Google goes cancer: improving outcome prediction for cancer patients by network-based ranking of marker genes

Predicting the clinical outcome of cancer patients based on the expression of marker genes in their tumors has received increasing interest in the past decade. Accurate predictors of outcome and response to therapy could be used to personalize and thereby improve therapy. However, state of the art methods used so far often found marker genes with limited prediction accuracy, limited reproducibility, and unclear biological relevance. To address this problem, we developed a novel computational approach to identify genes prognostic for outcome that couples gene expression measurements from primary tumor samples with a network of known relationships between the genes. Our approach ranks genes according to their prognostic relevance using both expression and network information in a manner similar to Google's PageRank. We applied this method to gene expression profiles which we obtained from 30 patients with pancreatic cancer, and identified seven candidate marker genes prognostic for outcome. Compared to genes found with state of the art methods, such as Pearson correlation of gene expression with survival time, we improve the prediction accuracy by up to 7%. Accuracies were assessed using support vector machine classifiers and Monte Carlo cross-validation. We then validated the prognostic value of our seven candidate markers using immunohistochemistry on an independent set of 412 pancreatic cancer samples. Notably, signatures derived from our candidate markers were independently predictive of outcome and superior to established clinical prognostic factors such as grade, tumor size, and nodal status. As the amount of genomic data of individual tumors grows rapidly, our algorithm meets the need for powerful computational approaches that are key to exploit these data for personalized cancer therapies in clinical practice.     

Design and current status of CONTINT: continuous versus interrupted abdominal wall closure after emergency midline laparotomy - a randomized controlled multicenter trial [NCT00544583

ABSTRACT: BACKGROUND: The optimal strategy for abdominal wall closure has been an issue of ongoing debate. Available studies do not specifically enroll patients who undergo emergency laparotomy and thus do not consider the distinct biological characteristics of these patients. The present randomized controlled trial evaluates the efficacy and safety of two commonly applied abdominal wall closure strategies in patients undergoing primary emergency midline laparotomy. Methods/design The CONTINT trial is a multicenter, open label, randomized controlled trial with a twogroup parallel design. Patients undergoing a primary emergency midline laparotomy are enrolled in the trial. The two most commonly applied strategies of abdominal wall closure after midline laparotomy are compared: the continuous, all-layer suture technique using slowly absorbable monofilament material (two Monoplus(R) loops) and the interrupted suture technique using rapidly absorbable braided material (Vicryl(R) sutures). The primary endpoint within the CONTINT trial is an incisional hernia within 12 months or a burst abdomen within 30 days after surgery. As reliable data on this primary endpoint is not available for patients undergoing emergency surgery, an adaptive interim analysis will be conducted after the inclusion of 80 patients, allowing early termination of the trial if necessary or modification of design characteristics such as recalculation of sample size. DISCUSSION: This is a randomized controlled multicenter trial with a two-group parallel design to assess the efficacy and safety of two commonly applied abdominal wall closure strategies in patients undergoing primary emergency midline laparotomy. Trial registration NCT00544583.     

Can mangroves keep pace with contemporary sea level rise? A global data review

Coastal vegetated wetlands such as mangrove forests provide multiple ecosystem services, though are potentially threatened by contemporary accelerated sea level rise (SLR), in addition to other immediate threats such as agriculture and coastal development. Several studies have revealed that mangroves are able to adapt to, and keep pace with local relative SLR through vertical surface elevation change (SEC), however data are lacking, with often only surface accretion rate (SAR) data available. We systematically review published studies of SEC and SAR from globally distributed monitoring sites using meta-analysis, and compare them with the Intergovernmental Panel on Climate Change Fifth Assessment Report (IPCC AR5) SLR scenarios. Hydro-geomorphic setting plays an important role, with basin mangroves potentially less vulnerable to SLR through land building processes. We find that SAR in both basin and fringe mangroves can cope with low SLR scenario (RCP 2.6) throughout the 100 years projection period. However, SAR can only keep pace with high SLR scenario (RCP 8.5) up to year 2070 and 2055 in basin and fringe mangrove settings respectively. These were associated with potential sediment accumulation of 41 cm and 29 cm respectively from the baseline. Mangrove degradation promoted lowering trends of SEC, while mangrove management such as rehabilitation practice stimulated positive trends of SEC. Mangrove ecosystems may be vulnerable to contemporary SLR in small island locations such as the Caribbean, East Africa and parts of the Indo-Pacific that are dominated by fringe mangroves and where SEC cannot keep pace with both low and high IPCC AR5 SLR scenarios. A global expansion of current mangrove surface elevation monitoring effort is urgently needed in order to better assess the vulnerability of mangroves, and the factors affecting their resiliency in the face of rising sea levels.     

Molecular pathogenesis of pancreatic cancer: advances and challenges

Pancreatic ductal adenocarcinoma (PDAC) is still a devastating and incurable disease with a median survival of 3-6 months and a 5-year survival rate of 1-4% when all stages are considered. Although crucial advances in our understanding of the molecular pathogenesis of the disease have been made, the exceptional aggressiveness of PDAC remains largely unexplained. Some key results will probably direct future PDAC research activities. For example, recent identification of pancreatic tumor stem cells has stimulated the debate over the cell of origin. Further, powerful new genetically engineered mouse models support the concept that stepwise progression of epithelial precursor lesions leads to invasive PDAC as a result of accumulating mutations in K-ras, INK4A/ARF, TP53 and DPC4; these models accentuate the initiating function of the K-ras mutation. Established PDAC exhibits all the classic hallmarks of cancer, including self-sufficiency in growth signals, insensitivity to anti-growth signals, evasion of apoptosis, limitless replicative potential, sustained angiogenesis, tissue invasion, and metastasis. This review provides an overview of the molecular machinery that PDAC utilizes to acquire these tumorigenic capacities. Moreover, recent advances have identified essential elements of key pathways partly recapitulating developmental signals, and of the tumor microenvironment that promotes tumor growth through the complex interplay of its different cellular components. In spite of progress in molecular research, there is still a dichotomy between the encouraging results obtained with targeted interference of numerous oncogenic pathways in vitro and a lack of significant improvement in clinical detection and survival. Thus our primary challenge remains to translate the solid knowledge of genetic and epigenetic alterations in PDAC into clinical tools which can be used for early diagnosis and effective therapy.     

Effect of land‐use and land‐cover change on mangrove blue carbon: A systematic review

Mangroves shift from carbon sinks to sources when affected by anthropogenic land‐use and land‐cover change (LULCC). Yet, the magnitude and temporal scale of these impacts are largely unknown. We undertook a systematic review to examine the influence of LULCC on mangrove carbon stocks and soil greenhouse gas (GHG) effluxes. A search of 478 data points from the peer‐reviewed literature revealed a substantial reduction of biomass (82% ± 35%) and soil (54% ± 13%) carbon stocks due to LULCC. The relative loss depended on LULCC type, time since LULCC and geographical and climatic conditions of sites. We also observed that the loss of soil carbon stocks was linked to the decreased soil carbon content and increased soil bulk density over the first 100 cm depth. We found no significant effect of LULCC on soil GHG effluxes. Regeneration efforts (i.e. restoration, rehabilitation and afforestation) led to biomass recovery after ~40 years. However, we found no clear patterns of mangrove soil carbon stock re‐establishment following biomass recovery. Our findings suggest that regeneration may help restore carbon stocks back to pre‐disturbed levels over decadal to century time scales only, with a faster rate for biomass recovery than for soil carbon stocks. Therefore, improved mangrove ecosystem management by preventing further LULCC and promoting rehabilitation is fundamental for effective climate change mitigation policy.     

Topological analysis of a haloacid permease of a Burkholderia sp. bacterium with a PhoA-LacZ reporter

Background  

2-Haloacids can be found in the natural environment as degradative products of natural and synthetic halogenated compounds. They can also be generated by disinfection of water and have been shown to be mutagenic and to inhibit glyceraldehyde-3-phosphate dehydrogenase activity. We have recently identified a novel haloacid permease Deh4p from a bromoacetate-degrading bacterium Burkholderia sp. MBA4. Comparative analyses suggested that Deh4p is a member of the Major Facilitator Superfamily (MFS), which includes thousands of membrane transporter proteins. Members of the MFS usually possess twelve putative transmembrane segments (TMS). Deh4p was predicted to have twelve TMS. In this study we characterized the topology of Deh4p with a PhoA-LacZ dual reporters system.     

Algorithms and software for support of gene identification experiments

MOTIVATION: Gene annotation is the final goal of gene prediction algorithms. However, these algorithms frequently make mistakes and therefore the use of gene predictions for sequence annotation is hardly possible. As a result, biologists are forced to conduct time-consuming gene identification experiments by designing appropriate PCR primers to test cDNA libraries or applying RT-PCR, exon trapping/amplification, or other techniques. This process frequently amounts to 'guessing' PCR primers on top of unreliable gene predictions and frequently leads to wasting of experimental efforts. RESULTS: The present paper proposes a simple and reliable algorithm for experimental gene identification which bypasses the unreliable gene prediction step. Studies of the performance of the algorithm on a sample of human genes indicate that an experimental protocol based on the algorithm's predictions achieves an accurate gene identification with relatively few PCR primers. Predictions of PCR primers may be used for exon amplification in preliminary mutation analysis during an attempt to identify a gene responsible for a disease. We propose a simple approach to find a short region from a genomic sequence that with high probability overlaps with some exon of the gene. The algorithm is enhanced to find one or more segments that are probably contained in the translated region of the gene and can be used as PCR primers to select appropriate clones in cDNA libraries by selective amplification. The algorithm is further extended to locate a set of PCR primers that uniformly cover all translated regions and can be used for RT-PCR and further sequencing of (unknown) mRNA.      

Divergent and reticulate processes in evolution of Ethiopian Lophuromys flavopunctatus species complex: evidence from mitochondrial and nuclear DNA differentiation patterns

Molecular study of mitochondrial and nuclear genes and cytogenetic analysis were performed to examine possible patterns of speciation in the diverse Lophuromys flavopunctatus species complex of Ethiopia. Phylogenetic analysis of mtDNA data resulted in an unresolved bush of ten deeply diverged haplotype groups corresponding to potential species either well supported by various types of character or 'cryptic'. The cytogenetic analysis showed representatives of five of these mtDNA lineages to share an identical karyotype (2 n  = 70, NFa = 84), that has not been found previously in Ethiopia. One of them, L.  cf.  sikapusi , being a member of the L. flavopunctatus species complex, demonstrates remarkable morphological similarity to representatives of another species complex, L. sikapusi s.l ., which might be considered as a result of convergent evolution in analogous environments. Analysis of RAPD data suggests that at least two mtDNA types might have been subject to interspecific transfer due to hybridization. In the case of two sympatric haplotypes of L. brunneus we may assume that the contemporary pattern of variation between them can be explained by relatively recent hybridization with another distinct species, L. flavopunctatus . The formation of two groups belonging to distinct mitochondrial lineages within northern populations could be associated with more complex processes including ancient hybridization.  © 2004 The Linnean Society of London, Biological Journal of the Linnean Society , 2004, 83 , 301–316.     

Improved preservation of rat epididymal sperm for high-resolution low-voltage scanning electron microscopy (HR-LVSEM)

Various fixation protocols were used in an attempt to improve preservation of rat epididymal sperm for high-resolution low-voltage scanning electron microscopy (HR-LVSEM). Wash solutions and fixatives of different composition and osmolarity were tested. Paraformaldehyde and glutaraldehyde concentrations were varied between 0.5% and 3%. Ruthenium red was tested as an additive in both primary fixation and postfixation, or in postfixation alone. HR-LVSEM revealed various degrees of ruffing, folding, blebbing, and peeling off of the plasma membrane, as well as holes of different sizes. The plasma membrane overlying the acrosome and the connecting piece proved to be particularly sensitive to varying fixation conditions. Consistent topographical differences were revealed among the different domains over the sperm head. Most of the differences were considered to be artifacts. Their consistency, however, suggests that structural and biochemical differences exist either within the membrane or in the structures subjacent to the membrane. Primary fixation turned out to be less critical than postfixation. Preservation of a smooth plasma membrane without holes could only be achieved when primary fixation in low aldehyde concentrations, with or without ruthenium red, was followed by postfixation with OsO₄ and 1,000 ppm ruthenium red. Examination of thin sections of the same material confirmed that even a considerable number of small holes are difficult to detect in transmission electron microscopy. These results show that with the recent increase in resolution of LVSEM there is need for further effort to improve sample processing. © 1993 Wiley-Liss, Inc.