Purifying selection of long dsRNA is the first line of defense against false activation of innate immunity

BACKGROUND

Mobile elements comprise a large fraction of metazoan genomes. Accumulation of mobile elements is bound to produce multiple putative double-stranded RNA (dsRNA) structures within the transcriptome. These endogenous dsRNA structures resemble viral RNA and may trigger false activation of the innate immune response, leading to severe damage to the host cell. Adenosine to inosine (A-to-I) RNA editing is a common post-transcriptional modification, abundant within repetitive elements of all metazoans. It was recently shown that a key function of A-to-I RNA editing by ADAR1 is to suppress the immunogenic response by endogenous dsRNAs.

RESULTS

Here, we analyze the transcriptomes of dozens of species across the Metazoa and identify a strong genomic selection against endogenous dsRNAs, resulting in their purification from the canonical transcriptome. This purifying selection is especially strong for long and nearly perfect dsRNAs. These are almost absent from mRNAs, but not pre-mRNAs, supporting the notion of selection due to cytoplasmic processes. The few long and nearly perfect structures found in human transcripts are weakly expressed and often heavily edited.

CONCLUSION

Purifying selection of long dsRNA is an important defense mechanism against false activation of innate immunity. This newly identified principle governs the integration of mobile elements into the genome, a major driving force of genome evolution. Furthermore, we find that most ADAR1 activity is not required to prevent an immune response to endogenous dsRNAs. The critical targets of ADAR1 editing are, likely, to be found mostly in non-canonical transcripts.

Differential lung ventilation for increased oxygenation during one lung ventilation for video assisted lung surgery

BACKGROUND

One lung ventilation (OLV) is the technique used during lung resection surgery in order to facilitate optimal surgical conditions. OLV may result in hypoxemia due to the shunt created. Several techniques are used to overcome the hypoxemia, one of which is continuous positive airway pressure (CPAP) to the non-dependent lung. Another technique is ventilating the non-dependent lung with a minimal volume, thus creating differential lung ventilation (DLV). In this study we compared the efficacy of CPAP to DLV during video assisted thoracoscopic lung resection.

PATIENTS AND METHOD

This is a prospective study of 30 adult patients undergoing elective video assisted thoracoscopic lung lobectomy. Each patient was ventilated in four modes: two lung ventilation, OLV, OLV + CPAP and OLV + DLV. Fifteen patients were ventilated with CPAP first and DLV next, and the other 15 were ventilated with DLV first and then CPAP. Five minutes separated each mode, during which the non-dependent lung was open to room air. We measured the patient's arterial blood gas during each mode of ventilation. The surgeons, who were blinded to the ventilation technique, were asked to assess the surgical conditions at each stage.

RESULTS

Oxygenation during OLV+ CPAP was significantly lower that OLV + DLV (p = 0.018). There were insignificant alterations of pH, PCO2 and HCO3 during the different ventilating modes. The surgeons' assessments of interference in the field exposure between OLV + CPAP or OLV + DLV was found to be insignificant (p = 0.073).

CONCLUSIONS

During OLV, DLV is superior to CPAP in improving patient's oxygenation, and may be used where CPAP failed.

TRIAL REGISTRATION

ClinicalTrials.gov NCT03563612 . Registered 9 June 2018, retrospectively (due to clerical error).

Retrosternal Block Use in the Treatment for Dyspnoea

We present a technique of retrosternal block for symptomatic treatment for dyspnoea of various aetiologies. In our experience with 20 patients, a retrosternal block using lignocaine improved symptoms within minutes. The block was easy to perform and was helpful when the patients’ symptoms were not relieved by conventional therapy. Prospective controlled studies are needed to further assess this simple and promising treatment.

Pre-reproductive stress and fluoxetine treatment in rats affect offspring A-to-I RNA editing, gene expression and social behavior

Adenosine to inosine RNA editing is an epigenetic process that entails site-specific modifications in double-stranded RNA molecules, catalyzed by adenosine deaminases acting on RNA (ADARs). Using the multiplex microfluidic PCR and deep sequencing technique, we recently showed that exposing adolescent female rats to chronic unpredictable stress before reproduction affects editing in the prefrontal cortex and amygdala of their newborn offspring, particularly at the serotonin receptor 5-HT2c (encoded by Htr2c). Here, we used the same technique to determine whether post-stress, pre-reproductive maternal treatment with fluoxetine (5 mg/kg, 7 days) reverses the effects of stress on editing. We also examined the mRNA expression of ADAR enzymes in these regions, and asked whether social behavior in adult offspring would be altered by maternal exposure to stress and/or fluoxetine. Maternal treatment with fluoxetine altered Htr2c editing in offspring amygdala at birth, enhanced the expression of Htr2c mRNA and RNA editing enzymes in the prefrontal cortex, and reversed the effects of pre-reproductive stress on Htr2c editing in this region. Furthermore, maternal fluoxetine treatment enhanced differences in editing of glutamate receptors between offspring of control and stress-exposed rats, and led to enhanced social preference in adult offspring. Our findings indicate that pre-gestational fluoxetine treatment affects patterns of RNA editing and editing enzyme expression in neonatal offspring brain in a region-specific manner, in interaction with pre-reproductive stress. Overall, these findings imply that fluoxetine treatment affects serotonergic signaling in offspring brain even when treatment is discontinued before gestation, and its effects may depend upon prior exposure to stress.

A-to-I RNA editing in the rat brain is age-dependent, region-specific and sensitive to environmental stress across generations

BACKGROUND

Adenosine-to-inosine (A-to-I) RNA editing is an epigenetic modification catalyzed by adenosine deaminases acting on RNA (ADARs), and is especially prevalent in the brain. We used the highly accurate microfluidics-based multiplex PCR sequencing (mmPCR-seq) technique to assess the effects of development and environmental stress on A-to-I editing at 146 pre-selected, conserved sites in the rat prefrontal cortex and amygdala. Furthermore, we asked whether changes in editing can be observed in offspring of stress-exposed rats. In parallel, we assessed changes in ADARs expression levels.

RESULTS

In agreement with previous studies, we found editing to be generally higher in adult compared to neonatal rat brain. At birth, editing was generally lower in prefrontal cortex than in amygdala. Stress affected editing at the serotonin receptor 2c (Htr2c), and editing at this site was significantly altered in offspring of rats exposed to prereproductive stress across two generations. Stress-induced changes in Htr2c editing measured with mmPCR-seq were comparable to changes measured with Sanger and Illumina sequencing. Developmental and stress-induced changes in Adar and Adarb1 mRNA expression were observed but did not correlate with editing changes.

CONCLUSIONS

Our findings indicate that mmPCR-seq can accurately detect A-to-I RNA editing in rat brain samples, and confirm previous accounts of a developmental increase in RNA editing rates. Our findings also point to stress in adolescence as an environmental factor that alters RNA editing patterns several generations forward, joining a growing body of literature describing the transgenerational effects of stress.

The effect of 'Out of hours surgery Service' in Israel on hip fracture fixation outcomes: a retrospective analysis

BACKGROUND

'Out of Hours Surgery Service' (OHSS) was implemented in Israel, amongst other reasons, in order to reduce the time interval between hospital admission and surgery and consequently improve outcomes. The OHSS is currently operated in the public hospitals in Israel. In this study we compared the data of patients before and after OHSS implementation to determine its efficacy in improving patient care.

METHODS

This is a retrospective observational study of 792 adult patients who underwent hip fracture surgery between 2002 and 2007 in a single hospital. The study population included two groups: patients that were operated before the implementation of the OHSS (2002-2004) and after the implementation of the OHSS (2005-2007). Data regarding all patients was collected using the institution's computer program. The following variables were analyzed: patients' demographics, time interval from hospitalization to surgery, causes for delaying surgery, post-operative length of hospitalization and mortality.

RESULTS

Patients in the post-OHSS group had more illnesses and higher ASA classification than those in the pre-OHSS group. The post-OHSS group had a significantly decreased length of stay in the hospital before and after the surgery. After adjusting for ASA score and age, the post-OHSS group was found to have decreased post-operative hospitalization and lower post-operative mortality. Surgery was delayed in pre-OHSS period mainly due to operating rooms unavailability.

CONCLUSION

Implementation of OHSS facilitated operating room availability, thus early operation and reduced post-operative mortality. In accordance with other studies, patient's outcome is greatly influenced by the time from admission to hip fracture surgery.

Abnormalities in A-to-I RNA editing patterns in CNS injuries correlate with dynamic changes in cell type composition

Adenosine to Inosine (A-to-I) RNA editing is a co- or post-transcriptional mechanism that modifies genomically encoded nucleotides at the RNA level. A-to-I RNA editing is abundant in the brain, and altered editing levels have been reported in various neurological pathologies and following spinal cord injury (SCI). The prevailing concept is that the RNA editing process itself is dysregulated by brain pathologies. Here we analyzed recent RNA-seq data, and found that, except for few mammalian conserved editing sites, editing is significantly higher in neurons than in other cell populations of the brain. We studied A-to-I RNA editing in stab wound injury (SWI) and SCI models and showed that the apparent under-editing observed after injury correlates with an approximately 20% reduction in the relative density of neurons, due to cell death and immune cell infiltration that may account for the observed under-editing. Studies of neuronal and astrocyte cultures and a computational analysis of SCI RNA-seq data further supported the possibility that a reduction in neuronal density is responsible for alterations in the tissue-wide editing patterns upon injury. Thus, our data suggest that the case for a mechanistic linkage between A-to-I RNA editing and brain pathologies should be revisited.

Activation-Induced Cytidine Deaminase Links Ovulation-Induced Inflammation and Serous Carcinogenesis

In recent years, the notion that ovarian carcinoma results from ovulation-induced inflammation of the fallopian tube epithelial cells (FTECs) has gained evidence. However, the mechanistic pathway for this process has not been revealed yet. In the current study, we propose the mutator protein activation-induced cytidine deaminase (AID) as a link between ovulation-induced inflammation in FTECs and genotoxic damage leading to ovarian carcinogenesis. We show that AID, previously shown to be functional only in B lymphocytes, is expressed in FTECs under physiological conditions, and is induced in vitro upon ovulatory-like stimulation and in vivo in carcinoma-associated FTECs. We also report that AID activity results in epigenetic, genetic and genomic damage in FTECs. Overall, our data provides new insights into the etiology of ovarian carcinogenesis and may set the ground for innovative approaches aimed at prevention and early detection.

Expanding preconception carrier screening for the Jewish population using high throughput microfluidics technology and next generation sequencing

Background

Genetic screening to identify carriers of autosomal recessive diseases has become an integral part of routine prenatal care. In spite of the rapid growth of known mutations, most current screening programs include only a small subset of these mutations, and are performed using diverse molecular techniques, which are generally labor-intensive and time consuming. We examine the implementation of the combined high-throughput technologies of specific target amplification and next generation sequencing (NGS), for expanding the carrier screening program in the Israeli Jewish population as a test case.

Methods

We compiled a panel of 370 germline mutations, causing 120 disorders, previously identified in affected Jewish individuals from different ethnicities. This mutation panel was simultaneously captured in 48 samples using a multiplex PCR-based microfluidics approach followed by NGS, thereby performing 17,760 individual assays in a single experiment.

Results

The sensitivity (measured with depth of at least 50×) and specificity of the target capture was 98 and 95 % respectively, leaving minimal rate of inconclusive tests per sample tested. 97 % of the targeted mutations present in the samples were correctly identified and validated.

Conclusion

Our methodology was shown to successfully combine multiplexing of target specific primers, samples indexing and NGS technology for population genetic screens. Moreover, it’s relatively ease of use and flexibility of updating the targets screened, makes it highly suitable for clinical implementation. This protocol was demonstrated in pre-conceptional screening for pan-Jewish individuals, but can be applied to any other population or different sets of mutations.

Electronic supplementary material

The online version of this article (doi:10.1186/s12920-016-0184-7) contains supplementary material, which is available to authorized users.

Reduced levels of protein recoding by A-to-I RNA editing in Alzheimer's disease

Adenosine to inosine (A-to-I) RNA editing, catalyzed by the ADAR enzyme family, acts on dsRNA structures within pre-mRNA molecules. Editing of the coding part of the mRNA may lead to recoding, amino acid substitution in the resulting protein, possibly modifying its biochemical and biophysical properties. Altered RNA editing patterns have been observed in various neurological pathologies. Here, we present a comprehensive study of recoding by RNA editing in Alzheimer's disease (AD), the most common cause of irreversible dementia. We have used a targeted resequencing approach supplemented by a microfluidic-based high-throughput PCR coupled with next-generation sequencing to accurately quantify A-to-I RNA editing levels in a preselected set of target sites, mostly located within the coding sequence of synaptic genes. Overall, editing levels decreased in AD patients' brain tissues, mainly in the hippocampus and to a lesser degree in the temporal and frontal lobes. Differential RNA editing levels were observed in 35 target sites within 22 genes. These results may shed light on a possible association between the neurodegenerative processes typical for AD and deficient RNA editing.

Abstract A34: Activation-induced cytidine deaminase links ovulation-induced inflammation and serous carcinogenesis

In recent years, the notion that serous ovarian carcinoma results from ovulation-induced inflammation of the fallopian tube epithelial cells (FTECs) has gained evidence. However, the mechanistic pathway that leads to mutagenesis and genomic instability has not been revealed yet. The mutator enzyme activation-induced cytidine deaminase (AID), which is known to be involved in the process of immunoglobulin somatic hypermutations, has also been recently implicated in inflammation-induced epithelial malignancies. In the current study, we propose that AID is a mechanistic link between ovulation-induced inflammation in FTECs and the genotoxic damage that leads to serous carcinogenesis.

We tested at the expression of AID in human fallopian tube tissues from patients with various gynecological pathologies, as well as in cultured FTECs in an experimental model mimicking normal ovulation. We also looked at the functional effects of AID up regulation in vitro by analyzing double strand DNA breaks, abasic sites, hypomethylation and chromosomal rearrangements. We also performed a comprehensive bioinformatic analysis of somatic mutations patterns in publically available serous carcinoma sequencing data in search of AID mutational fingerprints.

We show that AID, previously shown to be functional only in B lymphocytes, is expressed in human FTECs under physiological conditions, is induced in vitro upon ovulatory-like stimulation and is elevated in vivo under carcinogenesis-associated circumstances. We also report that AID activity results in epigenetic, genetic and genomic damage in FTECs.

Overall, our data provides new insights on the etiology of serous ovarian carcinogenesis and may set the ground for innovative approaches aimed at prevention and early-detection.

Citation Format: Stav Sapoznik, Keren Bahar-Shany, Hadar Brand, Yishay Pinto, Orshay Gabay, Efrat Glick-Saar, Chen Dor, Oranit Zadok, Iris Barshack, Adi Zundelevich, Einav Nili Gal-Yam, Yuval Yung, Ariel Hourvitz, Jacob Korach, Mario Beiner, Jasmine Jacob, Erez Y. Levanon, Michal Barak, Sarit Aviel-Ronen, Keren Levanon. Activation-induced cytidine deaminase links ovulation-induced inflammation and serous carcinogenesis. [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research: Exploiting Vulnerabilities; Oct 17-20, 2015; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2016;22(2 Suppl):Abstract nr A34.

Fmrp Interacts with Adar and Regulates RNA Editing, Synaptic Density and Locomotor Activity in Zebrafish

Fragile X syndrome (FXS) is the most frequent inherited form of mental retardation. The cause for this X-linked disorder is the silencing of the fragile X mental retardation 1 (fmr1) gene and the absence of the fragile X mental retardation protein (Fmrp). The RNA-binding protein Fmrp represses protein translation, particularly in synapses. In Drosophila, Fmrp interacts with the adenosine deaminase acting on RNA (Adar) enzymes. Adar enzymes convert adenosine to inosine (A-to-I) and modify the sequence of RNA transcripts. Utilizing the fmr1 zebrafish mutant (fmr1-/-), we studied Fmrp-dependent neuronal circuit formation, behavior, and Adar-mediated RNA editing. By combining behavior analyses and live imaging of single axons and synapses, we showed hyperlocomotor activity, as well as increased axonal branching and synaptic density, in fmr1-/- larvae. We identified thousands of clustered RNA editing sites in the zebrafish transcriptome and showed that Fmrp biochemically interacts with the Adar2a protein. The expression levels of the adar genes and Adar2 protein increased in fmr1-/- zebrafish. Microfluidic-based multiplex PCR coupled with deep sequencing showed a mild increase in A-to-I RNA editing levels in evolutionarily conserved neuronal and synaptic Adar-targets in fmr1-/- larvae. These findings suggest that loss of Fmrp results in increased Adar-mediated RNA editing activity on target-specific RNAs, which, in turn, might alter neuronal circuit formation and behavior in FXS.

The most frequent inherited mental retardation disorder is fragile X syndrome, which is characterized by learning disabilities, cognitive impairment, anxiety, and hyperactive behavior. The genetic cause of this disorder is the silencing of the fmr1 gene, which encodes the RNA-binding protein Fmrp. This protein inhibits the production of various proteins in the brain and interacts with the Adar enzyme, which converts the nucleotide A into I in RNAs. However, it is unclear by which mechanism the loss of Fmrp affects the sequence of neuronal genes and, ultimately, brain function. Here, we used the fmr1 mutant zebrafish (fmr1-/-), which enables high-throughput genetics and live imaging experiments in a transparent and evolutionarily conserved brain. We found that loss of Fmrp altered neuronal circuit formation. Furthermore, similar to human patients, the fmr1-/- larvae were hyperactive. Biochemical assays showed that Fmrp interacts with the Adar2a protein, which is increased in fmr1-/- larvae. Thus, we characterized global RNA editing in the zebrafish transcriptome and used a microfluidic-based high-throughput technique to accurately quantify RNA editing levels. Loss of Fmrp resulted in a mild increase in RNA editing in the coding sequences of conserved synaptic genes. These findings propose that altered RNA editing levels may affect neuronal and behavioral deficiencies in FXS.

Early rehabilitation treatment in newborns with congenital muscular torticollis

BACKGROUND

Congenital Muscular Torticollis (CMT) is the most common form of torticollis in infants; on clinical presentation it is classified into 3 types: 1) postural torticollis, with postural deformity only in the neck; 2) muscular torticollis, where neck deformity is associated with muscle tightness and restricted passive range of motion (ROM); and 3) sternomastoid tumor or pseudotumor, with a fibrotic, sternocleido-mastoid muscle mass and passive ROM limitations.

AIM

The aim of this study was to evaluate the physical therapy outcome of infants with CMT treated either by parents using a home exercise program, or by a physical therapist.

DESIGN

Longitudinal study.

SETTING

Outpatients with CMT at our Department of Physical Medicine and Rehabilitation.

POPULATION

Fifty consecutive newborns with CMT, referred by the primary pediatrician:

METHODS

In our study, 50 infants with CMT were evaluated and treated either by a physical therapist or by parents using a home program.

RESULTS

Sixteen females (32%) and 34 males (68%), aged 10.2 weeks (SD 6.66); 23 of the infants (46%) presented with more severe articular limitations than the others (P=0.002) and were therefore prescribed outpatient treatment by a physical therapist; the remaining 27 less severe cases (54%) were prescribed a home therapy program. 49 infants achieved full resolution after an average of 81.06 days (SD 64.05) of rehabilitation treatment. The group of patients who were treated at home achieved resolution more quickly (72.8 vs. 91.1 days), although statistical significance was not reached.

CONCLUSIONS

Infants with CMT who were treated early, either at home or in the outpatient clinic, completely recovered normal neck movement in a short time. It is important not to discharge patients until they have achieved full resolution of CMT symptoms to exclude the minimal risk of relapse.

CLINICAL REHABILITATION IMPACT

This study demonstrates the importance of early treatment in cases of congenital muscular torticollis.

Comparison of VivaSight double-lumen tube with a conventional double-lumen tube in adult patients undergoing video-assisted thoracoscopic surgery

The efficiency of a double-lumen tube depends on its position in the airways, which can be verified by fibreoptic bronchoscopy. The VivaSight DL is a single-use double-lumen tube with a camera embedded in the tube's right side. The view from the camera appears continuously on a monitor. In this prospective study of 71 adult patients, we compared intubation times using either the VivaSight DL or a conventional double-lumen tube. Median (IQR [range]) duration of intubation with visual confirmation of tube position was significantly reduced using the VivaSight DL compared with the conventional double-lumen tube (51 (42-60 [35-118]) s vs 264 (233-325 [160-490]) s, respectively, p < 0.0001). None of the patients allocated to the VivaSight DL required fibreoptic bronchoscopy during intubation or surgery. The VivaSight DL enables significantly more rapid intubation compared with the conventional double-lumen tube.

Autovalidation rates in an outpatient coagulation laboratory

INTRODUCTION

To determine the rates of autovalidation in our outpatient coagulation laboratory.

METHODS

We retrospectively identified all coagulation tests analyzed during the month of January 2014 from our laboratory information system (LIS) (N = 16 116), from around 800 000 active members of Clalit Health Services (a health maintenance organization). The integrated system includes a single centrifugation of all collection tubes, analyzers that rerun or reflex tests according to the test results, and a laboratory information system that sends orders to the analyzer, autovalidates test results, and automatically sends critical value results to a list for immediate physician communication. Reasons for technician validation are tests rerun for confirmation or because of analyzer errors and test results that require reflex testing. All other test results are sent automatically to the laboratory information system without the need for technician review.

RESULTS

There were 362 test results with analyzer errors, 91 results rerun for confirmation (thrombophilia test results outside the reference interval), and 50 tests with mixing studies and reflex testing for factor XI activity levels (total = 3.1%, 503/16116), resulting in an autovalidation rate of 96.9% (95% confidence interval - 96.6-97.2%).

CONCLUSIONS

We conclude that an integrated system can result in a high autovalidation rate in a high-volume outpatient coagulation laboratory.

Subcutaneous Emphysema following Emergent Surgical Conventional Tracheostomy

In maxillofacial surgery, tracheostomy is indicated in congenital, inflammatory, oncologic, or traumatic respiratory obstruction. In traumatic cases, however, it is sometimes hard to implement. We describe subcutaneous emphysema following emergent surgical conventional tracheostomy performed after stab injury to the floor of the mouth. We analyze the course that led to this complication and discuss suggestions on how to avoid it. In addition, we review the literature to improve our knowledge and practice regarding this entity. Massive subcutaneous neck emphysema occurred because ventilation started at the time when the hemorrhage was not completely managed and the tracheal tube was not fully secured. In traumatic cases with profound bleeding, hemorrhage management must be performed carefully. The recommendation not to ventilate until the hemorrhage is completely managed should be observed.

The use of VivaSight™ single lumen endotracheal tube in morbidly obese patients undergoing laparoscopic sleeve gastrectomy

Background

The population of obese patients is progressively growing and bariatric operations are becoming increasingly common. Morbidly obese patients require special anesthetic care and are often considered to be difficult to ventilate and intubate. The VivaSight™ Single Lumen tube is an endotracheal tube with a camera embedded in its tip. The view from the tip appears continuously on a monitor in the anesthesiologist's vicinity. The aim of this study was to assess the VivaSight™ in comparison with conventional endotracheal tube as an aid in the intubation and surveillance of tube position during surgery of obese patients.

Methods

This is a prospective study of 72 adult obese patients who underwent laparoscopic sleeve gastrectomy. The patients were randomly assigned to be intubated by either the VivaSight™ (40 patients, test group) or a conventional endotracheal tube (32 patients, control group). Data on the patients, the pre-operative airway evaluation, the endotracheal intubation and the post-operative outcome were collected and compared.

Results

The Mallampati scores were significantly higher in the test group than in the control group. Endotracheal intubation took 29 ± 10 and 24 ± 8 seconds using the VivaSight™ and a conventional tube respectively (p = 0.02). Three of the patients in the control group, while none of those in the test group, had soft tissue injury (p < 0.05).

Conclusion

We found the VivaSight™ SL to be helpful in the endotracheal intubation and continuous surveillance of tube position in morbidly obese patients undergoing laparoscopic sleeve gastrectomy.

Pulmonary Complications following Percutaneous Nephrolithotomy: A Prospective Study

INTRODUCTION

Pulmonary complications may occur in the post-operative period and are a significant cause of morbidity and mortality in patients undergoing anesthesia and surgery. Complication rates vary according to different procedures and different types of anesthesia and may be affected by the patient condition. The purpose of this study was to examine pulmonary complications following percutaneous nephrolithotomy (PCNL) and to search for associations between the pre- and intra-operative factors and the risk of post-operative pulmonary complications (PPC).

PATIENTS AND METHODS

This was a prospective observational study of 100 consecutive adult patients who underwent PCNL surgery. We collected data of the patient, surgery and anesthesia and analyzed it to find correlations with PPC.

RESULTS

Eight (8%) patients had PPC following PCNL, 7 patients had pneumothorax and 1 had atelectasis and pleural effusion. The latter patient died at post-operative day 24 due to respiratory failure. It was found that patients who had PCNL on the right kidney were at lower risk for PPC. In addition it was found that younger patients had a higher incidence of PPC.

CONCLUSIONS

Based on this study the most common type of post-operative complication following PCNL is pulmonary, with pneumothorax being the main complication. PPC may result in patient mortality. The side of the operation and the patient's age might affect the risk of PPC.

A-to-I RNA editing occurs at over a hundred million genomic sites, located in a majority of human genes

RNA molecules transmit the information encoded in the genome and generally reflect its content. Adenosine-to-inosine (A-to-I) RNA editing by ADAR proteins converts a genomically encoded adenosine into inosine. It is known that most RNA editing in human takes place in the primate-specific Alu sequences, but the extent of this phenomenon and its effect on transcriptome diversity are not yet clear. Here, we analyzed large-scale RNA-seq data and detected ∼1.6 million editing sites. As detection sensitivity increases with sequencing coverage, we performed ultradeep sequencing of selected Alu sequences and showed that the scope of editing is much larger than anticipated. We found that virtually all adenosines within Alu repeats that form double-stranded RNA undergo A-to-I editing, although most sites exhibit editing at only low levels (<1%). Moreover, using high coverage sequencing, we observed editing of transcripts resulting from residual antisense expression, doubling the number of edited sites in the human genome. Based on bioinformatic analyses and deep targeted sequencing, we estimate that there are over 100 million human Alu RNA editing sites, located in the majority of human genes. These findings set the stage for exploring how this primate-specific massive diversification of the transcriptome is utilized.

Automated analysis of immunoglobulin genes from high-throughput sequencing: life without a template

Background

Immunoglobulin (that is, antibody) and T cell receptor genes are created through somatic gene rearrangement from gene segment libraries. Immunoglobulin genes are further diversified by somatic hypermutation and selection during the immune response. Studying the repertoires of these genes yields valuable insights into immune system function in infections, aging, autoimmune diseases and cancers. The introduction of high throughput sequencing has generated unprecedented amounts of repertoire and mutation data from immunoglobulin genes. However, common analysis programs are not appropriate for pre-processing and analyzing these data due to the lack of a template or reference for the whole gene.

Results

We present here the automated analysis pipeline we created for this purpose, which integrates various software packages of our own development and others’, and demonstrate its performance.

Conclusions

Our analysis pipeline presented here is highly modular, and makes it possible to analyze the data resulting from high-throughput sequencing of immunoglobulin genes, in spite of the lack of a template gene. An executable version of the Automation program (and its source code) is freely available for downloading from our website: http://immsilico2.lnx.biu.ac.il/Software.html.

Core decompression and alendronate treatment of the osteonecrotic rat femoral head: computer-assisted analysis

Femoral head avascular necrosis is a process leading to femoral head deformity and osteoarthritic changes in the hip joint. Alendronate slows down bone resorption and remodelling in rats, while core decompression hastens the healing processes. We evaluated the influence of daily alendronate treatment on the rat femoral head shape after surgical osteonecrosis with core decompression, compared with controls. No differences were found in shape factor and femoral head height/length ratios. It was concluded that alendronate treatment slows down the process of replacing osteonecrotic bone by new bone and prevents early immature new bone collapse resulting from early revascularization because of core decompression.

Mini-ventilation for improved oxygenation during lung resection surgery

Lung separation is frequently used during lung resection to facilitate surgery and hypoxaemia may occur because of increasing pulmonary shunt. In this study, we tested a method of mini-ventilation to the non-dependent lung and compared it to continuous positive airway pressure (CPAP) to improve oxygenation during lung resection. Thirty-eight adult patients participated in this randomised, single-blinded crossover study. Following lung separation, mini-ventilation and CPAP of 5 cmH2O were alternately applied every 15 minutes to the non-dependent lung. Mini-ventilation was performed by a portable time-cycled ventilator with a respiratory rate of 8 breaths/minute and a tidal volume of 0.1 to 0.15 l. Arterial blood gases, peak inspiratory pressure, the dynamic compliance in the dependent lung and the surgeon's evaluation of the surgical field exposure were recorded. The arterial oxygen partial pressure was significantly higher during mini-ventilation compared to CPAP (379 vs 228 mmHg). No difference was noted in the dependent lung peak inspiratory pressure or in the dynamic compliance. The surgical conditions were similar with both methods in 53% of the patients, while the surgeon preferred CPAP in 44% and mini-ventilation in 3%. In conclusion, mini-ventilation is a simple method which improves oxygenation during lung resection. However due to interference with surgical field exposure, it should be reserved for cases in which CPAP does not relieve hypoxaemia.

Delayed awakening following inadvertent high-dose remifentanil infusion in a 13 year old patient

We report the case of a 13 year old patient who received 3.0 mg of remifentanil during a 50-minute surgical procedure as a result of a dosage miscalculation. The patient failed to awaken at the conclusion of the procedure and showed signs of opioid overdose. She recovered spontaneously two hours later.

[Anesthesia and peri-operative care of the elderly patient]

With raised life expectancy, there is a constant elevation in the percentage of elderly people in the general population. Consequently, the age of the surgical patient increases. This progressive process results in operating on patients who were considered 'too old for surgery' a decade ago. There are many physiological and pathological changes that take place in all body systems during aging. The function capacity of organs deteriorates, resulting in decreased capability to overcome surgical stress. As a result, the elderly surgical patients have higher rates of peri-operative morbidity and mortality. Anesthesia and peri-operative care should be customized to this population. Practicing management of older patients undergoing surgery will increase the experience of all caregivers and, in time, improve outcome.

Factors important in evolutionary shaping of immunoglobulin gene loci

Background

The extraordinary diversity characterizing the antibody repertoire is generated by both evolution and lymphocyte development. Much of this diversity is due to the existence of immunoglobulin (Ig) variable region gene segment libraries, which were diversified during evolution and, in higher vertebrates, are used in generating the combinatorial diversity of antibody genes. The aim of the present study was to address the following questions: What evolutionary parameters affect the size and structure of gene libraries? Are the number of genes in libraries of contemporary species, and the corresponding gene locus structure, a random result of evolutionary history, or have these properties been optimized with respect to individual or population fitness? If a larger number of genes or different genome structures do not increase the fitness, then the current structure is probably optimized.

Results

We used a simulation of variable region gene library evolution. We measured the effect of different parameters on gene library size and diversity, and the corresponding fitness. We found compensating relationships between parameters, which optimized Ig library size and diversity.

Conclusions

We conclude that contemporary species' Ig libraries have been optimized by evolution in terms of Ig sequence lengths, the number and diversity of Ig genes, and antibody-antigen affinities.

Ig gene diversification and selection in follicular lymphoma, diffuse large B cell lymphoma and primary central nervous system lymphoma revealed by lineage tree and mutation analyses

Follicular lymphoma (FL), diffuse large B cell lymphoma (DLBCL) and primary central nervous system lymphoma are B cell malignancies. FL and DLBCL have a germinal center origin. We have applied mutational analyses and a novel algorithm for quantifying shape properties of mutational lineage trees to investigate the nature of the diversification, somatic hypermutation and selection processes that affect B cell clones in these malignancies and reveal whether they differ from normal responses. Lineage tree analysis demonstrated higher diversification and mutations per cell in the lymphoma clones. This was caused solely by the longer diversification times of the malignant clones, as their recent diversification processes were similar to those of normal responses, implying similar mutation frequencies. Since previous analyses of antigen-driven selection were shown to yield false positives, we performed a corrected analysis of replacement and silent mutation patterns, which revealed selection against replacement mutations in the framework regions, responsible for the structural integrity of the B cell receptor, but not for positive selection for replacements in the complementary determining regions. Most replacements, however, were neutral or conservative, suggesting that if at all selection operates in these malignancies it is for structural B cell receptor integrity but not for antigen binding.

Somatic hypermutation and antigen-driven selection of B cells are altered in autoimmune diseases

B cells have been found to play a critical role in the pathogenesis of several autoimmune (AI) diseases. A common feature amongst many AI diseases is the formation of ectopic germinal centers (GC) within the afflicted tissue or organ, in which activated B cells expand and undergo somatic hypermutation (SHM) and antigen-driven selection on their immunoglobulin variable region (IgV) genes. However, it is not yet clear whether these processes occurring in ectopic GCs are identical to those in normal GCs. The analysis of IgV mutations has aided in revealing many aspects concerning B cell expansion, mutation and selection in GC reactions. We have applied several mutation analysis methods, based on lineage tree construction, to a large set of data, containing IgV productive and non-productive heavy and light chain sequences from several different tissues, to examine three of the most profoundly studied AI diseases - Rheumatoid Arthritis (RA), Multiple Sclerosis (MS) and Sjögren's Syndrome (SS). We have found that RA and MS sequences exhibited normal mutation spectra and targeting motifs, but a stricter selection compared to normal controls, which was more apparent in RA. SS sequence analysis results deviated from normal controls in both mutation spectra and indications of selection, also showing differences between light and heavy chain IgV and between different tissues. The differences revealed between AI diseases and normal control mutation patterns may result from the different microenvironmental influences to which ectopic GCs are exposed, relative to those in normal secondary lymphoid tissues.

Evidence for large diversity in the human transcriptome created by Alu RNA editing

Adenosine-to-inosine (A-to-I) RNA editing alters the original genomic content of the human transcriptome and is essential for maintenance of normal life in mammals. A-to-I editing in Alu repeats is abundant in the human genome, with many thousands of expressed Alu sequences undergoing editing. Little is known so far about the contribution of Alu editing to transcriptome complexity. Transcripts derived from a single edited Alu sequence can be edited in multiple sites, and thus could theoretically generate a large number of different transcripts. Here we explored whether the combinatorial potential nature of edited Alu sequences is actually fulfilled in the human transcriptome. We analyzed datasets of editing sites and performed an analysis of a detailed transcript set of one edited Alu sequence. We found that editing appears at many more sites than detected by earlier genomic screens. To a large extent, editing of different sites within the same transcript is only weakly correlated. Thus, rather than finding a few versions of each transcript, a large number of edited variants arise, resulting in immense transcript diversity that eclipses alternative splicing as mechanism of transcriptome diversity, although with less impact on the proteome.

Patients aged 80 and older undergoing orthopedic or urologic surgery: a prospective study focusing on perioperative morbidity and mortality

BACKGROUND

The population is progressively aging and an increasing number of elderly patients face surgical treatment.

OBJECTIVE

The current study was designed to examine the perioperative morbidity and mortality of elderly patients undergoing orthopedic or urologic surgery and look for predictors for adverse outcome.

METHODS

This is a prospective study of elderly patients, 80 years of age and older, who underwent elective or emergent orthopedic or urologic surgery in our institution during a 5-month period. Data were collected on age, gender, chronic diseases, number of regular medications, whether or not the patient was bedridden before surgery, American Society of Anesthesiologists (ASA) class, type of surgery and anesthesia, duration of hospitalization, and 30-day postoperative morbidity and mortality. We studied correlations between pre- and intraoperative parameters and postoperative complications.

RESULTS

During the study period, 39 patients underwent urologic surgery and 147 patients underwent orthopedic surgery. Age ranged from 80 to 98 years (85 +/- 4.2 years, mean +/- SD). One patient had an intraoperative complication, 5 patients had postoperative complications within 1 day of surgery, and 23 had complications within 1 month of surgery. Five (2.7%) patients, all of whom were operated urgently, died after surgery. Postoperative complications correlated significantly to poor ASA class (p = 0.01), urgency of the procedure (p = 0.03), and extent (p = 0.02) and duration (p = 0.01) of surgery. No significant correlation was found between outcome and any other pre- or intraoperative factors.

CONCLUSIONS

Elderly surgical patients with poor ASA class or following urgent, extensive or long surgery are at a higher risk for postoperative morbidity and mortality, mandating special perioperative care.

Maxillofacial trauma patient: coping with the difficult airway

Establishing a secure airway in a trauma patient is one of the primary essentials of treatment. Any flaw in airway management may lead to grave morbidity and mortality. Maxillofacial trauma presents a complex problem with regard to the patient's airway. By definition, the injury compromises the patient's airway and it is, therefore, must be protected. In most cases, the patient undergoes surgery for maxillofacial trauma or for other, more severe, life-threatening injuries, and securing the airway is the first step in the introduction of general anaesthesia. In such patients, we anticipate difficult endotracheal intubation and, often, also difficult mask ventilation. In addition, the patient is usually regarded as having a "full stomach" and has not been cleared of a C-spine injury, which may complicate airway management furthermore. The time available to accomplish the task is short and the patient's condition may deteriorate rapidly. Both decision-making and performance are impaired in such circumstances. In this review, we discuss the complexity of the situation and present a treatment approach.

[Surgical management of esophageal pathology: 6 years of experience in a single surgical department]

BACKGROUND

Esophageal diseases vary in relation to geographic and behavioral factors. Whether benign or malignant, these diseases interfere with food swallowing. Surgical treatment is variable and aims at restoring the alimentary tract continuity. In this research the authors retrospectively studied esophageal pathologies and their surgical treatment in their department over a 6 year period.

PATIENTS AND METHODS

The records of all patients who underwent surgery for esophageal pathology in a single surgical department at a referral center between January 2002 and December 2007 were reviewed. Data that was collected included patient age, gender, type of pathology, staging, type and length of surgery, length of hospital stay, post-operative morbidity and mortality.

RESULTS

During the study period, 186 patients were operated for esophageal pathology, 154 (83%) had malignant disease and 32 (17%) had benign disease. The distribution of malignancy types was: adenocarcinoma 57%, squamous cell carcinoma 27%, signet ring cell carcinoma 8%, and other 8%. Median length of post-operative hospital stay was 27 days. Thirty two percent of the patients experienced complications, including anastomotic leak (10%), respiratory (9.5%) or cardiac (2%) complications, and infection (7.5%), while 3% required re-operation. Postoperative mortality rate in the hospital was 6.5%.

CONCLUSIONS

The majority of patients undergoing esophageal surgery suffer malignancy, mainly adenocarcinoma. The surgery is extensive and is followed by a long recovery period, during which the patient is subject to a variety of complications. Mortality rate is significant yet comparable to centers around the world with high volume of esophageal operations.

Posterior reversible encephalopathy syndrome after combined general and spinal anesthesia with intrathecal morphine

We describe a patient who was in a stupor for several days after combined general-spinal anesthesia. Both clinical manifestations and magnetic resonance imaging findings were consistent with posterior reversible encephalopathy syndrome and resolved after the patient recovered spontaneously.

Perioperative morbidity and mortality in 80 years and older undergoing elective urology surgery - a prospective study

BACKGROUND AND PURPOSE

The number of octogenarians requiring surgery increases constantly. Data regarding perioperative morbidity and mortality in octogenarians is limited. Our aim was to assess surgery-related complications in octogenarians, undergoing urological surgery.

PATIENTS AND METHODS

We prospectively collected data from octogenarians and a control group of younger patients undergoing an elective urological surgery in our institution. Recorded data included: age, gender, American Society of Anesthesiologists (ASA) score, co-morbidities, number of medications, operation extent, anaesthesia type, surgery duration and perioperative morbidity and mortality.

RESULTS

Forty-seven octogenarians and 80 patients with a median age of 59 years (range 19-75) enrolled prospectively. Gender ratio, surgeries extent and median operative time were similar among groups. General anaesthesia was more prevalent in the control group. ASA classification and duration of hospitalization were significantly higher in octogenarians. The rate of intra-operative complications was significantly higher in the octogenarians group 6.38% versus 3.75% (p = 0.007), there was no significant difference in immediate post-operative and post-discharge complications among groups. One octogenarian patient died 2 days post-surgery, no death occurred in the control group.

CONCLUSIONS

Octogenarians have higher rate of intra-operative morbidity, leading to longer hospital stay. More experienced surgeons and anaesthetists should be involved in the operation; and careful surgical technique, tapered anaesthesia and higher level of post-operative monitoring should be applied for patients in this age.

Cerebral microemboli during hip fracture fixation: a prospective study

BACKGROUND

Recent studies have shown that cerebral fat microembolism takes place during surgery for hip or knee replacement. In this study, we examined the occurrence of cerebral microembolism, solid or gas, during a standard procedure of hip fracture fixation.

METHODS

This was a prospective study of patients who underwent urgent surgery with a dynamic hip screw for hip fracture fixation. During surgery, patients were monitored with transcranial Doppler for detection of microemboli from right and left middle cerebral arteries.

RESULTS

Twenty-two patients were included in the study; their median age was 82 yr (range, 51-97 yr). In nine (41%) patients, high intensity transient signals were recorded, indicating microemboli passage in the middle cerebral arteries. All nine patients had signals of both solid and gas emboli. One of these nine patients had a postoperative cerebrovascular accident.

CONCLUSIONS

The incidence of cerebral microemboli during urgent surgery for hip fracture fixation is considerable. This phenomenon is not confined to hip or knee replacement surgery. The clinical implications of this finding require further investigation.

IgTree: creating Immunoglobulin variable region gene lineage trees

Lineage trees describe the microevolution of cells within an organism. They have been useful in the study of B cell affinity maturation, which is based on somatic hypermutation of immunoglobulin genes in germinal centers and selection of the resulting mutants. Our aim was to create and implement an algorithm that can generate lineage trees from immunoglobulin variable region gene sequences. The IgTree program implements the algorithm we developed, and generates lineage trees. Original sequences found in experiments are assigned to either leaves or internal nodes of the tree. Each tree node represents a single mutation separating the sequences. The mutations that separate the sequences from each other can be point mutations, deletions or insertions. The program can deal with gaps and find potential reversion mutations. The program also enumerates mutation frequencies and sequence motifs around each mutation, on a per-tree basis. The algorithm has proven useful in several studies of immunoglobulin variable region gene mutations.

Antigen-driven selection in germinal centers as reflected by the shape characteristics of immunoglobulin gene lineage trees: a large-scale simulation study

During the immune response, the generation of memory B lymphocytes in germinal centers involves affinity maturation of the cells' antigen receptors, based on somatic hypermutation of receptor genes and antigen-driven selection of the resulting mutants. Affinity maturation is vital for immune protection, and is the basis of humoral immune learning and memory. Lineage trees of somatically hypermutated immunoglobulin genes often serve to qualitatively illustrate claims concerning the dynamics of affinity maturation in germinal centers. Here, we derive the quantitative relationships between parameters characterizing affinity maturation dynamics (proliferation, differentiation and mutation rates, initial affinity of the Ig to the antigen, and selection thresholds) and the mathematical properties of lineage trees, using a computer simulation which combines mathematical models for all mature B cell populations, stochastic models of hypermutation and selection, lineage tree generation and measurement of graphical tree characteristics. We identified seven key lineage tree properties, and found correlations of these with initial clone affinity and with the selection threshold. These two parameters were found to be the main factors affecting lineage tree shapes in both primary and secondary response trees. The results also confirm that recycling from centrocytes back to centroblasts is highly likely.

The biological basis of the bone-muscle inter-relationship in the algorithm of fracture healing

The biological cascade of fracture healing is intimately linked to the muscle envelope. It further depends on the preservation of stable, perpetual axial micromovements. The current study was designed to demonstrate that high molecular weight bioactive substances diffuse from the muscle envelope to initiate osteoinductive activity at experimental fracture sites. Forty-eight rats underwent an experimental fracture of the left tibia and stabilization with an intramedullary 20-gauge needle. The animals were divided into 4 groups (A-D) of 12 rats each according to the post-fracture treatment. In group A (control) no additional treatment was applied following fracture and intramedullary fixation. In groups B, C, and D, a nitrocellulose membrane of various sizes was wrapped around the fracture, separating the periosteum from the muscle envelope. The groups differed by the membrane pore size, allowing passage of the following molecular sizes: 50 kilodaltons (kDa), 12 to 14 kDa, and 3.5 kDa in groups B, C, and D, respectively. Four animals in each group were sacrificed 2, 5, and 10 weeks after the procedure for radiographic and histological evaluation of fracture healing. Radiographic evaluation revealed a decreased rate of bone synthesis that correlated with the nitrocellulose pore size. Morphological and functional analysis of the bone explants indicated poorly healed fractures in groups B, C, and D. Direct contact between fractured bone and its muscle envelope is essential for the biological sequence of new bone formation. The extent of obstruction between the fracture and its muscle envelope correlates with the delay in fracture healing.

A comparison of the Truview blade with the Macintosh blade in adult patients

The Truview blade facilitates a view of the vocal cords by indirect laryngoscopy. We prospectively compared the view obtained at laryngoscopy and intubating conditions of Truview (Group 1) or Macintosh (Group 2) blades in 170 patients who were scheduled to undergo general anaesthesia. We studied pre-operative airway evaluation, laryngoscopic view, duration of intubation, maximal force applied during intubation, anaesthetist's estimation of intubation effort on a 1-3 scale, bleeding, teeth and soft tissue damage, and postoperative stridor and hoarseness. The results demonstrated that, whilst the Truview produced a better laryngoscopic view and less maximal force applied during intubation, the duration of intubation was longer. No significant difference was found in the anaesthetist's estimation of intubation effort, tooth damage or postoperative stridor and hoarseness. Significantly fewer patients suffered bleeding and soft tissue damage following intubation with the Truview than with the Macintosh blade. The Truview blade is a useful option for tracheal intubation in patients with normal and anticipated difficult airways.

Low-Volume Interscalene Brachial Plexus Block for Post-Thoracotomy Shoulder Pain

OBJECTIVES

This study was designed to evaluate the effectiveness of low-volume interscalene brachial plexus block for post-thoracotomy ipsilateral shoulder pain and to compare it with nonsteroidal anti-inflammatory drug treatment.

DESIGN

Prospective nonblinded study.

SETTING

University hospital.

PARTICIPANTS

Sixty adult patients.

INTERVENTION

Patients who underwent elective thoracic surgery under combined epidural and general anesthesia, and after surgery were free of incisional pain but complaining of shoulder pain, were included in the study. They were selected in a sequential manner and placed into 2 groups of 30 patients each. Group 1 had a low-volume interscalene brachial plexus block, using 10 mL of bupivacaine 0.5%. Group 2 had an intramuscular injection of diclofenac sodium, 75 mg.

MEASUREMENTS AND MAIN RESULTS

Pain was measured during their stay in the postanesthesia care unit (PACU) by using a visual analog score (VAS). Opioids were administered when pain relief was incomplete. Pain intensity was re-estimated the next morning and patient satisfaction was scored. VAS was found to be significantly lower in the low-volume interscalene block group than in the diclofenac group at 30 minutes after treatment and when leaving PACU (p < 0.001 for both). Patients in the interscalene block group stayed longer in the PACU (p = 0.019), and significantly fewer required rescue opioids (p = 0.03). There was no significant difference between the groups in patient satisfaction with the pain treatment.

CONCLUSIONS

The authors concluded that low-volume interscalene brachial plexus block is a superior treatment for post-thoracotomy shoulder pain compared with diclofenac injection, although it requires a slightly longer stay in the PACU.

The pyruvate kinase isoenzyme M2 (Tu M2-PK) as a tumour marker for renal cell carcinoma

The M2 isoenzyme of pyruvate kinase (M2-PK) is specially expressed by tumour cells (Tu M2-PK) and has been detected in the peripheral blood of patients with renal cell carcinoma (RCC). We analysed the benefit of using Tu M2-PK as a tumour marker for primary detection of RCC by receiver operating characteristic (ROC) analysis. The area under the curve was 0.674, and the sensitivity, specificity and positive predictive value (PPV) were 44.4%, 87.5% and 88%, respectively, at the ROC optimal cut-off of 28.2 kU/L. We examined 71 patients. Since the marker sensitivity for detection of the early stages T1 and T2 was only 47% it is not suggested to use this marker for primary diagnosis of RCC. Its use as part of the confirmatory preoperative evaluation might be considered in view of its high PPV.