bluuebunny/crossref_metadata_2025 huggingface dataset:
The efforts of a federation of slum and shanty dwellers to secure land and improve housing in Moratuwa: from savings groups to citywide strategies
Authors: D'Cruz Celine , McGranahan Gordon , Sumithre Upali
Published: September 2009

In Moratuwa, Sri Lanka, the tsunami disaster of 2004 forced new ways of working on both organizations of the urban poor and local authorities. Building on this experience, an emerging federation of the urban poor (built on community savings groups) has been collaborating with local authorities to secure land and adequate housing in two deprived settlements unaffected by the tsunami. This article examines these recent initiatives and their citywide relevance. The federation (the Women’s Development Bank Federation) receives support from a local NGO (Janarukula) and is affiliated with an international confederation (Slum Dwellers International), whose principles are also evident in these improvement efforts. One of the two settlements is located on the periphery of Moratuwa, where land is plentiful and existing plots can be upgraded. The other is a central settlement, where land is scarcer and the federation has opted for multi-storey residences. Securing community control over the multi-storey development has proved difficult and has required far tighter collective action. Success in dense settlements is important, however, if the federation is to meet its goal of creating a citywide strategy.
Evaluation of Agri-environmental Measures
Authors: Ziolkowska Jadwiga
Published: September 2009

In this article, we discuss the implementation of two evaluation approaches—the Analytic Hierarchy Process and the cost-effectiveness analysis for political decision-making support in agri-environmental policy. The approaches represent two different ways of evaluation: hierarchical weighting for estimation of immeasurable environmental benefits and effectiveness analysis focused on economic aspects. These methods can be used separately; however, the combination of the approaches in one evaluation system can help to consider different economic and ecological aspects of environmental protection to a wider extent. The main objective of the article is to investigate which agri-environmental measures would be recommended for political strategies to maximize environmental benefits or else to minimize the realization costs of the measures. The investigation is based on results of a case study conducted in voivodship Subcarpathia in Poland including interviews with agricultural experts, agri-environmental advisors and farmers. The results show that the measures ‘Extensive meadow farming’ and ‘Organic farming’ denote the highest environmental benefits with regard to the envisaged environmental objectives defined in the National Agri-environmental Programme 2004–2006. The cost-effectiveness of agri-environmental measures is differentiated depending on the stakeholder group. The results can be helpful to support political decision-making processes considering simultaneously regional priorities of the environmental protection in rural areas.
Olive Entrepreneurship in the Southern Hemisphere
Authors: Alonso Abel D.
Published: September 2009

New Zealand's olive-growing industry has experienced continuous development in recent years; recent reports and success stories not only indicate progress achieved in quantity, but also, and more importantly, in quality. However, to date, research on this industry and particularly from entrepreneurs’ perspective is very limited. For example, little is known about the business goals of olive growers, or challenges they may face while developing their olive groves. The present case study explores these dimensions of olive growing in New Zealand using a quantitative approach.

The findings demonstrate the very developmental stage the olive growers are undergoing, as well as several challenges, including marketing issues, that are limiting the further development of olive growers’ operations. Implications include the need to strengthen marketing efforts of the olive oil product, both at a domestic and at an international level, particularly in view of the potential future increase of olive oil production in New Zealand.
Assessment of People's Participation under Watershed Development Programme in the State of Kerala, India
Authors: Chandran K. Madhava , Joseph E.J. , Chackacherry George
Published: September 2009

People's participation and the influence of socio-psychological characteristics of the beneficiaries on their participation were assessed under a watershed development project in the State of Kerala, India. The results indicate a ‘target-oriented’ approach, without much attention to social organization for promoting people's participation. Most of the beneficiaries of the project have medium level of participation in watershed-related activities. Socio-economic status, level of modernization and extension participation of the beneficiaries are the characteristics which can be used to discriminate between people with low, medium and high levels of participation. The five socio-psychological characteristics of beneficiaries in the study, together, explain 96.8 per cent of the variance observed in participation level between beneficiaries having less than one ha and those having more than 1 ha landholding. There exists potential for the implementing agencies of development projects for identifying and promoting such characteristics of the beneficiaries for improving their involvement under the project.
Rural Indian and Indigenous Australian Women Working Towards Empowerment
Authors: Moyle Tracey L. , Dollard Maureen F.
Published: September 2009

The aim of this article is to introduce and discuss the notion of a comparative study between India and Australia in the area of rural work psychology. It has been argued that there is enormous scope for work psychology to be applied to and contribute to rural development (Dollard et al. 2004). This article explores an aspect of work psychology in the form of personal and economic empowerment of women in rural communities by engaging women in group enterprise. A large body of research taken from developing countries explores entrepreneurial activity using micro-credit to overcome poverty, increase income and enhance well-being. No such comparison study has been introduced amongst indigenous women in Australia. Through the process of case study analysis, the empowerment of rural Indian women engaging in group enterprise is examined. This article explores the scope for future research for the inclusion and examination of indigenous women in income-generating activities within a rural and remote setting.
The Effects of Relocation on Wages
Authors: Hyder Asma
Published: September 2009

This article estimates the wage differentials between the natives and the relocated workers. Nationwide Pakistan Labor Force Survey 2005–06 has been used with a total sample of 10,401 working individuals. Two wage equations are estimated for those living in that area since birth or those who relocated during the last 10 years or so. Oaxaca-Binder methodology has been used for decomposition analysis. This decomposition analysis further helps to investigate the ‘treatment’ and ‘endowment effect’. The overall decomposition results are in favour of native workers.
When Facilities Become Excessive
Authors: Ramesh R. , Narayanasamy N.
Published: September 2009

Tamil Nadu is one of the very few states that have ensured domestic water supply in even the remotest of villages. The problem, as of now, is relating to proper management of water service delivery to reach all the households, and maintenance of the technical installations/facilities created. The target of government of India with regard to levels of service to rural areas is 55 litre per capita daily (lpcd); and the dream is being able to deliver 70 lpcd. An empirical verification was done to find out the adequacy of facilities to fulfill this dream. According to the findings of this study, there are excessive facilities in almost all the villages, to the extent that some of the villages get more than twice of the vision contemplated. This is because there is excessive physical infrastructure available for water supply in almost all the villages that were studied. This is resulting in excessive pumping of water from the ground, wastage, adding to the pumping charges in terms of electricity bill and maintenance of the facilities.
An Investigation of Pro-Poor Growth Index in Agriculture Sector of Pakistan—1984–85 to 2004–05
Authors: Zaman Khalid , Ahmad Mehboob
Published: September 2009

The aim of this study is to explore the interrelationship between agriculture growth, inequality and poverty in Pakistan. To this end, the study examines as to what extent the poor have benefited from growth while taking into account the magnitude of growth and the benefits of growth achieved by the poor from 1984–85 to 2004–05.The research concludes that the proportional reduction in poverty is an increasing function of the Pro-Poor Growth Index (PPGI) and Poverty Equivalent Growth Rate (PEGR) as proposed by Kakwani and Pernia (2000) and Kakwani and Son (2004). Results indicate that higher the PEGR, higher will be the poverty reduction.
Village Panchayats’ Common Lands
Authors: Malik Ajmer S.
Published: September 2009

The statutory authority pertaining to management of common lands lies with the state legislatures and administrations, which enact and effect laws pertaining to the subject of land including common lands. Hence, Haryana State has adopted ‘The Punjab Village Common Lands (Regulation) Act 1961.' The Punjab Village Common Lands (Regulation) Rules 1964 (for Haryana) provides an account of comprehensive details of various kinds of provisions necessary for regulating and managing the common lands in the state. Some relevant provisions to this effect are also made there in the Haryana Panchayati Raj Act-1994.

It is concluded that there is complete control of the State Government in managing the village common lands of the state. The State Government possesses all requisite executive and administrative powers for the said purpose. The executive authority vested in officials from secretariat to village levels enables the Government for effective management of shamlat land related affairs in the state. The Gram Panchayat is entrusted with the significant responsibility to perform all kinds of functions relating to the utilization, protection and preservation of these lands.

But inspite of an effective constitutional arrangement, it is found that a large area of common land in the state has remained unutilized mainly because of the absence of resources and innovative ideas in this regard. Therefore, there is an urgent need to evolve a policy measure for improving the potentiality of common lands to earn more income for the village panchayts in the state.
Shelly: A Case Study Focusing on Ethics and Counselor Wellness
Authors: Hendricks Bret , Bradley Loretta J. , Brogan W.Chuck , Brogan Charla
Published: September 2009

Counselors experience stress and anxiety as part of their profession. However, frequently counselors do not attend to their own needs regarding self-care and wellness, thus, placing themselves at risk of ethical violations relating to counselor impairment. In this article, a case study is presented with a correspondent wellness plan illustrating ways that counselors might implement self-care strategies to improve their wellness. The wellness treatment plan is written in conjunction with a physician, a cardiologist, who suggests simple ways to assess and monitor wellness.
Flexor pollicis longus primary repair: further experience with the tang technique and controlled active mobilization
Authors: GIESEN T. , SIROTAKOVA M. , COPSEY A. J. , ELLIOT D.
Published: September 2009

This study reports our treatment of divided flexor pollicis longus tendons by primary repair from January 2004 to September 2007. Fifty flexor pollicis longus repairs carried out using the Tang technique of three Tsuge sutures are reported in this study. A circumferential suture was not used routinely. Excellent or good results were observed in 78/82% of cases (White/Buck-Gramcko assessments, respectively). No patients ruptured repairs as a result of early active mobilization. No patients developed postoperative infections with wound and tendon dehiscence. One patient developed Chronic Regional Pain Syndrome Type 1. We have found this repair of the flexor pollicis longus tendon to be safe for early active mobilization and it is easier to perform than primary repair of this tendon using four strand Kessler-type core sutures and elaborate circumferential sutures, as reported previously.
Motion-stable flexor tendon repair with the Mantero technique in the distal part of the fingers
Authors: Schaller P. , Baer W.
Published: September 2009

Lacerated flexor digitorum profundus (FDP) tendons in zone 1 and distal zone 2 were reconstructed in 73 consecutive cases using the motion-stable Mantero technique during a 7-year period. Sixty-five (89%) of these patients were re-examined an average of 40 (26–82) months postoperatively. According to Moiemen and Elliot (2000) assessment by Strickland's original and modified criteria and in addition the Buck-Gramcko score showed excellent and good results of 54%, 72% and 91% respectively. In contrast, examination of the results measuring the range of movement of the distal interphalangeal (DIP) joint alone provided a more realistic assessment in DIP joint function after Mantero technique with excellent and good results of only 38%.
High-resolution ultrasonography of the cutaneous nerve branches in the hand and wrist
Authors: STOKVIS A. , VAN NECK J. W. , VAN DIJKE C. F. , VAN WAMEL A. , COERT J. H.
Published: September 2009

Ultrasonography can be used in the diagnosis of various neuropathies, including nerve injury. Nerves often involved in traumatic and iatrogenic injury are small cutaneous branches in the hand and wrist, which cannot be seen in detail using current ultrasound probes. This study explored the potential of high-resolution ultrasonography in seeing these nerve branches in the human. The VisualSonics Vevo 770 system with a 15–82.5 MHz probe was compared to a commonly used 5–12 MHz probe and ultrasound machine. The accuracy was validated by ultrasound guided dye injection into cadaver nerves, with subsequent anatomical dissection and verification. Results were confirmed in two healthy volunteers. The Vevo 770 system was able to accurately identify the small cutaneous nerves. It could also depict the median nerve and its fascicles in greater detail. This may be useful for clinical diagnosis, localisation and follow-up of neuropathies and nerve injuries.
Surface replacement trapeziometacarpal joint arthroplasty – early results
Authors: PENDSE A. , NISAR A. , SHAH S. Z. , BHOSALE A. , FREEMAN J. V. , CHAKRABARTI I.
Published: September 2009

This study reviews the results of Surface Replacement Trapeziometacarpal (SR TMC, Avanta®, San Diego, CA) total joint arthroplasty. Fifty patients (62 joints) were included in the study. Forty-three patients (54 joints) were seen at final follow up. Seven patients (eight joints) were interviewed over the phone. Seven patients were revised to trapeziectomy and ligament reconstruction with tendon interposition, five for aseptic loosening and two for dislocation. At final follow up, the mean Quick DASH score was 30.4 and the Sollerman Score was 77.3. Radiological review of the surviving 55 joints showed subsidence of four trapezial components in asymptomatic patients. Cumulative survival rate was 91% at 3 years. Eighty-five percent of the patients were satisfied with the outcome of their treatment.
Biomechanics of the wrist after proximal row carpectomy in cadavers
Authors: Zhu Y.-L. , Xu Y.-Q. , Ding J. , Li J. , Chen B. , Ouyang Y.-F.
Published: September 2009

We investigated the biomechanics of the radiocapitate joint after a proximal row carpectomy in six fresh-frozen cadaver wrists using super-low-pressure-sensitive film on a material testing system. The average pressure within the lunate fossa increased significantly from 23.2 to 136.4 N/cm2 with a sharp decrease in the contact area from 2.08 to 0.30 cm2 after a proximal row carpectomy. The cartilage of the proximal capitate had four sub-facets and therefore was not as smooth as the normal proximal lunate. We found that the wrist was overloaded after a proximal row carpectomy and the main cause was the anatomical mismatch of the radiocapitate articulation.
The role of an MMP inhibitor in the regulation of mechanical tension by Dupuytren’s disease fibroblasts
Authors: TOWNLEY W. A. , CAMBREY A. D. , KHAW P. T. , GROBBELAAR A. O.
Published: September 2009

Mechanical tension and contracture are two related facets of tissue biology. This study assessed the effect of ilomastat, a broad-spectrum matrix metalloprotease (MMP) inhibitor, on generation of tension by Dupuytren’s disease fibroblasts. Nodule and cord-derived fibroblasts were isolated from five patients with Dupuytren’s disease; flexor retinaculum acted as the control. A culture force monitor (CFM) provided an in vitro model of tissue organization to assess development of mechanical tension, lattice contraction and spatial remodelling by fibroblasts. Responses to ilomastat were compared to treatment with a control peptide. Nodule and cord-derived fibroblasts exhibited a two-fold increase in tension compared with flexor retinaculum. Ilomastat significantly inhibited development of tension by nodule and cord but not flexor retinaculum derived fibroblasts at 100 μM. These results imply that MMP activity mediates regulation of tensile strength by Dupuytren’s disease fibroblasts and may be an important therapeutic target in patients with Dupuytren’s disease.
Is revision bone grafting worthwhile after failed surgery for scaphoid nonunion? Minimum 8 year follow-up of 18 patients
Authors: REIGSTAD O. , THORKILDSEN R. , GRIMSGAARD C. , REIGSTAD A. , RØKKUM M.
Published: September 2009

Eighteen patients who underwent revision non-vascularized bone grafting and internal fixation after failed surgery for scaphoid nonunion were reviewed after a minimum of 8.2 years. Eleven of the nonunions were located in the middle and seven in the proximal third of the scaphoid. The mean interval between injury and the revision procedure was 6 years. Sixteen of the 18 nonunions healed, two after a third attempt. Three patients with healed nonunions and one patient with persistent nonunion required salvage procedures for progressive radiocarpal arthrosis. In the remaining 14 cases, the mean loss of wrist flexion/extension arc compared to the contralateral wrist was 36 °. Mean reduction of grip strength and key pinch was 9.3 kg and 0.9 kg respectively. The QuickDASH score was 18 and a visual analogue pain score was 21/100 at follow-up. Wrist degeneration increased in all but one case during the observation period. Thirteen of 16 patients with union and one patient with a persisting nonunion experienced moderate symptoms.
Analysis of NHSLA claims in hand and wrist surgery
Authors: Khan I. H. , Giddins G.
Published: September 2009

Claims for negligence are increasing in medical practice. We analysed data provided by the UK NHS Litigation Authority (NHSLA) on all hand and wrist surgery from 1995–2001. The numbers of claims increased from 13 to 40, but the number being successfully defended also increased from 2 to 13 during this period. Claims were most commonly attributed to errors at surgery (56%) or in outpatient clinics (24%). Strikingly the claims are clustered to a few common conditions, particularly the treatment of carpal tunnel syndrome (22%) and wrist fractures (48%). There were no claims related to complex hand surgery. We recommend better training for ‘routine surgery’, better description of distal radius fracture parameters at each clinic visit and better training in emergency departments (ED).
The addition of an upper-extremity curriculum in medical school education and its assessment
Authors: DAY C. S , AHN C. S , YU Y.
Published: September 2009

This study assessed the impact of changes made to address the inadequate upper-extremity education through preclinical medical school curriculum reform. After the administration of a new upper-extremity curriculum, which also increased the time devoted to three preclinical medical school courses from 7.25 to 21.25 hours, second-year medical students were evaluated for mastery of these concepts through a national validated objective examination, and attitude and skill through clinical confidence and subjective surveys. After implementation of the new upper-extremity curriculum, students had significantly greater confidence in their ability to perform a physical examination but not in identifying differential diagnoses of the upper-extremity. Students were more satisfied with the amount of time spent on the musculoskeletal system but their performance in the national examination did not change.
Epidermoid cysts in the hand
Authors: LINCOSKI C. J. , BUSH D. C. , MILLON S. J.
Published: September 2009

This study details our series of epidermoid cysts in the hand, characterising the incidence, clinical characteristics and recurrence rate after marginal excision. A historical cohort of 101 epidermoid cysts that were excised from a soft tissue or intraosseous location in the hand over a 27 year period were reviewed. The incidence of epidermoid cysts, patient age, sex, occupation, anatomic location, history of trauma, treatment complications and cyst recurrence rate were noted. Key findings of the study were as follows. Epidermoid cysts represented a significant portion of our relatively large series of hand tumours. The majority occurred in male patients, most often involving the soft tissues on the palmar aspect of the hand. Four percent were intraosseous epidermoid cysts. After excision with a marginal tumour margin we found that 11 cysts (11%) recurred.
TAPP2 links phosphoinositide 3-kinase signaling to B-cell adhesion through interaction with the cytoskeletal protein utrophin: expression of a novel cell adhesion-promoting complex in B-cell leukemia
Authors: Costantini Jennifer L. , Cheung Samuel M. S. , Hou Sen , Li Hongzhao , Kung Sam K. , Johnston James B. , Wilkins John A. , Gibson Spencer B. , Marshall Aaron J.
Published: September 2009

Tandem pleckstrin homology domain proteins (TAPPs) are recruited to the plasma membrane via binding to phosphoinositides produced by phosphoinositide 3-kinases (PI3Ks). Whereas PI3Ks are critical for B-cell activation, the functions of TAPP proteins in B cells are unknown. We have identified 40 potential interaction partners of TAPP2 in B cells, including proteins involved in cytoskeletal rearrangement, signal transduction and endocytic trafficking. The association of TAPP2 with the cytoskeletal proteins utrophin and syntrophin was confirmed by Western blotting. We found that TAPP2, syntrophin, and utrophin are coexpressed in normal human B cells and B-chronic lymphocytic leukemia (B-CLL) cells. TAPP2 and syntrophin expression in B-CLL was variable from patient to patient, with significantly higher expression in the more aggressive disease subset identified by zeta-chain–associated protein kinase of 70 kDa (ZAP70) expression and unmutated immunoglobulin heavy chain (IgH) genes. We examined whether TAPP can regulate cell adhesion, a known function of utrophin/syntrophin in other cell types. Expression of membrane-targeted TAPP2 enhanced B-cell adhesion to fibronectin and laminin, whereas PH domain–mutant TAPP2 inhibited adhesion. siRNA knockdown of TAPP2 or utrophin, or treatment with PI3K inhibitors, significantly inhibited adhesion. These findings identify TAPP2 as a novel link between PI3K signaling and the cytoskeleton with potential relevance for leukemia progression.
Allogeneic hematopoietic cell transplantation after conditioning with 131I–anti-CD45 antibody plus fludarabine and low-dose total body irradiation for elderly patients with advanced acute myeloid leukemia or high-risk myelodysplastic syndrome
Authors: Pagel John M. , Gooley Theodore A. , Rajendran Joseph , Fisher Darrell R. , Wilson Wendy A. , Sandmaier Brenda M. , Matthews Dana C. , Deeg H. Joachim , Gopal Ajay K. , Martin Paul J. , Storb Rainer F. , Press Oliver W. , Appelbaum Frederick R.
Published: September 2009

We conducted a study to estimate the maximum tolerated dose (MTD) of 131I–anti-CD45 antibody (Ab; BC8) that can be combined with a standard reduced-intensity conditioning regimen before allogeneic hematopoietic cell transplantation. Fifty-eight patients older than 50 years with advanced acute myeloid leukemia (AML) or high-risk myelodysplastic syndrome (MDS) were treated with 131I-BC8 Ab and fludarabine plus 2 Gy total body irradiation. Eighty-six percent of patients had AML or MDS with greater than 5% marrow blasts at the time of transplantation. Treatment produced a complete remission in all patients, and all had 100% donor-derived CD3+ and CD33+ cells in the blood by day 28 after the transplantation. The MTD of 131I-BC8 Ab delivered to liver was estimated to be 24 Gy. Seven patients (12%) died of nonrelapse causes by day 100. The estimated probability of recurrent malignancy at 1 year is 40%, and the 1-year survival estimate is 41%. These results show that CD45-targeted radiotherapy can be safely combined with a reduced-intensity conditioning regimen to yield encouraging overall survival for older, high-risk patients with AML or MDS. This study was registered at www.clinicaltrials.gov as #NCT00008177.
Follicular lymphoma cells induce T-cell immunologic synapse dysfunction that can be repaired with lenalidomide: implications for the tumor microenvironment and immunotherapy
Authors: Ramsay Alan G. , Clear Andrew J. , Kelly Gavin , Fatah Rewas , Matthews Janet , MacDougall Finlay , Lister T. Andrew , Lee Abigail M. , Calaminici Maria , Gribben John G.
Published: September 2009

An important hallmark of cancer progression is the ability of tumor cells to evade immune recognition. Understanding the relationship between neoplastic cells and the immune microenvironment should facilitate the design of improved immunotherapies. Here we identify impaired T-cell immunologic synapse formation as an active immunosuppressive mechanism in follicular lymphoma (FL) and diffuse large B-cell lymphoma (DLBCL). We found a significant reduction in formation of the F-actin immune synapse in tumor-infiltrating T cells (P < .01) from lymphoma patients compared with age-matched healthy donor cells. Peripheral blood T cells exhibited this defect only in patients with leukemic-phase disease. Moreover, we demonstrate that this T-cell defect is induced after short-term tumor cell contact. After 24-hour coculture with FL cells, previously healthy T cells showed suppressed recruitment of critical signaling proteins to the synapse. We further demonstrate repair of this defect after treatment of both FL cells and T cells with the immunomodulatory drug lenalidomide. Tissue microarray analysis identified reduced expression of the T-cell synapse signature proteins, including the cytolytic effector molecule Rab27A associated with poor prognosis, in addition to reduced T-cell numbers and activity with disease transformation. Our results highlight the importance of identifying biomarkers and immunotherapeutic treatments for repairing T-cell responses in lymphoma.
Mutation of the H-bond acceptor S119 in the ADAMTS13 metalloprotease domain reduces secretion and substrate turnover in a patient with congenital thrombotic thrombocytopenic purpura
Authors: Feys Hendrik B. , Pareyn Inge , Vancraenenbroeck Renee , De Maeyer Marc , Deckmyn Hans , Van Geet Chris , Vanhoorelbeke Karen
Published: September 2009

Hereditary thrombotic thrombocytopenic purpura is caused by mutations in adisintegrin and metalloprotease with thrombospondin motifs (ADAMTS13) resulting in defective processing of von Willebrand factor (VWF) that causes intravascular platelet aggregation culminating in thrombocytopenia with shistocytic anemia. In this study the functional and structural role of a recently identified ADAMTS13 metalloprotease domain mutation S119F was investigated. Secretion from heterologous cells was hampered but not completely eliminated. Secreted S119F was active toward multimeric VWF and FRETS-VWF73 but with abnormal kinetics, having a significantly reduced overall catalytic rate (kcat; 0.88 ± 0.04 s−1 vs 2.78 ± 0.11 s−1) and slightly smaller Michaelis constant (KM; 1.4 ± 0.2μM vs 2.3 ± 0.3μM). A computational model of the metalloprotease domain demonstrates both steric and polar interaction effects caused by S119F. Interestingly, mutant S119A has properties similar to S119F (kcat = 0.82 ± 0.03 s−1 and KM = 1.1 ± 0.1μM), allowing to assign distorted kinetics to the loss of the H-bond with conserved residue W262. We conclude that the S119-W262 H-bond is crucial for maximal turnover.
Anti-inflammatory effects of antibacterials on human bronchial epithelial cells
Authors: Zimmermann Gregor S , Neurohr Claus , Villena-Hermoza Heidrun , Hatz Rudolf , Behr Juergen
Published: September 2009

Background

Human Bronchial epithelial cells (hu-BEC) have been claimed to play a significant role in the pathogenesis of chronic inflammatory airway diseases like COPD. In this context IL-8 and GM-CSF have been shown to be key cytokines. Some antibiotics which are routinely used to treat lower respiratory tract infections have been shown to exert additional immunomodulatory or anti-inflammatory effects. We investigated whether these effects can also be detected in hu-BEC.

Methods

Hu-BEC obtained from patients undergoing lung resections were transferred to air-liquid-interface (ALI) culture. These cultures were incubated with cefuroxime (CXM, 10-62.5 mg/l), azithromycin (AZM, 0.1-1.5 mg/l), levofloxacin (LVX, 1-8 mg/l) and moxifloxacin (MXF, 1-16 mg/l). The spontaneous and TNF-α (10 ng/ml) induced expression and release of IL-8 and GM-CSF were measured using PCR and ELISA in the absence or presence of these antibiotics.

Results

The spontaneous IL-8 and GM-CSF release was significantly reduced with MXF (8 mg/l) by 37 ± 20% and 45 ± 31%, respectively (both p < 0.01). IL-8 release in TNF-α stimulated hu-BEC decreased by 16 ± 8% (p < 0.05) with AZM (1.5 mg/l). With MXF a concentration dependent decrease of IL-8 release was noted up to 39 ± 7% (p < 0.05). GM-CSF release from TNF-α stimulated hu-BEC was maximally decreased by 35 ± 24% (p < 0.01) with MXF (4 mg/l).

Conclusion

Using ALI cultures of hu-BEC we observed differential effects of antibiotics on spontaneous and TNF-α induced cytokine release. Our data suggest that MXF and AZM, beyond bactericidal effects, may attenuate the inflammatory process mediated by hu-BEC.
MetaTM - a consensus method for transmembrane protein topology prediction
Authors: Klammer Martin , Messina David N , Schmitt Thomas , Sonnhammer Erik LL
Published: September 2009

Background

Transmembrane (TM) proteins are proteins that span a biological membrane one or more times. As their 3-D structures are hard to determine, experiments focus on identifying their topology (i. e. which parts of the amino acid sequence are buried in the membrane and which are located on either side of the membrane), but only a few topologies are known. Consequently, various computational TM topology predictors have been developed, but their accuracies are far from perfect. The prediction quality can be improved by applying a consensus approach, which combines results of several predictors to yield a more reliable result.

Results

A novel TM consensus method, named MetaTM, is proposed in this work. MetaTM is based on support vector machine models and combines the results of six TM topology predictors and two signal peptide predictors. On a large data set comprising 1460 sequences of TM proteins with known topologies and 2362 globular protein sequences it correctly predicts 86.7% of all topologies.

Conclusion

Combining several TM predictors in a consensus prediction framework improves overall accuracy compared to any of the individual methods. Our proposed SVM-based system also has higher accuracy than a previous consensus predictor. MetaTM is made available both as downloadable source code and as DAS server at http://MetaTM.sbc.su.se
Defects in cellular sorting and retroviral assembly induced by GGA overexpression
Authors: Joshi Anjali , Nagashima Kunio , Freed Eric O
Published: September 2009

Background

We previously demonstrated that overexpression of Golgi-localized, γ-ear containing, Arf-binding (GGA) proteins inhibits retrovirus assembly and release by disrupting the function of endogenous ADP ribosylation factors (Arfs). GGA overexpression led to the formation of large, swollen vacuolar compartments, which in the case of GGA1 sequestered HIV-1 Gag.

Results

In the current study, we extend our previous findings to characterize in depth the GGA-induced compartments and the determinants for retroviral Gag sequestration in these structures. We find that GGA-induced structures are derived from the Golgi and contain aggresome markers. GGA overexpression leads to defects in trafficking of transferrin receptor and recycling of cation-dependent mannose 6-phosphate receptor. Additionally, we find that compartments induced by GGA overexpression sequester Tsg101, poly-ubiquitin, and, in the case of GGA3, Hrs. Interestingly, brefeldin A treatment, which leads to the dissociation of endogenous GGAs from membranes, does not dissociate the GGA-induced compartments. GGA mutants that are defective in Arf binding and hence association with membranes also induce the formation of GGA-induced structures. Overexpression of ubiquitin reverses the formation of GGA-induced structures and partially rescues HIV-1 particle production. We found that in addition to HIV-1 Gag, equine infectious anemia virus Gag is also sequestered in GGA1-induced structures. The determinants in Gag responsible for sequestration map to the matrix domain, and recruitment to these structures is dependent on Gag membrane binding.

Conclusion

These data provide insights into the composition of structures induced by GGA overexpression and their ability to disrupt endosomal sorting and retroviral particle production.
Quadruplex MAPH: improvement of throughput in high-resolution copy number screening
Authors: Tyson Jess , Majerus Tamsin MO , Walker Susan , Armour John AL
Published: September 2009

Background

Copy number variation (CNV) in the human genome is recognised as a widespread and important source of human genetic variation. Now the challenge is to screen for these CNVs at high resolution in a reliable, accurate and cost-effective way.

Results

Multiplex Amplifiable Probe Hybridisation (MAPH) is a sensitive, high-resolution technology appropriate for screening for CNVs in a defined region, for a targeted population. We have developed MAPH to a highly multiplexed format ("QuadMAPH") that allows the user a four-fold increase in the number of loci tested simultaneously. We have used this method to analyse a genomic region of 210 kb, including the MSH2 gene and 120 kb of flanking DNA. We show that the QuadMAPH probes report copy number with equivalent accuracy to simplex MAPH, reliably demonstrating diploid copy number in control samples and accurately detecting deletions in Hereditary Non-Polyposis Colorectal Cancer (HNPCC) samples.

Conclusion

QuadMAPH is an accurate, high-resolution method that allows targeted screening of large numbers of subjects without the expense of genome-wide approaches. Whilst we have applied this technique to a region of the human genome, it is equally applicable to the genomes of other organisms.
Ontology and diversity of transcript-associated microsatellites mined from a globe artichoke EST database
Authors: Scaglione Davide , Acquadro Alberto , Portis Ezio , Taylor Christopher A , Lanteri Sergio , Knapp Steven J
Published: September 2009

Background

The globe artichoke (Cynara cardunculusvar.scolymusL.) is a significant crop in the Mediterranean basin. Despite its commercial importance and its both dietary and pharmaceutical value, knowledge of its genetics and genomics remains scant. Microsatellite markers have become a key tool in genetic and genomic analysis, and we have exploited recently acquired EST (expressed sequence tag) sequence data (Composite Genome Project - CGP) to develop an extensive set of microsatellite markers.

Results

A unigene assembly was created from over 36,000 globe artichoke EST sequences, containing 6,621 contigs and 12,434 singletons. Over 12,000 of these unigenes were functionally assigned on the basis of homology withArabidopsis thalianareference proteins. A total of 4,219 perfect repeats, located within 3,308 unigenes was identified and the gene ontology (GO) analysis highlighted some GO term's enrichments among different classes of microsatellites with respect to their position. Sufficient flanking sequence was available to enable the design of primers to amplify 2,311 of these microsatellites, and a set of 300 was tested against a DNA panel derived from 28C. cardunculusgenotypes. Consistent amplification and polymorphism was obtained from 236 of these assays. Their polymorphic information content (PIC) ranged from 0.04 to 0.90 (mean 0.66). Between 176 and 198 of the assays were informative in at least one of the three available mapping populations.

Conclusion

EST-based microsatellites have provided a large set ofde novogenetic markers, which show significant amounts of polymorphism both between and within the three taxa ofC. cardunculus. They are thus well suited as assays for phylogenetic analysis, the construction of genetic maps, marker-assisted breeding, transcript mapping and other genomic applications in the species.
Enrichment of a set of microRNAs during the cotton fiber development
Authors: Kwak Pieter Bas , Wang Qin Qin , Chen Xu Sheng , Qiu Cheng Xiang , Yang Zhi Min
Published: September 2009

Background

Cotton (Gossypium hirsutum) is one of the most important economic crops and provides excellent fibers for textile manufacture. In addition to its industrial and agricultural importance, the fiber cell (plant trichome) also is a biological model system for exploring gene expression and regulation. Small RNAs regulate many aspects of plant growth and development. However, whether small RNAs are involved in regulation of fiber cell development is unknown.

Results

We adopted a deep sequencing approach developed by Solexa (Illumina Inc.) to investigate global expression and complexity of small RNAs during cotton fiber initiation and development. We constructed two small RNA libraries prepared from wild type (WT) and fuzz/lintless (fl Mutant in the WT background) cotton ovules, respectively. Each library was sequenced individually and generated more than 6-7 million short sequences, resulting in a total of over 13 million sequence reads. At least 22 conserved candidate miRNA families including 111 members were identified. Seven families make up the vast majority of expressed miRNAs in developing cotton ovules. In total 120 unique target genes were predicted for most of conserved miRNAs. In addition, we identified 2 cell-type-specific novel miRNA candidates in cotton ovules. Our study has demonstrated significant differences in expression abundance of miRNAs between the wild-type and mutant, and suggests that these differentially expressed miRNAs potentially regulate transcripts distinctly involved in cotton fiber development.

Conclusion

The present study is the first to deep sequence the small RNA population of G. hirsutum ovules where cotton fibers initiate and develop. Millions of unique miRNA sequences ranging from 18~28 nt in length were detected. Our results support the importance of miRNAs in regulating the development of different cell types and indicate that identification of a comprehensive set of miRNAs in cotton fiber cells would facilitate our understanding of the regulatory mechanisms for fiber cell initiation and elongation.
Evaluation of putative reference genes for gene expression normalization in soybean by quantitative real-time RT-PCR
Authors: Hu Ruibo , Fan Chengming , Li Hongyu , Zhang Qingzhu , Fu Yong-Fu
Published: September 2009

Background

Real-time quantitative reverse transcription PCR (RT-qPCR) data needs to be normalized for its proper interpretation. Housekeeping genes are routinely employed for this purpose, but their expression level cannot be assumed to remain constant under all possible experimental conditions. Thus, a systematic validation of reference genes is required to ensure proper normalization. For soybean, only a small number of validated reference genes are available to date.

Results

A systematic comparison of 14 potential reference genes for soybean is presented. These included seven commonly used (ACT2, ACT11, TUB4, TUA5, CYP, UBQ10, EF1b) and seven new candidates (SKIP16, MTP, PEPKR1, HDC, TIP41, UKN1, UKN2). Expression stability was examined by RT-qPCR across 116 biological samples, representing tissues at various developmental stages, varied photoperiodic treatments, and a range of soybean cultivars. Expression of all 14 genes was variable to some extent, but that of SKIP16, UKN1 and UKN2 was overall the most stable. A combination of ACT11, UKN1 and UKN2 would be appropriate as a reference panel for normalizing gene expression data among different tissues, whereas the combination SKIP16, UKN1 and MTP was most suitable for developmental stages. ACT11, TUA5 and TIP41 were the most stably expressed when the photoperiod was altered, and TIP41, UKN1 and UKN2 when the light quality was changed. For six different cultivars in long day (LD) and short day (SD), their expression stability did not vary significantly with ACT11, UKN2 and TUB4 being the most stable genes. The relative gene expression level of GmFTL3, an ortholog of Arabidopsis FT (FLOWERING LOCUS T) was detected to validate the reference genes selected in this study.

Conclusion

None of the candidate reference genes was uniformly expressed across all experimental conditions, and the most suitable reference genes are conditional-, tissue-specific-, developmental-, and cultivar-dependent. Most of the new reference genes performed better than the conventional housekeeping genes. These results should guide the selection of reference genes for gene expression studies in soybean.
A transcription-dependent increase in miniature EPSC frequency accompanies late-phase plasticity in cultured hippocampal neurons
Authors: Wiegert J Simon , Hofmann Frank , Bading Hilmar , Bengtson C Peter
Published: September 2009

Background

The magnitude and longevity of synaptic activity-induced changes in synaptic efficacy is quantified by measuring evoked responses whose potentiation requires gene transcription to persist for more than 2-3 hours. While miniature EPSCs (mEPSCs) are also increased in amplitude and/or frequency during long-term potentiation (LTP), it is not known how long such changes persist or whether gene transcription is required.

Results

We use whole-cell patch clamp recordings from dissociated hippocampal cultures to characterise for the first time the persistence and transcription dependency of mEPSC upregulation during synaptic potentiation. The persistence of recurrent action potential bursting in these cultures is transcription-, translation- and NMDA receptor-dependent thus providing an accessible model for long-lasting plasticity. Blockade of GABAA-receptors with bicuculline for 15 minutes induced action potential bursting in all neurons and was maintained in 50-60% of neurons for more than 6 hours. Throughout this period, the frequency but neither the amplitude of mEPSCs nor whole-cell AMPA currents was markedly increased. The transcription blocker actinomycin D abrogated, within 2 hours of burst induction, both action potential bursting and the increase in mEPSCs. Reversible blockade of action potentials during, but not after this 2 hour transcription period suppressed the increase in mEPSC frequency and the recovery of burst activity at a time point 6 hours after induction.

Conclusion

These results indicate that increased mEPSC frequency persists well beyond the 2 hour transcription-independent phase of plasticity in this model. This long-lasting mEPSC upregulation is transcription-dependent and requires ongoing action potential activity during the initial 2 hour period but not thereafter. Thus mEPSC upregulation may underlie the long term, transcription-dependent persistence of action potential bursting. This provides mechanistic insight to link gene candidates already identified by gene chip analysis to long lasting plasticity in this in vitro model.
Identification of flowering genes in strawberry, a perennial SD plant
Authors: Mouhu Katriina , Hytönen Timo , Folta Kevin , Rantanen Marja , Paulin Lars , Auvinen Petri , Elomaa Paula
Published: September 2009

Background

We are studying the regulation of flowering in perennial plants by using diploid wild strawberry (Fragaria vescaL.) as a model. Wild strawberry is a facultative short-day plant with an obligatory short-day requirement at temperatures above 15°C. At lower temperatures, however, flowering induction occurs irrespective of photoperiod. In addition to short-day genotypes, everbearing forms of wild strawberry are known. In 'Baron Solemacher' recessive alleles of an unknown repressor,SEASONAL FLOWERING LOCUS(SFL), are responsible for continuous flowering habit. Although flower induction has a central effect on the cropping potential, the molecular control of flowering in strawberries has not been studied and the genetic flowering pathways are still poorly understood. The comparison of everbearing and short-day genotypes of wild strawberry could facilitate our understanding of fundamental molecular mechanisms regulating perennial growth cycle in plants.

Results

We have searched homologs for 118Arabidopsisflowering time genes fromFragariaby EST sequencing and bioinformatics analysis and identified 66 gene homologs that by sequence similarity, putatively correspond to genes of all known genetic flowering pathways. The expression analysis of 25 selected genes representing various flowering pathways did not reveal large differences between the everbearing and the short-day genotypes. However, putative floral identity and floral integrator genesAP1andLFYwere co-regulated during early floral development.AP1mRNA was specifically accumulating in the shoot apices of the everbearing genotype, indicating its usability as a marker for floral initiation. Moreover, we showed that flowering induction in everbearing 'Baron Solemacher' and 'Hawaii-4' was inhibited by short-day and low temperature, in contrast to short-day genotypes.

Conclusion

We have shown that many central genetic components of the flowering pathways inArabidopsiscan be identified from strawberry. However, novel regulatory mechanisms exist, likeSFLthat functions as a switch between short-day/low temperature and long-day/high temperature flowering responses between the short-day genotype and the everbearing 'Baron Solemacher'. The identification of putative flowering gene homologs andAP1as potential marker gene for floral initiation will strongly facilitate the exploration of strawberry flowering pathways.