Widespread epistasis among beneficial genetic variants revealed by high-throughput genome editing.

The phenotypic effect of any genetic variant can be altered by variation at other genomic loci. Known as epistasis, these genetic interactions shape the genotype-phenotype map of every species, yet their origins remain poorly understood. To investigate this, we employed high-throughput genome editing to measure the fitness effects of 1,826 naturally polymorphic variants in four strains of Saccharomyces cerevisiae. About 31% of variants affect fitness, of which 24% have strain-specific fitness effects indicative of epistasis. We found that beneficial variants are more likely to exhibit genetic interactions and that these interactions can be mediated by specific traits such as flocculation ability. This work suggests that adaptive evolution will often involve trade-offs where a variant is only beneficial in some genetic backgrounds, potentially explaining why many beneficial variants remain polymorphic. In sum, we provide a framework to understand the factors influencing epistasis with single-nucleotide resolution, revealing widespread epistasis among beneficial variants.

Gene-by-environment interactions are pervasive among natural genetic variants.

Gene-by-environment (GxE) interactions, in which a genetic variant's phenotypic effect is condition specific, are fundamental for understanding fitness landscapes and evolution but have been difficult to identify at the single-nucleotide level. Although many condition-specific quantitative trait loci (QTLs) have been mapped, these typically contain numerous inconsequential variants in linkage, precluding understanding of the causal GxE variants. Here, we introduce BARcoded Cas9 retron precise parallel editing via homology (CRISPEY-BAR), a high-throughput precision genome editing strategy, and use it to map GxE interactions of naturally occurring genetic polymorphisms impacting yeast growth. We identified hundreds of GxE variants within condition-specific QTLs, revealing unexpected genetic complexity. Moreover, we found that 93.7% of non-neutral natural variants within ergosterol biosynthesis pathway genes showed GxE interactions, including many impacting antifungal drug resistance through diverse molecular mechanisms. In sum, our results suggest an extremely complex, context-dependent fitness landscape characterized by pervasive GxE interactions while also demonstrating massively parallel genome editing as an effective means for investigating this complexity.

A rare case of a retrocrural lymph node metastasis from a chromophobe renal cell cancer: complete thoracoscopic resection with a new multi-joint articulating surgical instrument.

We report a rare case of a 69-year-old man with a solitary retrocrural lymph node metastasis in the posterior mediastinum of an oligo-metastatic chromophobe renal cell cancer that was radically resected in a curative intent using new articulating Artisential® instruments.

Divergent patterns of selection on metabolite levels and gene expression.

BACKGROUND: Natural selection can act on multiple genes in the same pathway, leading to polygenic adaptation. For example, adaptive changes were found to down-regulate six genes involved in ergosterol biosynthesis-an essential pathway targeted by many antifungal drugs-in some strains of the yeast Saccharomyces cerevisiae. However, the impact of this polygenic adaptation on metabolite levels was unknown. Here, we performed targeted mass spectrometry to measure the levels of eight metabolites in this pathway in 74 yeast strains from a genetic cross. RESULTS: Through quantitative trait locus (QTL) mapping we identified 19 loci affecting ergosterol pathway metabolite levels, many of which overlap loci that also impact gene expression within the pathway. We then used the recently developed v-test, which identified selection acting upon three metabolite levels within the pathway, none of which were predictable from the gene expression adaptation. CONCLUSIONS: These data showed that effects of selection on metabolite levels were complex and not predictable from gene expression data. This suggests that a deeper understanding of metabolism is necessary before we can understand the impacts of even relatively straightforward gene expression adaptations on metabolic pathways.

Distribution pattern and penetration depth of doxorubicin after pressurized intraperitoneal aerosol chemotherapy (PIPAC) in a postmortem swine model.

BACKGROUND: Pressurized intraperitoneal aerosol chemotherapy (PIPAC) is a novel approach delivering intraperitoneal chemotherapy by means of a pressurized aerosol. This study was conducted to evaluate the distribution pattern of doxorubicin in the abdominal cavity after PIPAC in a postmortem swine model. METHODS: Doxorubicin was aerosolized through a Micropump© (MIP) into the peritoneal cavity of two swines at a pressure of 12 mm Hg CO2 and 32 °C. To measure the distribution of the drug, 9 different positions within the abdominal cavity were sampled. In-tissue doxorubicin penetration was evaluated using fluorescence microscopy on frozen thin sections. RESULTS: A maximum of drug penetration was observed in the area around the MIP. The penetration in the small intestine reached a depth of 349 ± 65 µm. Penetration depth in the right upper abdomen and left upper abdomen were 349 ± 65 and 140 µm ± 26 µm, respectively. Distant areas to the MIP showed variable penetration rates between 50 and 150 µm. CONCLUSIONS: Doxorubicin reached all areas within the peritoneum. Highest penetration rates were measured in the area around the Micropump. Further studies are warranted to evaluate and optimize the distribution and penetration of cytotoxic agent into the tissue after PIPAC.

Tailoring Supramolecular Nanofibers for Air Filtration Applications.

The demand of new materials and processes for nanofiber fabrication to enhance the performance of air filters is steadily increasing. Typical approaches to obtain nanofibers are based on top-down processes such as melt blowing, centrifugal spinning, and electrospinning of polymer materials. However, fabrication of polymer nanofibers is limited with respect to either a sufficiently high throughput or the smallest achievable fiber diameter. This study reports comprehensively on a fast and simple bottom-up process to prepare supramolecular nanofibers in situ inside viscose/polyester microfiber nonwovens. Here, selected small molecules of the materials class of 1,3,5-benzenetrisamides are employed. The microfiber-nanofiber composites exhibit a homogeneous nanofiber distribution and morphology throughout the entire nonwoven scaffold. Small changes in molecular structure and processing solvent have a strong influence on the final nanofiber diameter and diameter distribution and, consequently, on the filtration performance. Choosing proper processing conditions, microfiber-nanofiber composites with surprisingly high filtration efficiencies of particulate matter are obtained. In addition, the microfiber-nanofiber composite integrity at elevated temperatures was determined and revealed that the morphology of supramolecular nanofibers is maintained compared to that of the utilized polymer nonwoven.

Retrospective survival analysis of 237 consecutive patients with multiple pulmonary metastases from advanced renal cell carcinoma exclusively resected by a 1318-nm laser.

OBJECTIVES: Despite the introduction of new target drugs to treat pulmonary metastatic renal cell carcinoma (mRCC), complete surgical resection still generates significantly longer survival. We analysed the survival outcome for patients with pulmonary mRCC after extended laser metastasectomy with up to 110 metastases and systematic lymphadenectomy to assess the utility and value of laser resection in the respective patient groups even with high number of metastases. METHODS: Between 1996 and 2012, 237 patients (150 men, 87 women) underwent curative intended pulmonary laser metastasectomy of mRCC. A total of 2996 metastases (range: 1-110) were resected. Kaplan-Meier analysis was performed to assess overall survival in all 237 patients and for sub-groups. Multivariate analysis of prognostic factors was performed using Cox regression models. RESULTS: Two hundred and eight patients with R0-resection (88%) had 5-year overall survival rate and median overall survival of 54% and 69 months, respectively, significantly better than 7% and 19 months in those with incomplete resections (log-rank P < 0.00001). A mean of 13 metastases per patient were resected. Five-year survival for patients with 1, 2-5, 6-9, 10-29 or 30-110 metastases resected was 62, 59, 60, 43 and 40%, respectively. In multivariate Cox-regression of all 237 patients, only completeness of resection (P < 0.0001) and number of metastases (P = 0.0029) were independent factors. CONCLUSIONS: If complete resection is achieved, laser resection can remove even high numbers of metastases with considerable and comparable long-term survival known from previous reports. This tissue-saving technique allows repeated resections in case of recurrence.

Laser processing of electrospun PCL fiber mats for tissue engineering.

PURPOSE: Processing technologies for cutting and joining electrospun fiber mats are required to produce complex three-dimensional (3D) structures, like a scaffold for heart valve tissue engineering. The ability to bond very thin porous sheets, thus forming a stable 3D geometry, offers completely new design strategies such as organ-shaped scaffolds with void chambers inside. In this study, solvent, glue and laser bonding are compared with regard to their retention force and practicability. METHODS: For this purpose, samples were prepared by applying each bonding technique. In addition, two different ways of preparing the bonding site were investigated: a portion of mats were bonded by an L-joint and the others by a T-joint; then tensile testing was performed until tearing of the bonding occurred. Additionally, the edges of laser cut fiber mats were investigated in order to evaluate the influence of thermal effects of the laser beam and ongoing changes in pore structure. RESULTS: It was found that laser cut fiber mats were slightly deformed due to thermal effects, but still had an open, porous structure at the site of the cut. Results also show that joining of fiber mats by laser led to the best bonding result with highest retention force. Application of solvent and glue led to a nonuniform and noncontinuous bonding with lower retention forces. CONCLUSIONS: A first proof of concept for a heart valve-shaped scaffold was created by laser bonding. Thus, the laser is an advantageous tool for post-processing fiber mats and produce complex 3D structures for different applications.

Enhanced activity of meprin-α, a pro-migratory and pro-angiogenic protease, in colorectal cancer.

Meprin-α is a metalloprotease overexpressed in cancer cells, leading to the accumulation of this protease in a subset of colorectal tumors. The impact of increased meprin-α levels on tumor progression is not known. We investigated the effect of this protease on cell migration and angiogenesis in vitro and studied the expression of meprin-α mRNA, protein and proteolytic activity in primary tumors at progressive stages and in liver metastases of patients with colorectal cancer, as well as inhibitory activity towards meprin-α in sera of cancer patient as compared to healthy controls. We found that the hepatocyte growth factor (HGF)-induced migratory response of meprin-transfected epithelial cells was increased compared to wild-type cells in the presence of plasminogen, and that the angiogenic response in organ-cultured rat aortic explants was enhanced in the presence of exogenous human meprin-α. In patients, meprin-α mRNA was expressed in colonic adenomas, primary tumors UICC (International Union Against Cancer) stage I, II, III and IV, as well as in liver metastases. In contrast, the corresponding protein accumulated only in primary tumors and liver metastases, but not in adenomas. However, liver metastases lacked meprin-α activity despite increased expression of the corresponding protein, which correlated with inefficient zymogen activation. Sera from cancer patients exhibited reduced meprin-α inhibition compared to healthy controls. In conclusion, meprin-α activity is regulated differently in primary tumors and metastases, leading to high proteolytic activity in primary tumors and low activity in liver metastases. By virtue of its pro-migratory and pro-angiogenic activity, meprin-α may promote tumor progression in colorectal cancer.

Mutational status of KIT and PDGFRA and expression of PDGFRA are not associated with prognosis after curative resection of primary gastrointestinal stromal tumors (GISTs).

BACKGROUND: The aim of this study was to investigate if immunohistochemical expression and mutational status of KIT and PDGFRA in GISTs are associated with the clinical course and disease-free survival after curative resection of the primary tumor without adjuvant systemic therapy. METHODS: Paraffin-embedded tumor sections of 95 GISTs were analyzed for KIT and PDGFRA expression by immunohistochemistry. PDGFRA expression was judged using a scoring system subdividing tumors in negative/weak and strong immunoreactivity groups. For mutation analysis, exons 9, 10, 11, 13, and 17 of KIT and exons 10, 12, 14, and 18 of PDGFRA were sequenced. RESULTS: Of 95 R0-resected GISTs, 69% showed strong PDGFRA immunoreactivity. Gastric GISTs revealed a significantly higher rate of strong PDGFRA immunoreactivity (P = 0.01) and longer DFS (P = 0.015) than GISTs of the small intestine. KIT mutations were detected in 43 of 63 (68.3%) completely sequenced cases while PDGFRA mutations were identified in 6 cases (10%). In multivariate analysis, neither KIT/PDGFRA expression nor mutational status of KIT or PDGFRA were independent prognostic factors. Only mitotic rate predicted recurrence independently. CONCLUSION: Our data do not support the notion that expression of PDGFRA or mutations in KIT or PDGFRA are independent prognostic factors after curative resection of primary GIST.

An exceptionally DMSO-tolerant alcohol dehydrogenase for the stereoselective reduction of ketones.

A novel short-chain alcohol dehydrogenase from Paracoccus pantotrophus DSM 11072, which is applicable for hydrogen transfer, has been identified, cloned, and overexpressed in E. coli. The enzyme stereoselectively reduces several ketones in a sustainable substrate-coupled approach using 2-propanol (5% v/v) as hydrogen donor. The enzyme maintained its activity in organic co-solvents in biphasic as well as monophasic systems and was even active in micro-aqueous media (1% v/v aqueous buffer). In general, a higher conversion was observed at higher log P values of the solvent, however, DMSO, which exhibits the lowest log P value of all solvents investigated, was not only tolerated but led to a higher conversion and relative activity (110-210%). For example, the conversion after 24 h in 15% v/v DMSO was double that for the reaction performed in buffer. This tolerance to DMSO may be attributed to the ability of the wild-type strain to adapt and grow in media with high sulfur content.

Stereoselective bioreduction of bulky-bulky ketones by a novel ADH from Ralstonia sp.

Ketones with two bulky substituents, named bulky-bulky ketones, as well as less sterically demanding ketones were successfully reduced to the corresponding optically highly enriched alcohols using a novel identified recombinant short-chain alcohol dehydrogenase RasADH from Ralstonia sp. DSM 6428 overexpressed in E. coli.

One-way biohydrogen transfer for oxidation of sec-alcohols.

Quasi-irreversible oxidation of sec-alcohols was achieved via biocatalytic hydrogen transfer reactions using alcohol dehydrogenases employing selected ketones as hydrogen acceptors, which can only be reduced but not oxidized. Thus, only 1 equiv of oxidant was required instead of a large excess. For the oxidation of both isomers of methylcarbinols a single nonstereoselective short-chain dehydrogenase/reductase from Sphingobium yanoikuyae was identified and overexpressed in E. coli.

Color Doppler imaging predicts portal invasion by pancreatic adenocarcinoma.

BACKGROUND: Tumor infiltration of the intima of the portal vein (PV) and superior mesenteric vein (SMV) by pancreatic adenocarcinoma is classically considered a criterion for unsuitability for resection and poor prognosis. This study was performed to evaluate modern color duplex imaging (CDI) for the assessment of PV/SMV infiltration by pancreatic adenocarcinomas. METHOD: From 1994 to 2005, Whipple's procedure or pylorus-preserving pancreato-duodenectomy (PPPD) was performed in 303 patients with pancreatic adenocarcinoma; 35 of these underwent partial PV/SMV resection. Applying a previously reported CDI score, we evaluated the integrity of the echogenic border layer between the vein and tumor (mural demarcation) and maximum blood flow velocity (V (max)) in the PV segment in contact with the tumor. The results were compared to the final histological findings in the resected venous walls. RESULTS: CDI findings correlated well with the histological invasion grades. By measuring V (max )and evaluating mural demarcation, we observed a sensitivity of 66.7% and 100% and a specificity of 98.3% and 93.9%, respectively, in predicting full thickness vein invasion, including the intima. V (max) above 80 cm/s and lack of mural demarcation were predictors of PV/SMV invasion. The postoperative survival rates depended on the depth of tumor infiltration into the PV/SMV. CONCLUSIONS: Modern CDI is a reliable and valid technique for evaluation of morphological and hemodynamic parameters in the portal vein segment adjacent to pancreatic adenocarcinoma. Maximal blood-flow velocity in the portal segment in contact with the tumor and absence of the echogenic vessel-parenchymal sonographic interface are parameters predictive of tumor infiltration of the portal intima.

An efficient plasmid vector for expression cloning of large numbers of PCR fragments in Escherichia coli.

The described plasmid pEamTA was designed for parallel polymerase chain reaction (PCR) cloning of open reading frames (ORFs) in Escherichia coli. It relies on the well-known TA-cloning principle, and the "T-vector" can be generated from a plasmid preparation by digestion with the restriction enzyme Eam1105I. The single 3'-T-overhangs of the vector fragment are positioned in a way that A-tailed PCR-products beginning with the start-ATG of an ORF end up in optimal position for expression from a strong tac-promoter when ligated in correct orientation. The orientation of the insert can be checked via a reconstituted NdeI site (catATG) present in correct clones. The protocol works regardless of internal restriction sites of the PCR fragment, a major advantage when cloning a number of fragments in parallel. It also does not require 5'-primer extensions and finally delivers an expression clone for the preparation of untagged protein in less than a week.

Pichia pastoris "just in time" alternative respiration.

Alternative oxidases (Aox or Aod) are present in the mitochondria of plants, fungi and many types of yeast. These enzymes transfer electrons from the ubiquinol pool directly to oxygen without contributing to the proton transfer across the mitochondrial membrane. Alternative oxidases are involved in stress responses, programmed cell death and maintenance of the cellular redox balance. The alternative oxidase gene of the methylotrophic yeast Pichia pastoris was isolated and cloned to study its regulation and the effects of deregulation of the alternative respiration by overexpression or disruption of the gene. Both disruption and overexpression had negative effects on the biomass yield; however, the growth rate and substrate uptake rate of the strain overexpressing the alternative oxidase were slightly increased. These effects were even more pronounced when higher glucose concentrations were used. The occurrence of free intracellular radicals and cell death phenomena was investigated using dihydrorhodamine 123 and the TUNEL test. The results suggest a major contribution of the alternative oxidase to P. pastoris cell viability. The negative effects of deregulated alternative respiration clearly indicated the importance of precise regulation of the alternative oxidase in this yeast.

Engineering primary metabolic pathways of industrial micro-organisms.

Metabolic engineering is a powerful tool for the optimisation and the introduction of new cellular processes. This is mostly done by genetic engineering. Since the introduction of this multidisciplinary approach, the success stories keep accumulating. The primary metabolism of industrial micro-organisms has been studied for long time and most biochemical pathways and reaction networks have been elucidated. This large pool of biochemical information, together with data from proteomics, metabolomics and genomics underpins the strategies for design of experiments and choice of targets for manipulation by metabolic engineers. These targets are often located in the primary metabolic pathways, such as glycolysis, pentose phosphate pathway, the TCA cycle and amino acid biosynthesis and mostly at major branch points within these pathways. This paper describes approaches taken for metabolic engineering of these pathways in bacteria, yeast and filamentous fungi.