Dissection of DNA damage and repair pathways in live cells by femtosecond laser microirradiation and free-electron modeling.

Understanding and predicting the outcome of the interaction of light with DNA has a significant impact on the study of DNA repair and radiotherapy. We report on a combination of femtosecond pulsed laser microirradiation at different wavelengths, quantitative imaging, and numerical modeling that yields a comprehensive picture of photon-mediated and free-electron-mediated DNA damage pathways in live cells. Laser irradiation was performed under highly standardized conditions at four wavelengths between 515 nm and 1,030 nm, enabling to study two-photon photochemical and free-electron-mediated DNA damage in situ. We quantitatively assessed cyclobutane pyrimidine dimer (CPD) and γH2AX-specific immunofluorescence signals to calibrate the damage threshold dose at these wavelengths and performed a comparative analysis of the recruitment of DNA repair factors xeroderma pigmentosum complementation group C (XPC) and Nijmegen breakage syndrome 1 (Nbs1). Our results show that two-photon-induced photochemical CPD generation dominates at 515 nm, while electron-mediated damage dominates at wavelengths ≥620 nm. The recruitment analysis revealed a cross talk between nucleotide excision and homologous recombination DNA repair pathways at 515 nm. Numerical simulations predicted electron densities and electron energy spectra, which govern the yield functions of a variety of direct electron-mediated DNA damage pathways and of indirect damage by •OH radicals resulting from laser and electron interactions with water. Combining these data with information on free electron-DNA interactions gained in artificial systems, we provide a conceptual framework for the interpretation of the wavelength dependence of laser-induced DNA damage that may guide the selection of irradiation parameters in studies and applications that require the selective induction of DNA lesions.

PARP1 catalytic variants reveal branching and chain length-specific functions of poly(ADP-ribose) in cellular physiology and stress response.

Poly(ADP-ribosyl)ation regulates numerous cellular processes like genome maintenance and cell death, thus providing protective functions but also contributing to several pathological conditions. Poly(ADP-ribose) (PAR) molecules exhibit a remarkable heterogeneity in chain lengths and branching frequencies, but the biological significance of this is basically unknown. To unravel structure-specific functions of PAR, we used PARP1 mutants producing PAR of different qualities, i.e. short and hypobranched (PARP1\G972R), short and moderately hyperbranched (PARP1\Y986S), or strongly hyperbranched PAR (PARP1\Y986H). By reconstituting HeLa PARP1 knockout cells, we demonstrate that PARP1\G972R negatively affects cellular endpoints, such as viability, cell cycle progression and genotoxic stress resistance. In contrast, PARP1\Y986S elicits only mild effects, suggesting that PAR branching compensates for short polymer length. Interestingly, PARP1\Y986H exhibits moderate beneficial effects on cell physiology. Furthermore, different PARP1 mutants have distinct effects on molecular processes, such as gene expression and protein localization dynamics of PARP1 itself, and of its downstream factor XRCC1. Finally, the biological relevance of PAR branching is emphasized by the fact that branching frequencies vary considerably during different phases of the DNA damage-induced PARylation reaction and between different mouse tissues. Taken together, this study reveals that PAR branching and chain length essentially affect cellular functions, which further supports the notion of a 'PAR code'.

Highly standardized multicolor femtosecond fiber system for selective microphotomanipulation of deoxyribonucleic acid and chromatin.

We present a three-color femtosecond Er/Yb:fiber laser enabling highly specific and standardized nonlinear optical manipulation of live cells. The system simultaneously provides bandwidth-limited 80-fs pulses with identical intensity envelope centered at wavelengths of 515, 775, and 1035 nm in the focus of a confocal microscope. We achieve this goal by combining high-order dispersion control via, for example, chirped fiber Bragg gratings with proper bandwidth management in each nonlinear conversion step. Wavelength-selective and noninterfering induction of deoxyribonucleic acid (DNA) photoproducts and DNA strand breaks, as well as fluorescence photoactivation of a photoactivatable green fluorescent protein (PA-GFP)-histone fusion protein, are demonstrated. The capability to introduce different types of DNA lesions and perform photoswitching experiments in a selective manner is essential for quantitative studies on DNA repair and chromatin dynamics.

Analyzing structure-function relationships of artificial and cancer-associated PARP1 variants by reconstituting TALEN-generated HeLa PARP1 knock-out cells.

Genotoxic stress activates PARP1, resulting in the post-translational modification of proteins with poly(ADP-ribose) (PAR). We genetically deleted PARP1 in one of the most widely used human cell systems, i.e. HeLa cells, via TALEN-mediated gene targeting. After comprehensive characterization of these cells during genotoxic stress, we analyzed structure-function relationships of PARP1 by reconstituting PARP1 KO cells with a series of PARP1 variants. Firstly, we verified that the PARP1\E988K mutant exhibits mono-ADP-ribosylation activity and we demonstrate that the PARP1\L713F mutant is constitutively active in cells. Secondly, both mutants exhibit distinct recruitment kinetics to sites of laser-induced DNA damage, which can potentially be attributed to non-covalent PARP1-PAR interaction via several PAR binding motifs. Thirdly, both mutants had distinct functional consequences in cellular patho-physiology, i.e. PARP1\L713F expression triggered apoptosis, whereas PARP1\E988K reconstitution caused a DNA-damage-induced G2 arrest. Importantly, both effects could be rescued by PARP inhibitor treatment, indicating distinct cellular consequences of constitutive PARylation and mono(ADP-ribosyl)ation. Finally, we demonstrate that the cancer-associated PARP1 SNP variant (V762A) as well as a newly identified inherited PARP1 mutation (F304L\V762A) present in a patient with pediatric colorectal carcinoma exhibit altered biochemical and cellular properties, thereby potentially supporting human carcinogenesis. Together, we establish a novel cellular model for PARylation research, by revealing strong structure-function relationships of natural and artificial PARP1 variants.

Real-Time Cellular Imaging of Protein Poly(ADP-ribos)ylation.

Poly(ADP-ribos)ylation (PARylation) is an important posttranslational protein modification, and is involved in major cellular processes such as gene regulation and DNA repair. Its dysregulation has been linked to several diseases, including cancer. Despite its importance, methods to observe PARylation dynamics within cells are rare. By following a chemical biology approach, we developed a fluorescent NAD(+) analogue that proved to be a competitive building block for protein PARylation in vitro and in cells. This allowed us to directly monitor the turnover of PAR in living cells at DNA damage sites after near-infrared (NIR) microirradiation. Additionally, covalent and noncovalent interactions of selected target proteins with PAR chains were visualized in cells by using FLIM-FRET microscopy. Our results open up new opportunities for the study of protein PARylation in real time and in live cells, and will thus contribute to a better understanding of its significance in a cellular context.

Longitudinal assessment of colonoscopy quality indicators: a report from the Gastroenterology Practice Management Group.

BACKGROUND: There is increasing demand for colonoscopy quality measures for procedures performed in ambulatory surgery centers. Benchmarks such as adenoma detection rate (ADR) are traditionally reported as static, one-dimensional point estimates at a provider or practice level. OBJECTIVE: To evaluate 6-year variability of ADRs for 370 gastroenterologists from across the nation. DESIGN: Observational cross-sectional analysis. SETTING: Collaborative quality metrics database from 2007 to 2012. PATIENTS: Patients who underwent colonoscopies in ambulatory surgery centers. INTERVENTIONS: Colonoscopy. MAIN OUTCOME MEASUREMENTS: The number of colonoscopies with an adenomatous polyp divided by the total number of colonoscopies (ADR-T), inclusive of indication and patient's sex. RESULTS: Data from 368,157 colonoscopies were included for analysis from 11 practices. Three practice sites (5, 8, and 10) were significantly above and 2 sites (3, 7) were significantly below mean ADR-T, with a 95% confidence interval (CI). High-performing sites had 9.0% higher ADR-T than sites belonging to the lowest quartile (P < .001). The mean ADR-T remained stable for 9 of 11 sites. Regression analysis showed that the 2 practice sites where ADR-T varied had significant improvements in ADR-T during the 6-year period. For each, mean ADR-T improved an average of 0.5% per quarter for site 2 (P = .001) and site 3 (P = .021), which were average and low performers, respectively. LIMITATIONS: Summary-level data, which does not allow cross-reference of variables at an individual level. CONCLUSION: We found performance disparities among practice sites remaining relatively consistent over a 6-year period. The ability of certain sites to sustain their high-performance over 6 years suggests that further research is needed to identify key organizational processes and physician incentives that improve the quality of colonoscopy.

Femtosecond Cr:LiSAF and Cr:LiCAF lasers pumped by tapered diode lasers.

We report compact, low-cost and efficient Cr:Colquiriite lasers that are pumped by high brightness tapered laser diodes. The tapered laser diodes provided 1 to 1.2 W of output power around 675 nm, at an electrical-to-optical conversion efficiency of about 30%. Using a single tapered diode laser as the pump source, we have demonstrated output powers of 500 mW and 410 mW together with slope efficiencies of 47% and 41% from continuous wave (cw) Cr:LiSAF and Cr:LiCAF lasers, respectively. In cw mode-locked operation, sub-100-fs pulse trains with average power between 200 mW and 250 mW were obtained at repetition rates around 100 MHz. Upon pumping the Cr:Colquiriite lasers with two tapered laser diodes (one from each side of the crystal), we have observed scaling of cw powers to 850 mW in Cr:LiSAF and to 650 mW in Cr:LiCAF. From the double side pumped Cr:LiCAF laser, we have also obtained ~220 fs long pulses with 5.4 nJ of pulse energy at 77 MHz repetition rate. These are the highest energy levels reported from Cr:Colquiriite so far at these repetition rates. Our findings indicate that tapered diodes in the red spectral region are likely to become the standard pump source for Cr:Colquiriite lasers in the near future. Moreover, the simplified pumping scheme might facilitate efficient commercialization of Cr:Colquiriite systems, bearing the potential to significantly boost applications of cw and femtosecond lasers in this spectral region (750-1000 nm).

GIMAP5 maintains liver endothelial cell homeostasis and prevents portal hypertension.

Portal hypertension is a major contributor to decompensation and death from liver disease, a global health problem. Here, we demonstrate homozygous damaging mutations in GIMAP5, a small organellar GTPase, in four families with unexplained portal hypertension. We show that GIMAP5 is expressed in hepatic endothelial cells and that its loss in both humans and mice results in capillarization of liver sinusoidal endothelial cells (LSECs); this effect is also seen when GIMAP5 is selectively deleted in endothelial cells. Single-cell RNA-sequencing analysis in a GIMAP5-deficient mouse model reveals replacement of LSECs with capillarized endothelial cells, a reduction of macrovascular hepatic endothelial cells, and places GIMAP5 upstream of GATA4, a transcription factor required for LSEC specification. Thus, GIMAP5 is a critical regulator of liver endothelial cell homeostasis and, when absent, produces portal hypertension. These findings provide new insight into the pathogenesis of portal hypertension, a major contributor to morbidity and mortality from liver disease.

Vascular anomalies associated with hepatic shunting.

Congenital vascular anomalies affecting the liver have been described in the scientific literature for decades. Understanding these malformations begins with knowledge of hepatic vascular embryology. Surgeons have applied numerous classification systems to describe both intrahepatic and extrahepatic shunts, which can confuse the reader and clinician. In our experience, focusing on one classification system for extrahepatic shunts and one for intrahepatic shunts is better. Today many patients with these shunts carry good long-term prognosis thanks to advances in imaging to better detect shunts earlier and classify them. Timely intervention by skilled radiologists and surgeons have also limited complications arising from dynamic shunts and can avoid a liver transplant. Congenital hepatic shunts are not the only vascular condition affecting the liver. Hereditary hemorrhagic telangiectasia, also known as Osler Weber Rendu syndrome, particularly type 2, may have varying severity of hepatic involvement which warrants longitudinal care from an experienced hepatologist. Lastly, congenital hemangiomas, often first identified on the skin and oral mucosa, also can affect the liver. While most will resolve in infancy and childhood, the pediatric hepatologist must understand how and when to treat persistent lesions and their complications. This article serves as a concise reference to help clinicians better care for patients with these rare conditions.

Caspofungin resistant disseminated candidiasis in a 7-year-old girl with T cell lymphoma: a case report.

Immunocompromised patients are at increased risk of disseminated candidiasis. Guidelines for the treatment of invasive candidiasis were last published in 2009, but resistance to the recommended treatment has recently been described in the literature. Here we present the case of an immunocompromised child with T-cell lymphoma who died secondary to disseminated candidiasis despite prolonged antifungal therapy. Awareness of the increasing resistance patterns of Candida when caring for immunocompromised patients, especially pediatric patients, may improve treatment and create better patient outcomes.

Mechanical lithotripsy of pancreatic and biliary stones: complications and available treatment options collected from expert centers.

INTRODUCTION: PD and common bile duct (CBD) stones often require mechanical lithotripsy (ML) at ERCP for successful extraction. The frequency and spectrum of complications is not well described in the literature. AIM: To describe the frequency and spectrum of complications of ML. METHODS: A comprehensive retrospective review of cases requiring ML of large or resistant PC and/or CBD stones using a 46-point data questionnaire on type(s) of complication, treatment attempted, and success of treatment. The study involved 7 tertiary referral centers with 712 ML cases (643 biliary and 69 pancreatic). RESULTS: Overall incidence of complications were: 4-4% (31/712); 23/643 biliary, 8/69 pancreatic; 21 single, 10 multiple. Biliary complications: trapped (TR)/broken (BR) basket (N = 11), wire fracture (FX) (N = 8), broken (BR) handle (N = 7), perforation/duct injury (N = 3). Pancreatic complications: TR/BR basket (N = 7), wire FX (N = 4), BR handle (N = 5), pancreatic duct leak (N = 1). Endoscopic intervention successfully treated complications in 29/31 cases (93.5%). Biliary group treatments: sphincterotomy (ES) extension (N = 7), electrohydraulic lithotripsy (EHL) (N = 11), stent (N = 3), per-oral Soehendra lithotripsy (N = 8), surgery (N = 1), extracorporeal lithotripsy (N = 5), and dislodge stones/change basket (N = 4). Pancreatic group treatments: ES extension (N = 3), EHL (N = 2), stent (N = 5), Soehendra lithotriptor (N = 4), dislodge stones/change basket (N = 2), extracorporeal lithotripsy (ECL) (N = 1), surgery (N = 1). Perforated viscus patient died at 30 days. CONCLUSION: The majority of ML in expert centers involved the bile duct. The complication rate of pancreatic ML is threefold greater than biliary lithotripsy. The most frequent complication of biliary and pancreatic ML is trapped/broken baskets. Extension of ES and EHL are the most frequently utilized treatment options.

The underutilization of EUS-guided FNA in the lymph-node staging of non-small-cell lung cancer: perceptions of chest physicians in Wisconsin.

BACKGROUND: Recently, the American College of Chest Physicians (ACCP) published evidence-based guidelines for the invasive staging of non-small-cell lung cancer (NSCLC), which shows the potential value of transesophageal sampling by EUS-guided FNA (EUS-FNA). The objective of the study was to determine the perceptions and the clinical practice of chest physicians regarding EUS-FNA as a staging modality for NSCLC. METHODS: We mailed a questionnaire to all members of the ACCP in Wisconsin. RESULTS: Seventy-one of 173 members (41%) responded. Chest physicians were more likely to perceive positron emission tomography, transbronchial needle aspiration, transthoracic needle aspiration, and mediastinoscopy to be able to make a difference in managing patients with NSCLC instead of EUS-FNA (p=0.01). Of the 40 chest physicians who believed that EUS-FNA can change the management of NSCLC, only 8 (20%) have sent a patient for EUS-FNA in the past year. Our findings may not necessarily reflect the opinions of chest physicians in other areas of the United States. CONCLUSIONS: Many of the chest physicians surveyed do not believe EUS-FNA impacts the management of NSCLC. This limited awareness may represent a barrier to successful utilization of EUS-FNA in lung-cancer staging.