Parental transfer of the antimicrobial protein LBP/BPI protects Biomphalaria glabrata eggs against oomycete infections

Copyright: © 2013 Baron et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: This work was funded by ANR (ANR-07-BLAN-0214 and ANR-12-EMMA-00O7-01), CNRS and INRA. PvW was financially supported by the BBSRC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Peer reviewedPublisher PD

Treatment of advanced hepatocellular carcinoma with very low levels of amplitude-modulated electromagnetic fields

BACKGROUND: Therapeutic options for patients with advanced hepatocellular carcinoma (HCC) are limited. There is emerging evidence that the growth of cancer cells may be altered by very low levels of electromagnetic fields modulated at specific frequencies. METHODS: A single-group, open-label, phase I/II study was performed to assess the safety and effectiveness of the intrabuccal administration of very low levels of electromagnetic fields amplitude modulated at HCC-specific frequencies in 41 patients with advanced HCC and limited therapeutic options. Three-daily 60-min outpatient treatments were administered until disease progression or death. Imaging studies were performed every 8 weeks. The primary efficacy end point was progression-free survival >= 6 months. Secondary efficacy end points were progression-free survival and overall survival. RESULTS: Treatment was well tolerated and there were no NCI grade 2, 3 or 4 toxicities. In all, 14 patients (34.1%) had stable disease for more than 6 months. Median progression-free survival was 4.4 months (95% CI 2.1-5.3) and median overall survival was 6.7 months (95% CI 3.0-10.2). There were three partial and one near complete responses. CONCLUSION: Treatment with intrabuccally administered amplitude-modulated electromagnetic fields is safe, well tolerated, and shows evidence of antitumour effects in patients with advanced HCC. British Journal of Cancer (2011) 105, 640-648. doi:10.1038/bjc.2011.292 www.bjcancer.com Published online 9 August 2011 (C) 2011 Cancer Research U

Free energy estimation of short DNA duplex hybridizations

<p>Abstract</p> <p>Background</p> <p>Estimation of DNA duplex hybridization free energy is widely used for predicting cross-hybridizations in DNA computing and microarray experiments. A number of software programs based on different methods and parametrizations are available for the theoretical estimation of duplex free energies. However, significant differences in free energy values are sometimes observed among estimations obtained with various methods, thus being difficult to decide what value is the accurate one.</p> <p>Results</p> <p>We present in this study a quantitative comparison of the similarities and differences among four published DNA/DNA duplex free energy calculation methods and an extended Nearest-Neighbour Model for perfect matches based on triplet interactions. The comparison was performed on a benchmark data set with 695 pairs of short oligos that we collected and manually curated from 29 publications. Sequence lengths range from 4 to 30 nucleotides and span a large GC-content percentage range. For perfect matches, we propose an extension of the Nearest-Neighbour Model that matches or exceeds the performance of the existing ones, both in terms of correlations and root mean squared errors. The proposed model was trained on experimental data with temperature, sodium and sequence concentration characteristics that span a wide range of values, thus conferring the model a higher power of generalization when used for free energy estimations of DNA duplexes under non-standard experimental conditions.</p> <p>Conclusions</p> <p>Based on our preliminary results, we conclude that no statistically significant differences exist among free energy approximations obtained with 4 publicly available and widely used programs, when benchmarked against a collection of 695 pairs of short oligos collected and curated by the authors of this work based on 29 publications. The extended Nearest-Neighbour Model based on triplet interactions presented in this work is capable of performing accurate estimations of free energies for perfect match duplexes under both standard and non-standard experimental conditions and may serve as a baseline for further developments in this area of research.</p

Treatment of advanced hepatocellular carcinoma with very low levels of amplitude-modulated electromagnetic

BACKGROUND: Therapeutic options for patients with advanced hepatocellular carcinoma (HCC) are limited. There is emerging evidence that the growth of cancer cells may be altered by very low levels of electromagnetic fields modulated at specific frequencies. METHODS: A single-group, open-label, phase I/II study was performed to assess the safety and effectiveness of the intrabuccal administration of very low levels of electromagnetic fields amplitude modulated at HCC-specific frequencies in 41 patients with advanced HCC and limited therapeutic options. Three-daily 60-min outpatient treatments were administered until disease progression or death. Imaging studies were performed every 8 weeks. The primary efficacy end point was progression-free survival X6 months. Secondary efficacy end points were progression-free survival and overall survival. RESULTS: Treatment was well tolerated and there were no NCI grade 2, 3 or 4 toxicities. In all, 14 patients (34.1%) had stable disease for more than 6 months. Median progression-free survival was 4.4 months (95% CI 2.1 -5.3) and median overall survival was 6.7 months (95% CI 3.0 -10.2). There were three partial and one near complete responses. CONCLUSION: Treatment with intrabuccally administered amplitude-modulated electromagnetic fields is safe, well tolerated, and shows evidence of antitumour effects in patients with advanced HCC. British Journal of Cancer (2011Cancer ( ) 105, 640 -648. doi:10.1038Cancer ( /bjc.2011 Published online 9 August 2011 &amp; 2011 Cancer Research UK Keywords: hepatocellular carcinoma; phase II study; radiofrequency electromagnetic fields; tumour-specific modulation frequencies; 27.12 MHz Treatment of inoperable or metastatic solid tumours is a major challenge in oncology, which is limited by the small number of therapeutic agents that are both well tolerated and capable of longterm control of tumour growth. Hepatocellular carcinoma (HCC) is the second most common cause of cancer death in men and the sixth in women worldwide Therapies for HCC are limited. Resections of the primary tumour or liver transplantation are the preferred therapeutic approaches in patients who are surgical candidates The intrabuccal administration of low and safe levels of electromagnetic fields, which are amplitude-modulated at disease-specific frequencies (RF AM EMF) PATIENTS AND METHODS Patients The study was aimed at offering treatment to patients with ChildPugh A or B advanced HCC and limited therapeutic options. Patients were classified as having advanced disease if they were not eligible for surgical resection or had disease progression after surgical or locoregional therapies or had disease progression after chemotherapy or sorafenib therapy. Patients with measurable, inoperable HCC were eligible for enrolment. Previous local or systemic treatments were allowed as long as they were discontinued at least 4 weeks before enrolment. Inclusion criteria included Eastern Cooperative Oncology Group performance status of 0, 1, or 2 and biopsy-confirmed HCC. Also allowed were patients with no pathological confirmation of HCC with a level of a-fetoprotein higher than 400 ng ml À1 and characteristic imaging findings as assessed by multislice computer tomography (CT) scan or intravenous contrast ultrasound (US). As per the University of São Paulo Department of Transplantation and Liver Surgery guidelines, liver biopsies are avoided in patients eligible for transplant or with severely impaired liver function. Exclusion criteria included confirmed or suspected brain metastasis, Child -Pugh C, previous liver transplant, and pregnancy. Study design This was an investigator-initiated, single centre, uncontrolled phase I/II trial in patients with advanced HCC. The trial was approved by the local human investigation committee and conducted in accordance with the Declaration of Helsinki. Written informed consent was obtained from each patient. The protocol was registered: clinicaltrial.gov identifier no. NCT00534664. Translational Therapeutics Administration of AM EMFs The generator of AM EMFs consists of a battery-driven radiofrequency (RF) EMF generator connected to a 1.5 m long 50 O coaxial cable, to the other end of which a stainless-steel spoonshaped mouthpiece is connected via an impedance transformer ( We have previously reported the discovery of HCC-specific modulation frequencies in 46 patients with HCC using a patientbased biofeedback approach and shown the feasibility of using AM EMFs for the treatment of patients with cancer The treatment method consists of the administration of AM EMFs by means of an electrically conducting mouthpiece, which is Translational Therapeutics in direct contact with the oral mucosa ( Efficacy end points and disease assessment The primary end point of this trial was the proportion of patients progression-free at 6 months. Secondary end points were progression-free survival (PFS) (first day of treatment until progression of disease or death) and overall survival (OS) (first day of receiving treatment to death). Objective response was assessed using the Response Evaluation Criteria in Solid Tumours group classification for patients with disease assessed by either helical multiphasic CT (Therasse et al, 2000). Whenever contrastenhanced US radiological assessment was used, it was performed and reviewed by the same radiologist specialised in HCC (MCC) as this imaging modality is investigator dependent. Tumour measurements were performed at baseline and every 8 weeks. Only patients with at least one repeat tumour measurement during therapy were considered for response analysis. Throughout the study, lesions measured at baseline were evaluated using the same technique (CT or contrast-enhanced US). Overall tumour response was scored as a complete response (CR), partial response (PR), or stable disease (SD) if the response was confirmed at least 4 weeks later. Alpha-fetoprotein (AFP) levels were measured every 8 weeks in all patients throughout the study, but changes in AFP were not an end point for assessment of response. Pain was assessed according to the NCI-CTCAE v.3.0 (http://ctep.cancer.gov/protocolDevelopment/electronic_applications/docs/ctcaev3.pdf). Statistical analyses and efficacy assessment All eligible patients who began treatment were considered assessable for the primary and secondary end points. A Simon two-stage phase II minimax design was used (Simon, 1989) to evaluate the rate of progression-free survival at 6 months. The interim analysis was performed once enrolment into the first stage was completed. In the first stage, 23 patients were observed. If two or fewer patients had progression-free survival X6 months, the trial would be terminated early for lack of efficacy. If the progression-free survival of 3 or more of the first 23 patients was equal or greater than 6 months, then an additional 18 patients would be enrolled to a maximum of 41 patients. If eight or more of the 41 had PFS of at least 6 months, we would conclude that the treatment was efficacious. This design had a Type I error rate of 5% and a Type II error rate of 10% for the null hypothesis of a 6-month PFS rate of 10% vs the alternative of 27.5%. KaplanMeier estimates of survival, PFS, and duration of response were calculated with standard errors based on Greenwood&apos;s formula. These calculations were performed using the Proc Lifetest in SAS 9.2 (SAS Institute Inc., Cary, NC, USA). RESULTS Patient recruitment and follow-up From October 2005 to July 2007, 267 patients were assessed for eligibility ( Translational Therapeutics A total of 31 patients (75.6%) had radiological evidence of disease progression at the time of enrolment as defined by comparison of baseline imaging studies, with imaging studies obtained within the previous 6 months; 34 (82.9%) patients had received therapy before enrolment, five (14.6%) of them systemic chemotherapy or sorafenib Treatment efficacy Six of the first 23 patients (26.1%) had progression-free survival X6 months, which led us to continue enrolling patients up to the preplanned total of 41 patients A total of 28 patients were evaluable for tumour response Translational Therapeutics patients without biopsy-proven disease subsequently withdrew consent after 4.9 months to undergo liver transplantation. The patient died of progression of disease 9.4 months later before undergoing liver transplantation. One patient with Child -Pugh B disease had a partial response lasting 11.7 months and died of gastrointestinal bleeding. One patient died of disease progression at 44.6 months. Overall, there were six long-term survivors with an OS greater than 24 months and four long-term survivors with an OS greater than 3 years. Importantly, five of the six (83%) long-term survivors had radiological evidence of disease progression at the time of study enrolment In all, 11 patients reported pain before treatment initiation, 3 patients reported grade 3, 5 patients reported grade 2, and 3 patients grade 1. Five patients reported complete disappearance of pain and two patients reported decreased pain shortly after treatment initiation. Two patients reported no changes and two patients reported increased pain. There were no treatment-related grade 2, 3, or 4 toxicities. The only treatment-related adverse events were grade 1 mucositis (one patient) and grade 1 somnolence (one patient) over a total of 266.8 treatment months. DISCUSSION Treatment with AM EMFs did not show any significant toxicity despite long-term treatment. The lack of toxicity experienced by the 41 patients presented in this report as well as the 28 patients from our previous report These data are comparable to recent phase II studies evaluating the effectiveness of standard chemotherapy as well as novel targeted therapies in HCC The majority of patients enrolled in this study had either failed standard treatment options or had severely impaired liver function that limited their ability to tolerate any form of systemic or intrahepatic therapy. Indeed, 16 patients (39.0%) had Child -Pugh B8 or B9 disease. Among these patients, the median progressionfree survival was 4.4 months (95% CI 1.6 -7.6 months), which is identical to that of the entire group. Five of these 16 patients (31.3%) received therapy for more than 7.5 months, which indicates that this therapy is well tolerated even in patients with severely impaired liver function. Previous treatment with standard chemotherapy or sorafenib does not seem to impact the effectiveness of AM EMFs in the treatment of HCC. Indeed, three of the four patients who had a Translational Therapeutics partial response while receiving AM EMFs had received previous systemic therapies (chemotherapy and sorafenib) and one had received intrahepatic therapy with 131 I-lipiodol. Tumour shrinkage as assessed by radiological imaging as well as changes in AFP levels were documented in patients with advanced HCC receiving RF EMF modulated at HCC-specific frequencies administered by an intrabuccal probe. Antitumour activity in patients with advanced HCC was exemplified by partial responses observed in four patients (9.8%) and decreases in AFP levels greater than 20% in four patients. A total of 18 patients (43.9%) either had objective response or SD X6 months. Importantly, this therapeutic approach has long-lasting therapeutic effects in several patients with metastatic cancer. Two of these patients, one with recurrent thyroid cancer metastatic to the lungs Our phase I/II study has several limitations. First, only 19 of the 41 patients had biopsy-proven HCC, and the others were diagnosed by clinical criteria, an approach similar to that used in a recently reported phase II trial evaluating the clinical and biological effects of bevacizumab in unresectable HCC (Siegel et al, 2008). Importantly, analysis restricted to these 19 patients shows rates of progression-free survival at 6 months, median progression-free survival and OS that are similar to those without biopsyproven HCC Antitumour response is considered the primary end point for phase II studies to proceed to further investigations. Studies applying Cox proportional hazards analysis indicate that this end point is consistently associated with survival in trials of locoregional therapies for HCC (Llovet et al, 2002) and a recent consensus article suggests that randomised studies are necessary to capture the true efficacy of novel therapies in HCC (Llovet et al, 2008a). In summary, the encouraging findings from this study warrant a randomised study to determine the impact of AM EMFs on OS and time to symptomatic progression. ACKNOWLEDGEMENTS We thank Drs Al B Benson III, Northwestern University and Leonard B Saltz, Memorial Sloan-Kettering Cancer Center for reviewing the manuscript. There is clinical evidence that very low and safe levels of amplitude-modulated electromagnetic fields administered via an intrabuccal spoon-shaped probe may elicit therapeutic responses in patients with cancer. However, there is no known mechanism explaining the anti-proliferative effect of very low intensity electromagnetic fields. METHODS: To understand the mechanism of this novel approach, hepatocellular carcinoma (HCC) cells were exposed to 27.12 MHz radiofrequency electromagnetic fields using in vitro exposure systems designed to replicate in vivo conditions. Cancer cells were exposed to tumour-specific modulation frequencies, previously identified by biofeedback methods in patients with a diagnosis of cancer. Control modulation frequencies consisted of randomly chosen modulation frequencies within the same 100 Hz -21 kHz range as cancer-specific frequencies. RESULTS: The growth of HCC and breast cancer cells was significantly decreased by HCC-specific and breast cancer-specific modulation frequencies, respectively. However, the same frequencies did not affect proliferation of nonmalignant hepatocytes or breast epithelial cells. Inhibition of HCC cell proliferation was associated with downregulation of XCL2 and PLP2. Furthermore, HCC-specific modulation frequencies disrupted the mitotic spindle. CONCLUSION: These findings uncover a novel mechanism controlling the growth of cancer cells at specific modulation frequencies without affecting normal tissues, which may have broad implications in oncology. Conflict of interes

Aphids acquired symbiotic genes via lateral gene transfer

<p>Abstract</p> <p>Background</p> <p>Aphids possess bacteriocytes, which are cells specifically differentiated to harbour the obligate mutualist <it>Buchnera aphidicola </it>(γ-Proteobacteria). <it>Buchnera </it>has lost many of the genes that appear to be essential for bacterial life. From the bacteriocyte of the pea aphid <it>Acyrthosiphon pisum</it>, we previously identified two clusters of expressed sequence tags that display similarity only to bacterial genes. Southern blot analysis demonstrated that they are encoded in the aphid genome. In this study, in order to assess the possibility of lateral gene transfer, we determined the full-length sequences of these transcripts, and performed detailed structural and phylogenetic analyses. We further examined their expression levels in the bacteriocyte using real-time quantitative RT-PCR.</p> <p>Results</p> <p>Sequence similarity searches demonstrated that these fully sequenced transcripts are significantly similar to the bacterial genes <it>ldcA </it>(product, LD-carboxypeptidase) and <it>rlpA </it>(product, rare lipoprotein A), respectively. <it>Buchnera </it>lacks these genes, whereas many other bacteria, including <it>Escherichia coli</it>, a close relative of <it>Buchnera</it>, possess both <it>ldcA </it>and <it>rlpA</it>. Molecular phylogenetic analysis clearly demonstrated that the aphid <it>ldcA </it>was derived from a rickettsial bacterium closely related to the extant <it>Wolbachia </it>spp. (α-Proteobacteria, Rickettsiales), which are intracellular symbionts of various lineages of arthropods. The evolutionary origin of <it>rlpA </it>was not fully resolved, but it was clearly demonstrated that its double-ψ β-barrel domain is of bacterial origin. Real-time quantitative RT-PCR demonstrated that <it>ldcA </it>and <it>rlpA </it>are expressed 11.6 and 154-fold higher in the bacteriocyte than in the whole body, respectively. LdcA is an enzyme required for recycling murein (peptidoglycan), which is a component of the bacterial cell wall. As <it>Buchnera </it>possesses a cell wall composed of murein but lacks <it>ldcA</it>, a high level of expression of the aphid <it>ldcA </it>in the bacteriocyte may be essential to maintain <it>Buchnera</it>. Although the function of RlpA is not well known, conspicuous up-regulation of the aphid <it>rlpA </it>in the bacteriocyte implies that this gene is also essential for <it>Buchnera</it>.</p> <p>Conclusion</p> <p>In this study, we obtained several lines of evidence indicating that aphids acquired genes from bacteria via lateral gene transfer and that these genes are used to maintain the obligately mutualistic bacterium, <it>Buchnera</it>.</p

Life-History Evolution on Tropidurinae Lizards: Influence of Lineage, Body Size and Climate

The study of life history variation is central to the evolutionary theory. In many ectothermic lineages, including lizards, life history traits are plastic and relate to several sources of variation including body size, which is both a factor and a life history trait likely to modulate reproductive parameters. Larger species within a lineage, for example tend to be more fecund and have larger clutch size, but clutch size may also be influenced by climate, independently of body size. Thus, the study of climatic effects on lizard fecundity is mandatory on the current scenario of global climatic change. We asked how body and clutch size have responded to climate through time in a group of tropical lizards, the Tropidurinae, and how these two variables relate to each other. We used both traditional and phylogenetic comparative methods. Body and clutch size are variable within Tropidurinae, and both traits are influenced by phylogenetic position. Across the lineage, species which evolved larger size produce more eggs and neither trait is influenced by temperature components. A climatic component of precipitation, however, relates to larger female body size, and therefore seems to exert an indirect relationship on clutch size. This effect of precipitation on body size is likely a correlate of primary production. A decrease in fecundity is expected for Tropidurinae species on continental landmasses, which are predicted to undergo a decrease in summer rainfall

Striking HIV-1 Entry by Targeting HIV-1 gp41. But, Where Should We Target?

HIV-1 gp41 facilitates the viral fusion through a conformational switch involving the association of three C-terminal helices along the conserved hydrophobic grooves of three N-terminal helices coiled-coil. The control of these structural rearrangements is thought to be central to HIV-1 entry and, therefore, different strategies of intervention are being developed. Herewith, we describe a procedure to simulate the folding of an HIV-1 gp41 simplified model. This procedure is based on the construction of plausible conformational pathways, which describe protein transition between non-fusogenic and fusogenic conformations. The calculation of the paths started with 100 molecular dynamics simulations of the non-fusogenic conformation, which were found to converge to different intermediate states. Those presenting defined criteria were selected for separate targeted molecular dynamics simulations, subjected to a force constant imposing a movement towards the gp41 fusogenic conformation. Despite significant diversity, a preferred sequence of events emerged when the simulations were analyzed in terms of the formation, breakage and evolution of the contacts. We pointed out 29 residues as the most relevant for the movement of gp41; also, 2696 possible interactions were reduced to only 48 major interactions, which reveals the efficiency of the method. The analysis of the evolution of the main interactions lead to the detection of four main behaviors for those contacts: stable, increasing, decreasing and repulsive interactions. Altogether, these results suggest a specific small cavity of the HIV-1 gp41 hydrophobic groove as the preferred target to small molecules

Mechanisms and therapeutic applications of electromagnetic therapy in Parkinson's disease

© 2015 Vadalà et al. Electromagnetic therapy is a non-invasive and safe approach for the management of several pathological conditions including neurodegenerative diseases. Parkinson's disease is a neurodegenerative pathology caused by abnormal degeneration of dopaminergic neurons in the ventral tegmental area and substantia nigra pars compacta in the midbrain resulting in damage to the basal ganglia. Electromagnetic therapy has been extensively used in the clinical setting in the form of transcranial magnetic stimulation, repetitive transcranial magnetic stimulation, high-frequency transcranial magnetic stimulation and pulsed electromagnetic field therapy which can also be used in the domestic setting. In this review, we discuss the mechanisms and therapeutic applications of electromagnetic therapy to alleviate motor and non-motor deficits that characterize Parkinson's disease