Benefits and limitations of volumetric modulated arc therapy in treating bilateral breast cancer with regional lymph nodes

Purpose: The study was performed comparing dosimetric characteristics of volumetric modulated arc therapy (VMAT) and field-in-field (FiF) techniques on a patient with synchronous bilateral breast carcinoma. Methods: The patients with bilateral breast cancer treatment were included in this study. A total dose of 40.05 Gy in 15 fractions was prescribed to the Planning Target Volume (PTV) of the whole bilateral breast cancer with the supraclavicular and infraclavicular nodes, with a complementary boost of 10 Gy in 4 fractions to the surgical bed (PTVboost). For both radiotherapy techniques, several VxGy parameters were analyzed for the PTVs, together with the Conformity index (CI), the Homogeneity index (HI) and the critical organs at risk (OARs), lungs and heart. Results: The patient was treated by the VMAT technique and the daily treatment time was less than 20 minutes with daily CBCT imaging. In the VMAT plan, the PTV 95% dose covered 38.89 ± 0.81 Gy, compared to 37.26 ± 1.02 Gy in the FiF technique. The VMAT plan improved the dose homogeneity index and lower dose in lung towards high dose region. Conclusion: The study demonstrates the viability of the VMAT technique in the treatment of bilateral breast cancer. The introduced single isocentric VMAT technique is fast to deliver and it increases the dose homogeneity of the target volume with some limitations. The treatment was well tolerated, without interruption of the treatment courses caused by treatmentrelated toxicities

Gamma evaluation with Octavius 4D phantom for pretreatment of modern radiotherapy treatment techniques

Purpose: In modern radiotherapy techniques such as intensity-modulated radiation therapy (IMRT) and volume modulated arc therapy (VMAT), the quality assurance (QA) process is vital. The goal of the study was to verify the treatment planning dose delivered during delivery of complex treatment plans. The QA standard is to perform patient-specific comparisons between planned doses and doses measured in a phantom. Materials and Methods: Ninety-five complex IMRT and VMAT plans for different pathologies planned using Eclipse treatment planning system (TPS). The Octavius 4D phantom has been used to verify patient specific quality assurance of all VMAT plans calculating with different algorithms. Conclusion: Overall, good agreement was observed between measured and calculated doses in most cases with gamma values above 1 in >95% of measured points in volumetric 3D analysis and 1 in >90% in 2D analysis. The Octavius 4D phantom is an effective and efficient method for patient specific QA

Cell-Free DNA as a Diagnostic and Prognostic Biomarker in Pediatric Rhabdomyosarcoma.

PURPOSE: Total cell-free DNA (cfDNA) and tumor-derived cfDNA (ctDNA) can be used to study tumor-derived genetic aberrations. We analyzed the diagnostic and prognostic potential of cfDNA and ctDNA, obtained from pediatric patients with rhabdomyosarcoma. METHODS: cfDNA was isolated from diagnostic plasma samples from 57 patients enrolled in the EpSSG RMS2005 study. To study the diagnostic potential, shallow whole genome sequencing (shWGS) and cell-free reduced representation bisulphite sequencing (cfRRBS) were performed in a subset of samples and all samples were tested using droplet digital polymerase chain reaction to detect methylated RASSF1A (RASSF1A-M). Correlation with outcome was studied by combining cfDNA RASSF1A-M detection with analysis of our rhabdomyosarcoma-specific RNA panel in paired cellular blood and bone marrow fractions and survival analysis in 56 patients. RESULTS: At diagnosis, ctDNA was detected in 16 of 30 and 24 of 26 patients using shallow whole genome sequencing and cfRRBS, respectively. Furthermore, 21 of 25 samples were correctly classified as embryonal by cfRRBS. RASSF1A-M was detected in 21 of 57 patients. The presence of RASSF1A-M was significantly correlated with poor outcome (the 5-year event-free survival [EFS] rate was 46.2% for 21 RASSF1A-M‒positive patients, compared with 84.9% for 36 RASSF1A-M‒negative patients [P < .001]). RASSF1A-M positivity had the highest prognostic effect among patients with metastatic disease. Patients both negative for RASSF1A-M and the rhabdomyosarcoma-specific RNA panel (28 of 56 patients) had excellent outcome (5-year EFS 92.9%), while double-positive patients (11/56) had poor outcome (5-year EFS 13.6%, P < .001). CONCLUSION: Analyzing ctDNA at diagnosis using various techniques is feasible in pediatric rhabdomyosarcoma and has potential for clinical use. Measuring RASSF1A-M in plasma at initial diagnosis correlated significantly with outcome, particularly when combined with paired analysis of blood and bone marrow using a rhabdomyosarcoma-specific RNA panel

Molecular adaptation of a plant-bacterium outer membrane protease towards plague virulence factor Pla

<p>Abstract</p> <p>Background</p> <p>Omptins are a family of outer membrane proteases that have spread by horizontal gene transfer in Gram-negative bacteria that infect vertebrates or plants. Despite structural similarity, the molecular functions of omptins differ in a manner that reflects the life style of their host bacteria. To simulate the molecular adaptation of omptins, we applied site-specific mutagenesis to make Epo of the plant pathogenic <it>Erwinia pyrifoliae </it>exhibit virulence-associated functions of its close homolog, the plasminogen activator Pla of <it>Yersinia pestis</it>. We addressed three virulence-associated functions exhibited by Pla, i.e., proteolytic activation of plasminogen, proteolytic degradation of serine protease inhibitors, and invasion into human cells.</p> <p>Results</p> <p>Pla and Epo expressed in <it>Escherichia coli </it>are both functional endopeptidases and cleave human serine protease inhibitors, but Epo failed to activate plasminogen and to mediate invasion into a human endothelial-like cell line. Swapping of ten amino acid residues at two surface loops of Pla and Epo introduced plasminogen activation capacity in Epo and inactivated the function in Pla. We also compared the structure of Pla and the modeled structure of Epo to analyze the structural variations that could rationalize the different proteolytic activities. Epo-expressing bacteria managed to invade human cells only after all extramembranous residues that differ between Pla and Epo and the first transmembrane β-strand had been changed.</p> <p>Conclusions</p> <p>We describe molecular adaptation of a protease from an environmental setting towards a virulence factor detrimental for humans. Our results stress the evolvability of bacterial β-barrel surface structures and the environment as a source of progenitor virulence molecules of human pathogens.</p

Mapping the sex determination locus in the hāpuku (Polyprion oxygeneios) using ddRAD sequencing

Background&nbsp; Hāpuku (Polyprion oxygeneios) is a member of the wreckfish family (Polyprionidae) and is highly regarded as a food fish. Although adults grow relatively slowly, juveniles exhibit low feed conversion ratios and can reach market size in 1&ndash;2 years, makingP. oxygeneiosa strong candidate for aquaculture. However, they can take over 5years to reach sexual maturity in captivity and are not externally sexually dimorphic, complicating many aspects of broodstock management. Understanding the sex determination system ofP. oxygeneiosand developing accurate assays to assign genetic sex will contribute significantly towards its full-scale commercialisation.&nbsp; Results&nbsp; DNA from parents and sexed offspring (n = 57) from a single family of captive bredP. oxygeneioswas used as a template for double digestion Restriction-site Associated DNA (ddRAD) sequencing. Two libraries were constructed usingSbfI&ndash;SphI andSbfI &ndash;NcoI restriction enzyme combinations, respectively. Two runs on an Illumina MiSeq platform generated 70,266,464 raw reads, identifying 19,669 RAD loci. A combined sex linkage map (1367cM) was constructed based on 1575 Single Nucleotide Polymorphism (SNP) markers that resolved into 35 linkage groups. Sex-specific linkage maps were of similar size (1132 and 1168cM for male and female maps respectively). A single major sex-determining locus, found to be heterogametic in males, was mapped to linkage group 14. Several markers were found to be in strong linkage disequilibrium with the sex-determining locus. Allele-specific PCR assays were developed for two of these markers, SphI6331 and SphI8298, and demonstrated to accurately differentiate sex in progeny within the same pedigree. Comparative genomic analyses indicated that many of the linkage groups within theP. oxygeneiosmap share a relatively high degree of homology with those published for the European seabass (Dicentrarchus labrax).&nbsp; Conclusion&nbsp; P. oxygeneioshas an XX/XY sex determination system. Evaluation of allele-specific PCR assays, based on the two SNP markers most closely associated with phenotypic sex, indicates that a simple molecular assay for sexingP. oxygeneiosshould be readily attainable. The high degree of synteny observed withD. labraxshould aid further molecular genetic study and exploitation of hāpuku as a food fish

The interactive effects of arbuscular mycorrhiza and plant growth-promoting rhizobacteria synergistically enhance host plant defences against pathogens

Belowground interactions between plant roots, mycorrhizal fungi and plant growth-promoting rhizobacteria (PGPR) can improve plant health via enhanced nutrient acquisition and priming of the plant immune system. Two wheat cultivars differing in their ability to form mycorrhiza were (co)inoculated with the mycorrhizal fungus Rhizophagus irregularis and the rhizobacterial strain Pseudomonas putida KT2440. The cultivar with high mycorrhizal compatibility supported higher levels of rhizobacterial colonization than the low compatibility cultivar. Those levels were augmented by mycorrhizal infection. Conversely, rhizobacterial colonization of the low compatibility cultivar was reduced by mycorrhizal arbuscule formation. Single inoculations with R. irregularis or P. putida had differential growth effects on both cultivars. Furthermore, while both cultivars developed systemic priming of chitosan-induced callose after single inoculations with R. irregularis or P. putida, only the cultivar with high mycorrhizal compatibility showed a synergistic increase in callose responsiveness following co-inoculation with both microbes. Our results show that multilateral interactions between roots, mycorrhizal fungi and PGPR can have synergistic effects on growth and systemic priming of wheat

Genome-wide, high-content siRNA screening identifies the Alzheimer's genetic risk factor FERMT2 as a major modulator of APP metabolism

Genome-wide association studies (GWASs) have identified 19 susceptibility loci for Alzheimer’s disease (AD). However, understanding how these genes are involved in the pathophysiology of AD is one of the main challenges of the “post-GWAS” era. At least 123 genes are located within the 19 susceptibility loci; hence, a conventional approach (studying the genes one by one) would not be time- and cost-effective. We therefore developed a genome-wide, high-content siRNA screening approach and used it to assess the functional impact of gene under-expression on APP metabolism. We found that 832 genes modulated APP metabolism. Eight of these genes were located within AD susceptibility loci. Only FERMT2 (a β3-integrin co-activator) was also significantly associated with a variation in cerebrospinal fluid Aβ peptide levels in 2886 AD cases. Lastly, we showed that the under-expression of FERMT2 increases Aβ peptide production by raising levels of mature APP at the cell surface and facilitating its recycling. Taken as a whole, our data suggest that FERMT2 modulates the AD risk by regulating APP metabolism and Aβ peptide production

Current understanding of the human microbiome

Author Posting. © The Author(s), 2018. This is the author's version of the work. It is posted here by permission of Nature Publishing Group for personal use, not for redistribution. The definitive version was published in Nature Medicine 24 (2018): 392–400, doi:10.1038/nm.4517.Our understanding of the link between the human microbiome and disease, including obesity, inflammatory bowel disease, arthritis and autism, is rapidly expanding. Improvements in the throughput and accuracy of DNA sequencing of the genomes of microbial communities associated with human samples, complemented by analysis of transcriptomes, proteomes, metabolomes and immunomes, and mechanistic experiments in model systems, have vastly improved our ability to understand the structure and function of the microbiome in both diseased and healthy states. However, many challenges remain. In this Review, we focus on studies in humans to describe these challenges, and propose strategies that leverage existing knowledge to move rapidly from correlation to causation, and ultimately to translation.Many of the studies described here in our laboratories were supported by the NIH, NSF, DOE, and the Alfred P. Sloan Foundation.2018-10-1