BaSDAS: a web-based pooled CRISPR-Cas9 knockout screening data analysis system

We developed the BaSDAS (Barcode-Seq Data Analysis System), a GUI-based pooled knockout screening data analysis system, to facilitate the analysis of pooled knockout screen data easily and effectively by researchers with limited bioinformatics skills. The BaSDAS supports the analysis of various pooled screening libraries, including yeast, human, and mouse libraries, and provides many useful statistical and visualization functions with a user-friendly web interface for convenience. We expect that BaSDAS will be a useful tool for the analysis of genome-wide screening data and will support the development of novel drugs based on functional genomics information.

BaSDAS: a web-based pooled CRISPR-Cas9 knockout screening data analysis system

We developed the BaSDAS (Barcode-Seq Data Analysis System), a GUI-based pooled knockout screening data analysis system, to facilitate the analysis of pooled knockout screen data easily and effectively by researchers with limited bioinformatics skills. The BaSDAS supports the analysis of various pooled screening libraries, including yeast, human, and mouse libraries, and provides many useful statistical and visualization functions with a user-friendly web interface for convenience. We expect that BaSDAS will be a useful tool for the analysis of genome-wide screening data and will support the development of novel drugs based on functional genomics information.

Bile Acid Nuclear Receptor Farnesoid X Receptor: Therapeutic Target for Nonalcoholic Fatty Liver Disease

Nonalcoholic fatty liver disease (NAFLD) is one of the causes of fatty liver, occurring when fat is accumulated in the liver without alcohol consumption. NAFLD is the most common liver disorder in advanced countries. NAFLD is a spectrum of pathology involving hepatic steatosis with/without inflammation and nonalcoholic steatohepatitis with accumulation of hepatocyte damage and hepatic fibrosis. Recent studies have revealed that NAFLD results in the progression of cryptogenic cirrhosis that leads to hepatocarcinoma and cardiovascular diseases such as heart failure. The main causes of NAFLD have not been revealed yet, metabolic syndromes including obesity and insulin resistance are widely accepted for the critical risk factors for the pathogenesis of NAFLD. Nuclear receptors (NRs) are transcriptional factors that sense environmental or hormonal signals and regulate expression of genes, involved in cellular growth, development, and metabolism. Several NRs have been reported to regulate genes involved in energy and xenobiotic metabolism and inflammation. Among various NRs, farnesoid X receptor (FXR) is abundantly expressed in the liver and a key regulator to control various metabolic processes in the liver. Recent studies have shown that NAFLD is associated with inappropriate function of FXR. The impact of FXR transcriptional activity in NAFLD is likely to be potential therapeutic strategy, but still requires to elucidate underlying potent therapeutic mechanisms of FXR for the treatment of NAFLD. This article will focus the physiological roles of FXR and establish the correlation between FXR transcriptional activity and the pathogenesis of NAFLD.

SFannotation: A Simple and Fast Protein Function Annotation System

Owing to the generation of vast amounts of sequencing data by using cost-effective, high-throughput sequencing technologies with improved computational approaches, many putative proteins have been discovered after assembly and structural annotation. Putative proteins are typically annotated using a functional annotation system that uses extant databases, but the expansive size of these databases often causes a bottleneck for rapid functional annotation. We developed SFannotation, a simple and fast functional annotation system that rapidly annotates putative proteins against four extant databases, Swiss-Prot, TIGRFAMs, Pfam, and the non-redundant sequence database, by using a best-hit approach with BLASTP and HMMSEARCH.

Effects of Propofol on Phenylephrine Induced Vascular Smooth Muscle Contraction in Rat Thoracic Aorta / 대한마취과학회지

BACKGROUND: Propofol decreases arterial blood pressure. This has been ascribed to vasodilation and decreased cardiac output occuring separately or in combination. The goal of the present study was to assess the effects of propofol on the phenylephrine induced vasoconstriction in rat thoracic aortic rings. METHODS: All aortic rings were removed endothelium and isometric tension was recorded under a resting tension of 3 g. Isolated aortic rings were precontracted with phenylephrine (0.3micrometer) and propofol (1 to 100micrometer) was added cumulatively. We induced the phenylephrine preconstriction after treatment of verapamil 10micrometer in the other vascular rings. RESULTS: Propofol (1 to 100micrometer) attenuated phenylephrine (0.3micrometer) induced preconstriction dose-dependently. The administration of propofol (1 and 10micrometer) did not change the tonic constriction. The contractile response were significantly attenuated in verapamil pretreated rings but propofol did not affect on constriction in all dose range. CONCLUSIONS: Propofol attenuated phenylephrine precontracted rat thoracic aortic rings with inhibition of Ca2+ movement through the L-type calcium channel in the sarcolemmal membrane.

Comparison of the Effect of Epinephrine Concentration during Caudal Epidural Anesthesia / 대한마취과학회지

BACKGROUND: The advantages of addition of epinephrine to local anesthetics during caudal epidural anesthesia are core intense block, prolonged duration of anesthesia and reduction of systemic toxic effect of local anesthetics. The currently recommended concentration of epinephrine is 1 : 200,000, but absorbed epinephrines cause unwanted hemodynamic changes, so we attempted to ascertain the minimum effective concentrations of epinephrine during caudal epidural anesthesia. METHODS: Ninty patients classified ASA physical status I or II scheduled for perianal surgery were studied. These patients were divided into four groups who received 20 ml of 2% lidocaine with epinephrine concentrations of 1 : 100,000, 1 : 200,000, 1 : 400,000 or 1 : 800,000 respectively. Before and during anesthesia, patients' mean arterial pressure (MAP) and heart rate (HR) were measured. Caudal anesthesia was performed with patients in the jack-knife position. A 3 ml test dose was administered initially and then the remaining local anesthetics were injected slowly. The onset of analgesia, duration of analgesia, and other complications were observed. RESULTS: The onset of analgesia was slowest in the 1 : 800,000 group. The duration of analgesia was longest in the 1 : 100,000 group. There were no significant difference in MAP changes, but HR increased significantly in the 1 : 100,000 group compared to the 1 : 200,00 group. There were no systemic toxic symptoms for local anesthetics except that 1 patient, who was in the 1 : 100,000 group, had symptoms of palpitation and headache, considered to be the unwanted pharmacologic effects of epinephrine. CONCLUSION: We concluded that the 1 : 400,000 epinephrine concentration can be used during caudal epidural anesthesia.

Hemodynamic Effects of Hepatic Cooling and Portal Decompression during Hepatic Resection with Portal Triad Clamping / 대한마취과학회지

BACKGROUND: Portal triad clamping (PTC) during hepatic resection (Pringle maneuver, PM) can afford reduced intraoperative bleeding and bloodless surgical field. But inflow obstruction of blood to liver during PM can bring hemodynamic changes to the patient. This study was designed to evaluate the hemodynamic changes before, during and after PM application during hepatic resection. We also compared the hemodynamic effects of hepatic cooling before PM with/without portal decompression during PM. METHODS: The patients were divided into three groups; PM (P group, n=9), PM after hepatic cooling with 400 ml of 4oC lactated Ringer's solution (LR) (C+P group, n=13), PM after hepatic cooling and portal decompression with portocaval shunt (C+P+S group, n=7). Systemic vascular resistance index (SVRI), cardiac index (CI) and mean arterial pressure (MAP) were measured before, during and after PM. RESULTS: Portal pressure of C+P+S group (208.3+/-36.6 mmH2O) was lower than P (487.3+/-92.9 mmH2O) and C P (553.6+/-77.0 mmH2O) group during PM. CIs of P and C P group were decreased (15, 13% respectively) during PM. After reperfusion, CIs and SVRIs of P, C+P and C+P+S group were all increased (CI; 33, 26, 50%, SVRI; 30, 40, 50%, respectively) than end of PM. CONCLUSION: PM itself doesn't make abrupt hemodynamic change. Hepatic cooling with 4oC LR (400 ml) before PM increases MAP because of increased SVRI. Reperfusion after PM for 50 minutes, hemodynamic depression could occur by decreased SVRI, especially in case of decompressed portal pressure with portocaval shunt during PM.

Hemodynamic Effects of Hepatic Cooling and Portal Decompression during Hepatic Resection with Portal Triad Clamping / 대한마취과학회지

BACKGROUND: Portal triad clamping (PTC) during hepatic resection (Pringle maneuver, PM) can afford reduced intraoperative bleeding and bloodless surgical field. But inflow obstruction of blood to liver during PM can bring hemodynamic changes to the patient. This study was designed to evaluate the hemodynamic changes before, during and after PM application during hepatic resection. We also compared the hemodynamic effects of hepatic cooling before PM with/without portal decompression during PM. METHODS: The patients were divided into three groups; PM (P group, n=9), PM after hepatic cooling with 400 ml of 4oC lactated Ringer's solution (LR) (C+P group, n=13), PM after hepatic cooling and portal decompression with portocaval shunt (C+P+S group, n=7). Systemic vascular resistance index (SVRI), cardiac index (CI) and mean arterial pressure (MAP) were measured before, during and after PM. RESULTS: Portal pressure of C+P+S group (208.3+/-36.6 mmH2O) was lower than P (487.3+/-92.9 mmH2O) and C P (553.6+/-77.0 mmH2O) group during PM. CIs of P and C P group were decreased (15, 13% respectively) during PM. After reperfusion, CIs and SVRIs of P, C+P and C+P+S group were all increased (CI; 33, 26, 50%, SVRI; 30, 40, 50%, respectively) than end of PM. CONCLUSION: PM itself doesn't make abrupt hemodynamic change. Hepatic cooling with 4oC LR (400 ml) before PM increases MAP because of increased SVRI. Reperfusion after PM for 50 minutes, hemodynamic depression could occur by decreased SVRI, especially in case of decompressed portal pressure with portocaval shunt during PM.

Spectral Analysis of Heart Rate and Blood Pressure Variability during Hemorrhage in Propofol-Anesthetized Rats / 대한마취과학회지

BACKGROUND: This study was aimed to elucidate the effect of propofol anesthesia on circulatory response to hemorrhage in rats by power spectral analysis of heart rate and blood pressure variability. METHODS: Nineteen male Sprague-Dawley rats weighing 350-580 g were divided into propofol (2 mg/kg, iv)-anesthetized (P, n=10) and saline control (C, n=9) groups. Blood pressure signal was digitized at 500 Hz for 5 min at basal, during hemorrhage and after hemorrhage. The signal was analyzed with fast Fourier transform algorithm to yield power spectra of systolic (SPV) and diastolic (DPV) blood pressure and cycle length variability (HRV). Very low frequency (VLF, 0.02-0.26 Hz), low frequency (LF, 0.26-0.75 Hz), high frequency (HF, 0.75-5.00 Hz) powers, LF/HF ratio and total power were obtained. Powers of each band were expressed as percent of total power. RESULTS: Blood pressure was decreased during hemorrhage in C and with a greater magnitude in P. Heart rate tended to increase during hemorrhage in C, but was not changed in P. LF powers of SPV in P was decreased after propofol injection. Hemorrhage decreased LF and increased HF. LF powers of DPV in P was decreased after propofol injection. Hemorrhage caused a further decrease in LF. LF powers of HRV in P was decreased after propofol injection. Hemorrhage caused a further decrease in LF. Powers of SPV, DPV and HRV in C were not changed by hemorrhage. LF/HF of SPV, DPV and HRV were decreased during hemorrhage in P, but not in C. CONCLUSIONS: These results suggest that propofol depressed sympathetic activity to diminish peripheral vascular tone and hemorrhage under propofol anesthesia resulted in a greater blood pressure fall due to impaired sympathetic compensation including attenuated baroreflex mechanism.

Effects of L-Arginine and N-Nitro-L-Arginine Metheylester Treatment on Vasodilation of Propofol in Rat Thoracic Aortic Rings / 대한마취과학회지

BACKGROUND: Propofol decreases arterial blood pressure. This has been ascribed to vasodilation and decreased cardiac output occurring separately or in combination. This study investigated the relaxant effects of propofol and the effects of L-arginine and L-NAME on the vasodilation of propofol in rat thoracic aortic rings. METHODS: Isolated aortic rings were precontracted with phenylephrine (0.01 micrometer -10 micrometer) cumulatively and 10 minutes before the precontracted phenylephrine treatment, propofol was added cumulatively (1 micrometer-10 micrometer). The effects of L-NAME and L-arginine were evaluated by applying L-NAME (10 micrometer) and L-arginine (10 micrometer) after added propofol and before precontracted phenylephrine. RESULTS: A low concentration of propofol (1 micrometer) did not reduce phenylephrine-induced contraction but a high concentration of propofol (over 10 micrometer) reduced it significantly. Propofol also relaxed rat thoracic aortic rings in an endothelium independent manner. The L-NAME and L-arginine treatment did not affect the propofol-induced relaxation. CONCLUSIONS: Propofol was shown to have a biphasic vasoactive effect on rat thoracic aorta rings. The vasodilation effect of propofol was not related to the production of nitric oxide.

A Total Intravenous Anesthetic Experience of Pediatric Living Related Liver Transplantation with Propofol: A case report / 대한마취과학회지

We have experienced one case of anesthesia for living related liver transplantation with propofol. The recipient was 18-month-old girl and 10.5 kg. She was suffered from congenital liver disease (biliary atresia). We decided propofol as an anesthetic agent of the recipient with permission of the recipient's parents. Total anesthetic time was about 13 hours and anhepatic phase was 110 min. Careful attention was paid to prevent infection, hypothermia, hepatic artery thrombosis and to keep proper lung function. Hemodynamic changes were relatively stable throughout the operation and postoperative mechanical ventilatory support was required for about 2 days.

A Total Intravenous Anesthetic Experience of Pediatric Living Related Liver Transplantation with Propofol: A case report / 대한마취과학회지

We have experienced one case of anesthesia for living related liver transplantation with propofol. The recipient was 18-month-old girl and 10.5 kg. She was suffered from congenital liver disease (biliary atresia). We decided propofol as an anesthetic agent of the recipient with permission of the recipient's parents. Total anesthetic time was about 13 hours and anhepatic phase was 110 min. Careful attention was paid to prevent infection, hypothermia, hepatic artery thrombosis and to keep proper lung function. Hemodynamic changes were relatively stable throughout the operation and postoperative mechanical ventilatory support was required for about 2 days.

Effects of L-NAME, Aminoguanidine and Hydroxocobalamin on Aortic Contractile Responses in Endotoxemic Rats during Halothane Administration / 대한마취과학회지

BACKGROUND: Recent studies demonstrated that volatile anesthetics suppress the NO-cGMP system in the vascular system. It has been known that the hemodynamic changes produced by volatile anesthetics in septic patients are mediated by upregulation of iNOS leading to excessive release of NO. The mechanisms underlying suppression of the NO-cGMP system by anesthetics are still controversial. It has been elucidated that nitric oxide synthase (NOS) plays a major role in the regulatory function in the L-arginine-NO system. So we examined the effects of NOS inhibitor (L-NAME, aminoguanidine) and NO scavenger (hydroxocobalamin) on vascular smooth muscle contractile function in lipopolysaccharide (LPS)-treated rat aorta during halothane administration. METHODS: Aortic ring preparations were obtained from LPS-treated (1.5 mg/kg, ip, for 18 h) rats. We evaluated the effects of hydroxocobalamin, L-NAME and aminoguanidine on contractile responses to phenylephrine during halothane (1 & 2 MAC) administration respectively. Statistical significances (P<0.05) were analyzed according to data characterictics by repeated measures ANOVA test and student's t-test. RESULTS: The contractile responses to phenylephrine in LPS-treated rats aorta were significantly (P<0.05) increased in the presence of hydroxocobalamin and L-NAME. During the halothane (1 and 2 MAC) administration, the contractile responses to phenylephrine in LPS-treated rats aorta were increased significantly (P<0.05) in the presence of hydroxocobalamin and L-NAME. CONCLUSIONS: From these results, it is suggested that hydroxocobalamin and L-NAME may be useful in the therapy of septic shock.

An Evaluation of Caudal Anesthesia / 대한마취과학회지

Caudal anesthesia appears to be a safe and reliable technique for surgical anesthesia as well as an alternative to narcotics for postoperative analgesia for procedure below umbilicus. From January 1990 to December 1992, we examined the trend and distribution of the 1038 cases of caudal anesthesia retrospectively according to year, age, surgieal department, type of operation, operation time, local anesthetics and suecess rate. Annual numbers of caudal anesthesia increased with years and the first decade of life was the greatest number. The most common department and operation time were general surgery and 30~60 minutes. 2% or 1% lidocaine with epinephrine was the major local anesthetics used during caudal anesthesia and overall success rate was 95.5%.

Mananagement of Cancer Pain Using Portable Infusor / 대한마취과학회지

Continuous epidural analgesia with morphine via portable infusor(Baxter Infusor, BI) is a good technique for the management of intractable cancer pain. The method of subcutaneous tunnelling with portable infusor has been widely used for the cancer pain management. We examined the doses of morphine, duration of subcutaneous tunnelling, side effects, age distribution and causes of pain. The mean initial dose of morphine was 6.09 and the last 24.02 mg. Mean duration of subcutaneous tunnelling was 53.71 days and voiding difficulty, pruritus, respiratory depression were observed. Most of the patients were at the ages of 6th decade and the most common cause of pain was stomach cancer. It is suggested that the management of intractable cancer pain with epidural morphine through subcutaneous tunnelling via portable infusor is satisfactory and reliable.

Effects of Stellate Ganglion Blocks for Sudden Deafness / 대한마취과학회지

Forty-four patients with sudden sensorineural hearing loss were treated with stellate ganglion block. The results were as follows. The results showed highest incidence in the decade between 30 and 50 years. The incidence of unilateral involvement were 40 cases (90.9%), among them 26 cases (59.1%) were right side. Among 44 patients 8 (18.2%) showed complete recovery, 9 (20.5%) partial recovery and 16 cases (36.4%) slight improvement by pure tone gain. These results showed a relative superiority of stellate ganglion block to other therapeutic regimens such as vasodilators, corticosteroids, anticoagulants etc. The time interval from onset of symptoms to start of stellate ganglion block seems to be important. Prognosis was slight poor in cases of sudden hearing loss with vertigo.

Spectral Analysis of EEG during Inhalation of Halothane, Enflurane, and Isoflurane in the Rat / 대한마취과학회지

The dose-related effects of halothane, enflurane, and isoflurane on the rat EEG were evaluated qusntitstively by spectral analysis of the EEG recorded from the rat skull. The anesthetics were inhaled by animal ventilator into 10L glass bottle, in which the preparated rats were placed, at various concentrations, and then bipolar EEG was recorded from the rat skull and its spectrum was calculated by power speetral analysis. The density of each spectral bands (delta 1-3.25, theta 3.5-7.75, alpha 8-12.25, and beta 13-31.75Hz), total density, delta ratio, spectral edge frequency, and medisn power frequency were derived from the spectra. With inspection of conventional EEG, 1.5 MAC of hslothane revealed spindles, but higher dose decreased the amplitude. 1.5 MAC of enflurane revealed a lot of spike waves but 2.0 MAC revealed several spike waves and decreased the amplitude, and 1.5 MAC isoflurane revealed isolated spike waves but 2.0 MAC revealed cerebro- electrical silence. In quantitative spectral analysis of EEG, significant EEG changes were identified during inhalation of all anestheties. In halothane dominent frequencies in EEG were delta waves at 1.5 MAC and 2.0 MAC. In enflurane dominent waves in EEG were theta waves at 1.5 MAC and 2.0 MAC and in isoflurane those were theta waves. Taken together, these findings suggest that analysis for EEG parameters derived from power spectral analysis could be applied to determine the depth of halothane, enflurane, and isoflurane anesthesia.

Effects of Volatile Anesthetics on Isolated Rings of Thoracic Aorta in Rats / 대한마취과학회지

Halothane, enflurane, and isoflurane are generally regarded as vasodilators. This property has been attributed to a direct action on vascular smooth muscle or the inhibition of vasoconstricition by endogenous neurohumoral substances. Because of the importance of the endothelium in determining of modulating the vascular responses of a wide vareity of agents, vascular effects of halothane, enflurane and isoflaurane on isolated rings of thoracic aorta in Sprague-Dawley rats were studied in the presence and absence of intact endothelium. Halothane, enflurane and isoflurane induced relaxation on thoraeic aortic rings precan-tracted with 50mM KCl both with and without endothelium. Halothane also induced vasodilation in both aortic rings precontracted with 10-6 M phenylephrine. And enflurane and isoflurane induced vasodilation in denuded aortic rings precontracted with phenylephrine. But endothelium intact rings demonstrsted significant(p<0.05) vasoconstriction at low concentrations of both enflurane and isoflurane followed by vasodilation at higher concentra- tion precontracted with phenyephrine. These results suggest that at low concentration and intact rings, enflurane and isoflurane eause vasoconstriction through inhibition of basal EDRF production and /or stimulation of the release of an endothelium derived constricting factor. At higher concentration, a direct vasodilating effect of the anesthetic predominance.

Effects of Pentoxifylline on Hemorrhagic Shock in Cats / 대한마취과학회지

It was reported that pentoxifylline(PTX) improved tissue oxygenation and increased survival rate in animal models of hemorrhagic shock. The authors investigated the salutary effects of PTX on hemodynamics, oxygen transport and tissue metabolism in animal models of hemorrhagic shock. 18 anesthetized cats were subjected to hemorrhage to MABP of 40-45 mmHg and this pressure was maintained for 120 minutes. After this period, normal saline was administered in a volume double the original shed blood volume over 30 minutes. Thereafter the cats were observed for 120 minutes. Drug-treated cats received at 25 mg/kg i.v. bolus of PTX at the beginning of hemorrhage, followed by a continuous infusion of 25 mg/kg/hr throughout the experiment. PTX had no effect on MABP, pH(a-cv), P(cv-a) CO2 and lactic acid value but, PTX group had more rapid HR and higher PcvO, than placebo group(P<0.05). In addition, we found that pH(a-cv) and P(cv-a) CO2 changes occurred more rapidly than lactic acid changes(P<0.05) after hemorrhagic shock. So, pH(a-cv) and P(cv-a) CO2 changes might be considered as useful parameters for early detection of derangement of tissue oxygenation in shock states. It was concluded that PTX had no effects on indices of representing tissue oxygenation except improvement of central venous oxygen tension in this feline hemorrhagic shock model. Further studies are needed.

Comparison of Two Methods of Axillary Brachial Plexus Block / 대한마취과학회지

Comparison of the perivascular and paresthetic techniques of axillary brachial plexus block was made in two groups of 40 patients undergiong elective upper limb surgery. The results were as follows. Complete block were 16 cases(80%) in perivascular group, 17 cases(85%) in paresthetic group and total failure was abscent. Among incomplete block, radial nerve were 6 cases, ulnar never 2 cases and median nerve 1 case. There is no statistical difference between the two techniques. It is suggested that the axillary brachial plexus block is best suited for surgery of the forearm and hand, especially when surgery is in the area innervated by the median and ulnar nerves.