has been difficult to access. The data obtained from such an approach may potentially useful in prognosis, diagnosis, and monitoring of treatment response.
Combined fluticasone furoate/vilanterol reduces decline in lung function following inhaled allergen 23 h after dosing in adult asthma: a randomised, controlled trial
Authors: Oliver Amanda , Quinn Dean , Goldfrad Caroline , van Hecke Benjamin , Ayer Jonathan , Boyce Malcolm
Published: June 2012

Background

There is a need for preventative asthma maintenance therapy that provides lasting bronchoprotection against allergen provocation. Fluticasone furoate (FF) is a novel inhaled once‐daily corticosteroid, being investigated as monotherapy for asthma and in combination with vilanterol (VI), a novel inhaled once‐daily long‐acting beta‐agonist, for asthma and chronic obstructive pulmonary disease.

Methods

In a crossover study of 52 subjects with mild asthma, FF/VI 100/25mcg and FF 100 dosed once‐daily in the evening for 28 days were compared with placebo to evaluate their capacity to provide bronchoprotection against the early asthmatic response (EAR) stimulated by an inhaled allergen challenge. Bronchoprotection was assessed by change from post‐saline baseline in weighted mean (wm) forced expiratory volume in 1 s (FEV1) for the first 2 h post‐allergen challenge, which was on Day 29 (22–23 h post final dose on Day 28). The EAR was also assessed using maximum percent decrease from post‐saline baseline and minimum absolute FEV1; the incidence of adverse events was a secondary endpoint.

Results

FF/VI 100/25 and FF 100 both provided significant bronchoprotection against the EAR for all endpoints assessed. For wmFEV1 over the first 2 h post‐allergen challenge, a 162 mL (95% CI, 87 to 237 mL) difference was observed between placebo and FF 100, while a 145 mL (95% CI, 69 to 222 mL) difference was observed between placebo and FF/VI 100/25 treatment. No difference between active treatments was observed (−17 mL; 95% CI, –91 to 57 mL). Both treatments were well tolerated.

Conclusions

FF 100 alone and in combination with VI 25 provides significant bronchoprotection against the EAR in subjects with mild asthma. That this protection is provided at the trough of dosing, i.e. 23 h post last dose, supports the utility of FF 100 and FF/VI 100/25 as viable once‐daily therapies.

Trial registration

ClinicalTrials.gov identifier: NCT01128569, GSK Study number: HZA113090
Immunoglobulin genes and diversity: what we have learned from domestic animals
Authors: Sun Yi , Liu Zhancai , Ren Liming , Wei Zhiguo , Wang Ping , Li Ning , Zhao Yaofeng
Published: June 2012

This review focuses on the diversity of immunoglobulin (Ig) genes and Ig isotypes that are expressed in domestic animals. Four livestock species—cattle, sheep, pigs, and horses—express a full range of Ig heavy chains (IgHs), including μ, δ, γ, ϵ, and α. Two poultry species (chickens and ducks) express three IgH isotypes, μ, υ, and α, but not δ. The κ and λ light chains are both utilized in the four livestock species, but only the λ chain is expressed in poultry. V(D)J recombination, somatic hypermutation (SHM), and gene conversion (GC) are three distinct mechanisms by which immunoglobulin variable region diversity is generated. Different domestic animals may use distinct means to diversify rearranged variable regions of Ig genes.
Systems modeling and simulation applications for critical care medicine
Authors: Dong Yue , Chbat Nicolas W , Gupta Ashish , Hadzikadic Mirsad , Gajic Ognjen
Published: June 2012

Critical care delivery is a complex, expensive, error prone, medical specialty and remains the focal point of major improvement efforts in healthcare delivery. Various modeling and simulation techniques offer unique opportunities to better understand the interactions between clinical physiology and care delivery. The novel insights gained from the systems perspective can then be used to develop and test new treatment strategies and make critical care delivery more efficient and effective. However, modeling and simulation applications in critical care remain underutilized. This article provides an overview of major computer-based simulation techniques as applied to critical care medicine. We provide three application examples of different simulation techniques, including a) pathophysiological model of acute lung injury, b) process modeling of critical care delivery, and c) an agent-based model to study interaction between pathophysiology and healthcare delivery. Finally, we identify certain challenges to, and opportunities for, future research in the area.
High Incidence of Vertebral Fractures in Children With Acute Lymphoblastic Leukemia 12 Months After the Initiation of Therapy
Authors: Alos Nathalie , Grant Ronald M. , Ramsay Timothy , Halton Jacqueline , Cummings Elizabeth A. , Miettunen Paivi M. , Abish Sharon , Atkinson Stephanie , Barr Ronald , Cabral David A. , Cairney Elizabeth , Couch Robert , Dix David B. , Fernandez Conrad V. , Hay John , Israels Sara , Laverdière Caroline , Lentle Brian , Lewis Victor , Matzinger MaryAnn , Rodd Celia , Shenouda Nazih , Stein Robert , Stephure David , Taback Shayne , Wilson Beverly , Williams Kathryn , Rauch Frank , Siminoski Kerry , Ward Leanne M.
Published: June 2012

Purpose

Vertebral fractures due to osteoporosis are a potential complication of childhood acute lymphoblastic leukemia (ALL). To date, the incidence of vertebral fractures during ALL treatment has not been reported.

Patient and Methods

We prospectively evaluated 155 children with ALL during the first 12 months of leukemia therapy. Lateral thoracolumbar spine radiographs were obtained at baseline and 12 months. Vertebral bodies were assessed for incident vertebral fractures using the Genant semiquantitative method, and relevant clinical indices such as spine bone mineral density (BMD), back pain, and the presence of vertebral fractures at baseline were analyzed for association with incident vertebral fractures.

Results

Of the 155 children, 25 (16%; 95% CI, 11% to 23%) had a total of 61 incident vertebral fractures, of which 32 (52%) were moderate or severe. Thirteen (52%) of the 25 children with incident vertebral fractures also had fractures at baseline. Vertebral fractures at baseline increased the odds of an incident fracture at 12 months by an odds ratio of 7.3 (95% CI, 2.3 to 23.1; P = .001). In addition, for every one standard deviation reduction in spine BMD Z-score at baseline, there was 1.8-fold increased odds of incident vertebral fracture at 12 months (95% CI, 1.2 to 2.7; P = .006).

Conclusion

Children with ALL have a high incidence of vertebral fractures after 12 months of chemotherapy, and the presence of vertebral fractures and reductions in spine BMD Z-scores at baseline are highly associated clinical features.
Pilot Study of Nelarabine in Combination With Intensive Chemotherapy in High-Risk T-Cell Acute Lymphoblastic Leukemia: A Report From the Children's Oncology Group
Authors: Dunsmore Kimberly P. , Devidas Meenakshi , Linda Stephen B. , Borowitz Michael J. , Winick Naomi , Hunger Stephen P. , Carroll William L. , Camitta Bruce M.
Published: June 2012

Purpose

Children's Oncology Group study AALL00P2 was designed to assess the feasibility and safety of adding nelarabine to a BFM 86–based chemotherapy regimen in children with newly diagnosed T-cell acute lymphoblastic leukemia (T-ALL).

Patients and Methods

In stage one of the study, eight patients with a slow early response (SER) by prednisone poor response (PPR; ≥ 1,000 peripheral blood blasts on day 8 of prednisone prephase) received chemotherapy plus six courses of nelarabine 400 mg/m2 once per day; four patients with SER by high minimal residual disease (MRD; ≥ 1% at day 36 of induction) received chemotherapy plus five courses of nelarabine; 16 patients with a rapid early response (RER) received chemotherapy without nelarabine. In stage two, all patients received six 5-day courses of nelarabine at 650 mg/m2 once per day (10 SER patients [one by MRD, nine by PPR]) or 400 mg/m2 once per day (38 RER patients; 12 SER patients [three by MRD, nine by PPR]).

Results

The only significant difference in toxicities was decreased neutropenic infections in patients treated with nelarabine (42% with v 81% without nelarabine). Five-year event-free survival (EFS) rates were 73% for 11 stage one SER patients and 67% for 22 stage two SER patients treated with nelarabine versus 69% for 16 stage one RER patients treated without nelarabine and 74% for 38 stage two RER patients treated with nelarabine. Five-year EFS for all patients receiving nelarabine (n = 70) was 73% versus 69% for those treated without nelarabine (n = 16).

Conclusion

Addition of nelarabine to a BFM 86–based chemotherapy regimen was well tolerated and produced encouraging results in pediatric patients with T-ALL, particularly those with a SER, who have historically fared poorly.
Nomogram to Predict the Benefit of Radiation for Older Patients With Breast Cancer Treated With Conservative Surgery
Authors: Albert Jeffrey M. , Liu Diane D. , Shen Yu , Pan I-Wen , Shih Ya-Chen Tina , Hoffman Karen E. , Buchholz Thomas A. , Giordano Sharon H. , Smith Benjamin D.
Published: June 2012

Purpose

The role of radiation therapy (RT) after conservative surgery (CS) remains controversial for older patients with breast cancer. Guidelines based on recent clinical trials have suggested that RT may be omitted in selected patients with favorable disease. However, it is not known whether this recommendation should extend to other older women. Accordingly, we developed a nomogram to predict the likelihood of long-term breast preservation with and without RT.

Methods

We used Surveillance, Epidemiology, and End Results–Medicare data to identify 16,092 women age 66 to 79 years treated with CS between 1992 and 2002, using claims to identify receipt of RT and subsequent mastectomy. Time to mastectomy was estimated using the Kaplan-Meier method. Cox proportional hazards models determined the effect of covariates on mastectomy-free survival (MFS). A nomogram was developed to predict 5- and 10-year MFS, given associated risk factors, and bootstrap validation was performed.

Results

With a median follow-up of 7.2 years, the overall 5- and 10-year MFS rates were 98.1% (95% CI, 97.8% to 98.3%) and 95.4% (95% CI, 94.9% to 95.8%), respectively. In multivariate analysis, age, race, tumor size, estrogen receptor status, and receipt of RT were predictive of time to mastectomy and were incorporated into the nomogram. Nodal status was also included given a significant interaction with RT. The resulting nomogram demonstrated good accuracy in predicting MFS, with a bootstrap-corrected concordance index of 0.66.

Conclusion

This clinically useful tool predicts 5- and 10-year MFS among older women with early breast cancer using readily available clinicopathologic factors and can aid individualized clinical decision making by estimating predicted benefit from RT.
High-Fat Diet Increases LH Pulse Frequency and Kisspeptin-Neurokinin B Expression in Puberty-Advanced Female Rats
Authors: Feng Li Xiao , Lin Yuan Shao , Kinsey-Jones James S. , O'Byrne Kevin T.
Published: June 2012

To investigate whether the advancement of puberty in response to high-fat diet (HFD) results from a concomitant increase in LH pulse frequency and kisspeptin (Kiss1) and neurokinin B (NKB) signaling in the hypothalamus, blood samples were collected on postnatal day (pnd) 28, 32, or 36 for LH measurement and vaginal opening monitored as a marker of puberty in female rats fed with HFD or standard chow from weaning. Quantitative RT-PCR was used to determine Kiss1 and kisspeptin receptor (Kiss1r) mRNA levels in brain punches of the medial preoptic area and the arcuate nucleus (ARC), and NKB and NKB receptor (NK3R) mRNA levels in the ARC. There was a gradual increase in LH pulse frequency from pnd 28, reaching significance by pnd 36 in control diet-fed rats. The advancement of puberty by approximately 6 d (average pnd 34) in rats fed HFD was associated with an earlier onset of the higher LH pulse frequency that was already extant on pnd 28. The increased levels of expression of Kiss1 in the medial preoptic area and ARC, and NKB in the ARC, associated with pubertal onset were similarly advanced in HFD-fed rats. These data suggest that the earlier accelerated GnRH pulse generator frequency and advanced puberty with obesogenic diets might be associated with premature up-regulation of kisspeptin and NKB signaling in the hypothalamus of the female rat.
Immunoregulatory Natural Killer Cells Suppress Autoimmunity by Down-Regulating Antigen-Specific CD8+ T Cells in Mice
Authors: Ehlers Margret , Papewalis Claudia , Stenzel Wiebke , Jacobs Benedikt , Meyer Klaus L. , Deenen René , Willenberg Holger S. , Schinner Sven , Thiel Annette , Scherbaum Werner A. , Ullrich Evelyn , Zitvogel Laurence , Schott Matthias
Published: June 2012

Natural killer (NK) cells belong to the innate immune system. Besides their role in antitumor immunity, NK cells also regulate the activity of other cells of the immune system, including dendritic cells, macrophages, and T cells, and may, therefore, be involved in autoimmune processes. The aim of the present study was to clarify the role of NK cells within this context. Using two mouse models for type 1 diabetes mellitus, a new subset of NK cells with regulatory function was identified. These cells were generated from conventional NK cells by incubation with IL-18 and are characterized by the expression of the surface markers CD117 (also known as c-Kit, stem cell factor receptor) and programmed death (PD)-ligand 1. In vitro analyses demonstrated a direct lysis activity of IL-18-stimulated NK cells against activated insulin-specific CD8+ T cells in a PD-1/PD-ligand 1-dependent manner. Flow cytometry analyses revealed a large increase of splenic and lymphatic NK1.1+/c-Kit+ NK cells in nonobese diabetic mice at 8 wk of age, the time point of acceleration of adaptive cytotoxic immunity. Adoptive transfer of unstimulated and IL-18-stimulated NK cells into streptozotocin-treated mice led to a delayed diabetes development and partial disease prevention in the group treated with IL-18-stimulated NK cells. Consistent with these data, mild diabetes was associated with increased numbers of NK1.1+/c-Kit+ NK cells within the islets. Our results demonstrate a direct link between innate and adaptive immunity in autoimmunity with newly identified immunoregulatory NK cells displaying a potential role as immunosuppressors.
RelB/NF-κB2 Regulates Corticotropin-Releasing Hormone in the Human Placenta
Authors: Wang Bingbing , Parobchak Nataliya , Rosen Todd
Published: June 2012

Placental CRH may be part of a clock that governs the length of human gestation. The mechanism underlying differential regulation of CRH in the human placenta is poorly understood. We report here that constitutively activated RelB/nuclear factor-κB2 (NF-κB)-2 (p100/p52) acts as an endogenous stimulatory signal to regulate CRH by binding to an NF-κB enhancer of CRH gene promoter in the human placenta. Nuclear staining of NF-κB2 and RelB in villous syncytiotrophoblasts and cytotrophoblasts was coupled with cytoplasmic CRH in syncytial knots of cytotrophoblasts. Chromatin immunoprecipitation identified that CRH gene associated with both RelB and NF-κB2 (p52). Dexamethasone increased synthesis and nuclear translocation of RelB and NF-κB2 (p52) and their association with the CRH gene. In contrast, progesterone, a down-regulator of placental CRH, repressed NF-κB2 (p100) processing, nuclear translocation of RelB and NF-κB2 (p52), and their association with the CRH gene. Luciferase reporter assay determined that the NF-κB enhancer of CRH was sufficient to regulate transcriptional activity of a heterologous promoter in primary cytotrophoblasts. RNA interference-mediated repression of RelB or NF-κB2 resulted in significant inhibition of CRH at both transcriptional and translational levels and prevented the dexamethasone-mediated up-regulation of CRH transcription and translation. These results suggest that the noncanonical NF-κB pathway regulates CRH production in the human placenta and is responsible for the positive regulation of CRH by glucocorticoids.
Research Resource: dkCOIN, the National Institute of Diabetes, Digestive and Kidney Diseases (NIDDK) Consortium Interconnectivity Network: A Pilot Program to Aggregate Research Resources Generated by Multiple Research Consortia
Authors: McKenna Neil J. , Howard Christopher L. , Aufiero Michael , Easton-Marks Jeremy , Steffen David L. , Becnel Lauren B. , Magnuson Mark A. , McIndoe Richard A. , Cartailler Jean-Philippe
Published: June 2012

The National Institute of Diabetes, Digestive and Kidney Diseases (NIDDK) supports multiple basic science consortia that generate high-content datasets, reagent resources, and methodologies, in the fields of kidney, urology, hematology, digestive, and endocrine diseases, as well as metabolic diseases such as diabetes and obesity. These currently include the Beta Cell Biology Consortium, the Nuclear Receptor Signaling Atlas, the Diabetic Complications Consortium, and the Mouse Metabolic Phenotyping Centers. Recognizing the synergy that would accrue from aggregating information generated and curated by these initiatives in a contiguous informatics network, we created the NIDDK Consortium Interconnectivity Network (dkCOIN; www.dkcoin.org). The goal of this pilot project, organized by the NIDDK, was to establish a single point of access to a toolkit of interconnected resources (datasets, reagents, and protocols) generated from individual consortia that could be readily accessed by biologists of diverse backgrounds and research interests. During the pilot phase of this activity dkCOIN collected nearly 2000 consortium-curated resources, including datasets (functional genomics) and reagents (mouse strains, antibodies, and adenoviral constructs) and built nearly 3000 resource-to-resource connections, thereby demonstrating the feasibility of further extending this database in the future. Thus, dkCOIN promises to be a useful informatics solution for rapidly identifying useful resources generated by participating research consortia.
Research Resource: Whole Transcriptome RNA Sequencing Detects Multiple 1α,25-Dihydroxyvitamin D3-Sensitive Metabolic Pathways in Developing Zebrafish
Authors: Craig Theodore A. , Zhang Yuji , McNulty Melissa S. , Middha Sumit , Ketha Hemamalini , Singh Ravinder J. , Magis Andrew T. , Funk Cory , Price Nathan D. , Ekker Stephen C. , Kumar Rajiv
Published: June 2012

The biological role of vitamin D receptors (VDR), which are abundantly expressed in developing zebrafish (Danio rerio) as early as 48 h after fertilization, and before the development of a mineralized skeleton and mature intestine and kidney, is unknown. We probed the role of VDR in developing zebrafish biology by examining changes in expression of RNA by whole transcriptome shotgun sequencing (RNA-seq) in fish treated with picomolar concentrations of the VDR ligand and hormonal form of vitamin D3, 1α,25-dihydroxyvitamin D3 [1α,25(OH)2D3)].We observed significant changes in RNAs of transcription factors, leptin, peptide hormones, and RNAs encoding proteins of fatty acid, amino acid, xenobiotic metabolism, receptor-activator of NFκB ligand (RANKL), and calcitonin-like ligand receptor pathways. Early highly restricted, and subsequent massive changes in more than 10% of expressed cellular RNA were observed. At days post fertilization (dpf) 2 [24 h 1α,25(OH)2D3-treatment], only four RNAs were differentially expressed (hormone vs. vehicle). On dpf 4 (72 h treatment), 77 RNAs; on dpf 6 (120 h treatment) 1039 RNAs; and on dpf 7 (144 h treatment), 2407 RNAs were differentially expressed in response to 1α,25(OH)2D3. Fewer RNAs (n = 481) were altered in dpf 7 larvae treated for 24 h with 1α,25(OH)2D3vs. those treated with hormone for 144 h. At dpf 7, in 1α,25(OH)2D3-treated larvae, pharyngeal cartilage was larger and mineralization was greater. Changes in expression of RNAs for transcription factors, peptide hormones, and RNAs encoding proteins integral to fatty acid, amino acid, leptin, calcitonin-like ligand receptor, RANKL, and xenobiotic metabolism pathways, demonstrate heretofore unrecognized mechanisms by which 1α,25(OH)2D3 functions in vivo in developing eukaryotes.
Six3 cooperates with Hedgehog signaling to specify ventral telencephalon by promoting early expression of Foxg1a and repressing Wnt signaling
Authors: Carlin Dan , Sepich Diane , Grover Vandana K. , Cooper Michael K. , Solnica-Krezel Lilianna , Inbal Adi
Published: June 2012

Six3 exerts multiple functions in the development of anterior neural tissue of vertebrate embryos. Whereas complete loss of Six3 function in the mouse results in failure of forebrain formation, its hypomorphic mutations in human and mouse can promote holoprosencephaly (HPE), a forebrain malformation that results, at least in part, from abnormal telencephalon development. However, the roles of Six3 in telencephalon patterning and differentiation are not well understood. To address the role of Six3 in telencephalon development, we analyzed zebrafish embryos deficient in two out of three Six3-related genes, six3b and six7, representing a partial loss of Six3 function. We found that telencephalon forms in six3b;six7-deficient embryos; however, ventral telencephalic domains are smaller and dorsal domains are larger. Decreased cell proliferation or excess apoptosis cannot account for the ventral deficiency. Instead, six3b and six7 are required during early segmentation for specification of ventral progenitors, similar to the role of Hedgehog (Hh) signaling in telencephalon development. Unlike in mice, we observe that Hh signaling is not disrupted in embryos with reduced Six3 function. Furthermore, six3b overexpression is sufficient to compensate for loss of Hh signaling in isl1- but not nkx2.1b-positive cells, suggesting a novel Hh-independent role for Six3 in telencephalon patterning. We further find that Six3 promotes ventral telencephalic fates through transient regulation of foxg1a expression and repression of the Wnt/β-catenin pathway.
Cellular reprogramming – lowering gravity on Waddington's epigenetic landscape
Authors: Takahashi Kazutoshi
Published: June 2012

During development, cell fate is specified precisely through programming by multiple complex elements and processes, including chromatin modifications that result in epigenetic marks. Once determined, cell fate is specified further only through maturation processes, which include differentiation and senescence. However, recent studies have shown that it is possible to influence cell fate through artificial manipulation. For example, the exogenous expression of a set of transcription factors can result in the reprogramming of differentiated skin fibroblasts to a pluripotent state. In addition, recent reports have demonstrated the directed reprogramming of one type of differentiated somatic cell to another type of differentiated somatic cell, without rejuvenation to a pluripotent state. Reprogramming factors blur the boundaries between different cell fates, which can never meet, as if the hierarchy were flattened by ‘lowering gravity’. Although attempts to use direct reprogramming to generate certain cell types, such as those found in the kidneys and the lungs, have remained unsuccessful, recent advances suggest that we are nearing the identification of determinants that allow cells to be directly reprogrammed into cell types from all organs in the not too distant future. This Commentary summarises our current knowledge on cellular reprogramming, and more specifically, recent advances in direct reprogramming to generate a variety of cell types.
Functional coupling of microtubules to membranes – implications for membrane structure and dynamics
Authors: Stephens David J.
Published: June 2012

The microtubule network dictates much of the spatial patterning of the cytoplasm, and the coupling of microtubules to membranes controls the structure and positioning of organelles and directs membrane trafficking between them. The connection between membranes and the microtubule cytoskeleton, and the way in which organelles are shaped and moved by interactions with the cytoskeleton, have been studied intensively in recent years. In particular, recent work has expanded our thinking of this topic to include the mechanisms by which membranes are shaped and how cargo is selected for trafficking as a result of coupling to the cytoskeleton. In this Commentary, I will discuss the molecular basis for membrane–motor coupling and the physiological outcomes of this coupling, including the way in which microtubule-based motors affect membrane structure, cargo sorting and vectorial trafficking between organelles. Whereas many core concepts of these processes are now well understood, key questions remain about how the coupling of motors to membranes is established and controlled, about the regulation of cargo and/or motor loading and about the control of directionality.
A test of alternate models for increased tissue nitrogen isotope ratios during fasting in hibernating arctic ground squirrels
Authors: Lee Trixie N. , Buck C. Loren , Barnes Brian M. , O'Brien Diane M.
Published: June 2012

We describe two models explaining the increase in tissue nitrogen isotope ratios (δ15N) that occurs during fasting in animals. The catabolic model posits that protein breakdown selectively removes the lighter isotope of nitrogen (14N) from catabolized tissues, causing an increase in the proportion of heavy nitrogen isotope (15N). The anabolic model posits that protein synthesis during fasting results in elevated δ15N values, as the unreplaced loss of 14N to urea results in a higher proportion of 15N in plasma amino acids used for protein synthesis. We effected a range of lean mass loss in arctic ground squirrels (Urocitellus parryii) fasting during hibernation before collecting organ and muscle tissues for analysis of δ15N values. The catabolic model predicts increased δ15N values in both liver and muscle, since these tissues undergo significant catabolism during hibernation. The anabolic model predicts no change in muscle, but an increase in δ15N values in liver, which has high levels of protein synthesis during euthermic phases of hibernation. We found a significant increase in liver δ15N values and no change in muscle δ15N values with lean mass loss, which supports the anabolic model. Heart, small intestine, and brown adipose tissue also increased in δ15N values, indicating protein synthesis in these organ tissues during hibernation. Urine was 3.8‰ lighter than plasma, and both urine and plasma increased in δ15N values with lean mass loss. This study helps clarify the mechanisms causing δ15N change during nutritional stress, thus increasing its utility for physiological research and reconciling previously contradictory results.
Visuo-motor transformations involved in the escape response to looming stimuli in the crab Neohelice (=Chasmagnathus) granulata
Authors: Oliva Damián , Tomsic Daniel
Published: June 2012

Escape responses to directly approaching predators represent one instance of the animals' ability for collision avoidance. Usually, such responses can be easily evoked in the laboratory using two dimensional computer simulations of approaching objects, known as looming stimuli. Therefore, escape behaviors are considered useful models for the study of computations performed by the brain to efficiently transform visual information into organized motor patterns. The escape response of the crab Neohelice (previously Chasmagnathus) granulata offers an opportunity to investigate the processing of looming stimuli and its transformation into complex motor patterns. Here we studied the escape performance of this crab to a variety of different looming stimuli. The response always consisted of a vigorous run away from the stimulus. However, the moment at which it was initiated, as well as the developed speed, closely matched the expansion dynamics of each particular stimulus. Thus, we analyzed the response events as a function of several variables that could theoretically be used by the crab (angular size, angular velocity, etc.). Our main findings were: a) the decision to initiate the escape run is made when the stimulus angular size increases by 7°. b) The escape run is not a ballistic kind of response, as its speed is adjusted concurrently with changes in the optical stimulus variables. c) The speed of the escape run can be faithfully described by a phenomenological input-output relation based on the stimulus angular increment and angular velocity of the stimulus.
Sticky Wages: Evidence from Quarterly Microeconomic Data
Authors: Bihan Hervé Le , Montornès Jérémi , Heckel Thomas
Published: June 2012

Using an original micro-dataset from France, we investigate nominal wage stickiness. Nominal wage changes are found to occur at a quarterly frequency of around 38 percent over our sample period, and to be to a large extent staggered across establishments, and very synchronized within establishments. We carry out an econometric analysis of wage changes based on a two-threshold sample selection model. Our results are that the timing of wage adjustments is time-dependent as opposed to state-dependent, there is evidence of predetermination in wage changes, and both backward and forward-looking behavior is relevant in wage setting. (JEL E24, E52, J31)
Identification and functional characterization of the nascent RNA contacting residues of the hepatitis C virus RNA-dependent RNA polymerase
Authors: Vaughan Robert , Fan Baochang , You Jin-Sam , Kao C. Cheng
Published: June 2012

Understanding how the hepatitis C virus (HCV) RNA-dependent RNA polymerase (RdRp) interacts with nascent RNA would provide valuable insight into the virus's mechanism for RNA synthesis. Using a peptide mass fingerprinting method and affinity capture of peptides reversibly cross-linked to an alkyn-labeled nascent RNA, we identified a region below the Δ1 loop in the fingers domain of the HCV RdRp that contacts the nascent RNA. A modification protection assay was used to confirm the assignment. Several mutations within the putative nascent RNA binding region were generated and analyzed for RNA synthesis in vitro and in the HCV subgenomic replicon. All mutations tested within this region showed a decrease in primer-dependent RNA synthesis and decreased stabilization of the ternary complex. The results from this study advance our understanding of the structure and function of the HCV RdRp and the requirements for HCV RNA synthesis. In addition, a model of nascent RNA interaction is compared with results from structural studies.
Three Frameworks for Service Research: Exploring Multilevel Governance in Nested, Networked Systems
Authors: Spohrer Jim , Piciocchi Paolo , Bassano Clara
Published: June 2012

Three frameworks are recommended to analyze multilevel governance across a spectrum of complex human systems, including nations, states, cities, universities, hospitals, hotels, and homes, with which service researchers are concerned. This spectrum of complex human systems can be seen as instances of nested, networked holistic service systems that provision whole service to the people inside them and depend heavily on shared systems of rules to change over time. Increasingly, service researchers benefit from improved analysis/design frameworks for complex human systems that (1) improve multilevel governance, making it more likely that local optimizations contribute to global resilience and sustainability, and (2) can integrate across diverse disciplines, systems, and cultures. Three frameworks are considered: service science, management, engineering, and design (SSME+D); viable systems approach (VSA); and institutional analysis and development (IAD). Each framework has a focal building block (rule-rich entity architectures)—namely, a service system (SSME+D), a viable system (VSA), and a polycentric system (IAD). Our goals are to (1) provide a conceptual foundation and recommended methodology to illustrate the type of future empirical work that might someday provide more efficient and effective ways to compare, contrast, and search for improved service research frameworks and entity architectures, and (2) encourage service researchers to move beyond dyads, be they provider-to-customer, business-to-business, or even government-to-citizen, and toward a view of multilevel rule-rich nested, networked systems in the wild.