Genome characterization of a novel Burkholderia cepacia complex genomovar isolated from dieback affected mango orchards

We characterized the genome of the antibiotic resistant, caseinolytic and non-hemolytic Burkholderia sp. strain TJI49, isolated from mango trees (Mangifera indica L.) with dieback disease. This isolate produced severe disease symptoms on the indicator plants. Next generation DNA sequencing and short-read assembly generated the 60X deep 7,631,934 nucleotide draft genome of Burkholderia sp. TJI49 which comprised three chromosomes and at least one mega plasmid. Genome annotation studies revealed a total 8,992 genes, out of which 8,940 were protein coding genes. Comparative genomics and phylogenetics identified Burkholderia sp. TJI49 as a distinct species of Burkholderia cepacia complex (BCC), closely related to B. multivorans ATCC17616. Genome-wide sequence alignment of this isolate with replicons of BCC members showed conservation of core function genes but considerable variations in accessory genes. Subsystem-based gene annotation identified the active presence of wide spread colonization island and type VI secretion system in Burkholderia sp. TJI49. Sequence comparisons revealed (a) 28 novel ORFs that have no database matches and (b) 23 ORFs with orthologues in species other than Burkholderia, indicating horizontal gene transfer events. Fold recognition of novel ORFs identified genes encoding pertactin autotransporter-like proteins (a constituent of type V secretion system) and Hap adhesion-like proteins (involved in cell–cell adhesion) in the genome of Burkholderia sp. TJI49. The genomic characterization of this isolate provided additional information related to the ‘pan-genome’ of Burkholderia species.     

Measurement of the circumferential mechanical properties of the umbilical vein: experimental and numerical analyses

Coronary artery disease is responsible for almost 30% of all deaths worldwide. The saphenous vein and umbilical vein (UV) are the most common veins using for treatment as a coronary artery bypass graft (CABG). The mechanical properties of UV belonging to its long-term patency for CABG are very important. However, there is a lack of knowledge on the linear elastic and nonlinear hyperelastic mechanical properties of the UV. In this study, three stress definitions (second Piola–Kichhoff stress, engineering stress and true stress) and four strain definitions (Almansi–Hamel strain, Green–St Venant strain, engineering strain and true strain) are used to determine the elastic modulus, maximum stress and strain of eight human UVs under circumferential loading. The nonlinear mechanical behaviour of the UV is computationally investigated using Mooney–Rivlin hyperelastic model. A numerical finite element analysis is also carried out to simulate the constitutive modelling versus its numerical results. The results show that the Almansi–Hamel strain definition overestimates the elastic modulus while Green–St Venant strain definition underestimates the elastic modulus at different stress definitions. The true stress–true strain definition, which gives more accurate measurements of the tissue's response using the instantaneous values, reveals the Young's modulus and maximum stress of 2.18 and 6.01 MPa, respectively. The Mooney–Rivlin material model is well represented by the nonlinear mechanical behaviour of the UV. The findings of this study could have implications not only for understanding the extension and rupture mechanism of UV but also for interventions and surgeries, including balloon angioplasty, bypass and stenting.     

Identifying Probable Suicide Clusters in Wales Using National Mortality Data

Background

Up to 2% of suicides in young people may occur in clusters i.e., close together in time and space. In early 2008 unprecedented attention was given by national and international news media to a suspected suicide cluster among young people living in Bridgend, Wales. This paper investigates the strength of statistical evidence for this apparent cluster, its size, and temporal and geographical limits.

Methods and findings

The analysis is based on official mortality statistics for Wales for 2000–2009 provided by the UK''s Office for National Statistics (ONS). Temporo-spatial analysis was performed using Space Time Permutation Scan Statistics with SaTScan v9.1 for suicide deaths aged 15 and over, with a sub-group analysis focussing on cases aged 15–34 years. These analyses were conducted for deaths coded by ONS as: (i) suicide or of undetermined intent (probable suicides) and (ii) for a combination of suicide, undetermined, and accidental poisoning and hanging (possible suicides). The temporo-spatial analysis did not identify any clusters of suicide or undetermined intent deaths (probable suicides). However, analysis of all deaths by suicide, undetermined intent, accidental poisoning and accidental hanging (possible suicides) identified a temporo-spatial cluster (p = 0.029) involving 10 deaths amongst 15–34 year olds centred on the County Borough of Bridgend for the period 27^th December 2007 to 19^th February 2008. Less than 1% of possible suicides in younger people in Wales in the ten year period were identified as being cluster-related.

Conclusions

There was a possible suicide cluster in young people in Bridgend between December 2007 and February 2008. This cluster was smaller, shorter in duration, and predominantly later than the phenomenon that was reported in national and international print media. Further investigation of factors leading to the onset and termination of this series of deaths, in particular the role of the media, is required.     

Validation of Verbal Autopsy Tool for Ascertaining the Causes of Stillbirth

Objective

To assess performance of the WHO revised verbal autopsy tool for ascertaining the causes of still birth in comparison with reference standard cause of death ascertained by standardized clinical and supportive data.

Methods

All stillbirths at a tertiary hospital in Karachi, Pakistan were prospectively recruited into study from August 2006- February 2008. The reference standard cause of death was established by two senior obstetricians within 48 hours using the ICD coding system. Verbal autopsy interviews using modified WHO tool were conducted by trained health workers within 2- 6 weeks of still birth and the cause of death was assigned by second panel of obstetricians. The performance was assessed in terms of sensitivity, specificity and Kappa.

Results

There were 204 still births. Of these, 80.8% of antepartum and 50.5% of intrapartum deaths were correctly diagnosed by verbal autopsy. Sensitivity of verbal autopsy was highest 68.4%, (95%CI: 46-84.6) for congenital malformation followed by obstetric complication 57.6%, (95%CI: 25-84.2). The specificity for all major causes was greater than 90%. The level of agreement was high (kappa=0.72) for anomalies and moderate (k=0.4) for all major causes of still birth, except asphyxia.

Conclusion

Our results suggest that verbal autopsy has reasonable validity in identifying and discriminating between causes of stillbirth in Pakistan. On the basis of these findings, we feel it has a place in resource constrained areas to inform strategic planning and mobilization of resources to attain Millennium Development Goals.     

Blood-Borne Hepatitis in Opiate Users in Iran: A Poor Outlook and Urgent Need to Change Nationwide Screening Policy

Objective

Iran has the highest rate of opiate use worldwide. However, most opiate users are not screened for hepatitis virus infections. This study aimed to provide accurate, detailed data on the size of the opiate user population at risk of developing these infections.

Method

This seroprevalence study was conducted in the city of Shiraz, southern Iran. All participants were screened for HBV, HCV and HIV infection. The data were analyzed with SPSS.

Result

Among 569 participants, 233 (40.9%) were injection drug users (IDU), 369 (64.8%) were heterosexual, 84 (14.7%) were bisexual and 15 (2.6%) were homosexual. One hundred nine (19.1%) were HCV antibody-positive, 18 (3.1%) were HBS antigen-positive, 72 (12.6%) were HBc antibody-positive and 23 (4%) were HIV-positive. Among IDU compared to non-IDU, positivity rates for HBS antigen (5.5 vs 1.4%), HBc antibody (22.7 vs 5.6%), HCV antibody (40.3 vs 4.4%) and HIV (7.7 vs 1.4%) were higher (P < 0.05). Most patients with HBV (80.7%) and HCV infection (83.4%) were HIV-negative. In the cumulative analysis, only history of imprisonment was a statistically significant determinant of infection by HCV or HBV in opiate users.

Conclusion

The current policy of screening only HIV-positive drug users for HBV and HCV in Iran misses most cases of HBV and HCV infection. We therefore recommend urgent revision of the nationwide protocol by the Ministry of Health in Iran to implement routine screening of all opiate users and especially IDU for these viruses, regardless of their HIV status.     

Refolding of a membrane protein in a microfluidics reactor

Membrane protein production for structural studies is often hindered by the formation of non-specific aggregates from which the protein has to be denatured and then refolded to a functional state. We developed a new approach, which uses microfluidics channels, to refold protein correctly in quantities sufficient for structural studies. Green fluorescent protein (GFP), a soluble protein, and bacteriorhodopsin (BR), a transmembrane protein, were used to demonstrate the efficiency of the process. Urea-denatured GFP refolded as the urea diffused away from the protein, forming in the channel a uniform fluorescent band when observed by confocal microscopy. Sodium dodecyl sulphate-denatured BR refolded within the channel on mixing with detergent–lipid mixed micelles. The refolding, monitored by absorbance spectroscopy, was found to be flow rate dependent. This potential of microfluidic reactors for screening protein-folding conditions and producing protein would be particularly amenable for high-throughput applications required in structural genomics. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Exogenous Application of Melatonin Induces Tolerance to Salt Stress by Improving the Photosynthetic Efficiency and Antioxidant Defense System of Maize Seedling

Journal of Plant Growth Regulation - Melatonin is a ubiquitous signaling plant hormone that plays a crucial role in regulating the growth and development of plants under stress conditions. Since a...     

Solitary Renal Fossa Recurrence of Renal Cell Carcinoma After Nephrectomy

Renal cell carcinoma without metastasis responds well to surgical excision but is known to recur postnephrectomy. In a small but significant number of patients this recurrence is not accompanied by metastasis, which is important as these people benefit from further surgery. We examined 20 articles from the current literature to ascertain how best to treat this condition. Surgical management renders better results than conservative or medical therapies. Readily available investigations such as blood tests and computed tomography can help determine the right patients for surgery in an evidence-based fashion. Current findings have allowed us to suggest a protocol for the treatment of solitary renal fossa recurrence of postnephrectomy renal cell carcinoma. There are further opportunities for study in validating our protocol, and in novel renal cell carcinoma treatment strategies that have not been tested on solitary renal fossa recurrences.Key words: Renal cancer, Recurrence, Nephrectomy, Complications, ManagementKidney cancers represent 2% of cancers worldwide; the most common type is renal cell carcinoma. Curative treatment of localized disease is a nephrectomy. Following surgery, recurrence can happen locally with an incidence of 1.61%.^1–5 A solitary renal fossa local recurrence is rare but important to distinguish from local recurrence with metastasis, which would not benefit from surgical resection. The 5-year survival postresection of local recurrence for those without metastasis compared with those with metastasis was 62% compared with 0%.⁴ The kidneys are bordered by the colon, spleen, liver, stomach, and associated neurovascular structures, all of which may be invaded in this form of recurrence; specific morbidity is related to the invasion and subsequent resection of these organs. General morbidity is caused by the surgery itself, with pain, infection, and hemorrhage being major contributors (Figure 1). This article explains predictive factors in recurrence, useful diagnostic modalities, and management, and provides recommendations and highlights opportunities for further study.Open in a separate windowFigure 1Computed tomography image of a patient with renal fossa recurrence of renal cancer after nephrectomy. Of note is the large mass identifiable in the spleen.     

Stochastic model for tumor control probability: effects of cell cycle and (a)symmetric proliferation

Background

Estimating the required dose in radiotherapy is of crucial importance since the administrated dose should be sufficient to eradicate the tumor and at the same time should inflict minimal damage on normal cells. The probability that a given dose and schedule of ionizing radiation eradicates all the tumor cells in a given tissue is called the tumor control probability (TCP), and is often used to compare various treatment strategies used in radiation therapy.

Method

In this paper, we aim to investigate the effects of including cell-cycle phase on the TCP by analyzing a stochastic model of a tumor comprised of actively dividing cells and quiescent cells with different radiation sensitivities. Moreover, we use a novel numerical approach based on the method of characteristics for partial differential equations, validated by the Gillespie algorithm, to compute the TCP as a function of time.

Results

We derive an exact phase-diagram for the steady-state TCP of the model and show that at high, clinically-relevant doses of radiation, the distinction between active and quiescent tumor cells (i.e. accounting for cell-cycle effects) becomes of negligible importance in terms of its effect on the TCP curve. However, for very low doses of radiation, these proportions become significant determinants of the TCP. We also present the results of TCP as a function of time for different values of asymmetric division factor.

Conclusion

We observe that our results differ from the results in the literature using similar existing models, even though similar parameters values are used, and the reasons for this are discussed.