Ion channels modulate ion flux across cell membranes, activate signal transduction pathways, and influence cellular transport—vital biological functions that are inexorably linked to cellular processes that go awry during carcinogenesis. Indeed, deregulation of ion channel function has been implicated in cancer-related phenomena such as unrestrained cell proliferation and apoptotic evasion. As the prototype for ligand-gated ion channels, nicotinic acetylcholine receptors (nAChRs) have been extensively studied in the context of neuronal cells but accumulating evidence also indicate a role for nAChRs in carcinogenesis. Recently, variants in the nAChR genes CHRNA3, CHRNA5, and CHRNB4 have been implicated in nicotine dependence and lung cancer susceptibility. Here, we silenced the expression of these three genes to investigate their function in lung cancer. We show that these genes are necessary for the viability of small cell lung carcinomas (SCLC), the most aggressive type of lung cancer. Furthermore, we show that nicotine promotes SCLC cell viability whereas an α3β4-selective antagonist, α-conotoxin AuIB, inhibits it. Our findings posit a mechanism whereby signaling via α3/α5/β4-containing nAChRs promotes lung carcinogenesis.
nicotinic acetylcholine receptor; ligand-gated ion channel; lung cancer; small cell lung carcinoma; CHRNA5
Salmonella enterica serovar Typhimurium definitive type 2 (DT2) is host restricted to Columba livia (rock or feral pigeon) but is also closely related to S. Typhimurium isolates that circulate in livestock and cause a zoonosis characterized by gastroenteritis in humans. DT2 isolates formed a distinct phylogenetic cluster within S. Typhimurium based on whole-genome-sequence polymorphisms. Comparative genome analysis of DT2 94-213 and S. Typhimurium SL1344, DT104, and D23580 identified few differences in gene content with the exception of variations within prophages. However, DT2 94-213 harbored 22 pseudogenes that were intact in other closely related S. Typhimurium strains. We report a novel in silico approach to identify single amino acid substitutions in proteins that have a high probability of a functional impact. One polymorphism identified using this method, a single-residue deletion in the Tar protein, abrogated chemotaxis to aspartate in vitro. DT2 94-213 also exhibited an altered transcriptional profile in response to culture at 42°C compared to that of SL1344. Such differentially regulated genes included a number involved in flagellum biosynthesis and motility.
Whereas Salmonella enterica serovar Typhimurium can infect a wide range of animal species, some variants within this serovar exhibit a more limited host range and altered disease potential. Phylogenetic analysis based on whole-genome sequences can identify lineages associated with specific virulence traits, including host adaptation. This study represents one of the first to link pathogen-specific genetic signatures, including coding capacity, genome degradation, and transcriptional responses to host adaptation within a Salmonella serovar. We performed comparative genome analysis of reference and pigeon-adapted definitive type 2 (DT2) S. Typhimurium isolates alongside phenotypic and transcriptome analyses, to identify genetic signatures linked to host adaptation within the DT2 lineage.
Objective The main objective of this study was to evaluate the value of free-run electromyography (f-EMG) monitoring of cranial nerves (CNs) VII, IX, X, XI, and XII in skull base surgeries performed using endoscopic endonasal approach (EEA) to reduce iatrogenic CN deficits.
Design We retrospectively identified 73 patients out of 990 patients who had EEA in our institution who had at least one CN monitored. In each CN group, we classified patients who had significant (SG) f-EMG activity as group I and those who did not as group II.
Results We monitored a total of 342 CNs. A total of 62 nerves had SG f-EMG activity including CN VII = 18, CN IX = 16, CN X = 13, CN XI = 5, and CN XII = 10. No nerve deficit was found in the nerves that had significant activity during procedure. A total of five nerve deficits including (CN IX = 1, CN X = 2, CN XII = 2) were observed in the group that did not display SG f-EMG activity during surgery.
Conclusions f-EMG seems highly sensitive to surgical manipulations and in locating CNs. It seems to have limited value in predicting postoperative neurological deficits. Future studies to evaluate the EMG of lower CNs during EEA procedures need to be done with both f-EMG and triggered EMG.
electromyography; lower cranial nerves; endoscopic endonasal approach; skull base surgery
Modern DNA sequencing technologies enable geneticists to rapidly identify genetic variation among many human genomes. However, isolating the minority of variants underlying disease remains an important, yet formidable challenge for medical genetics. We have developed GEMINI (GEnome MINIng), a flexible software package for exploring all forms of human genetic variation. Unlike existing tools, GEMINI integrates genetic variation with a diverse and adaptable set of genome annotations (e.g., dbSNP, ENCODE, UCSC, ClinVar, KEGG) into a unified database to facilitate interpretation and data exploration. Whereas other methods provide an inflexible set of variant filters or prioritization methods, GEMINI allows researchers to compose complex queries based on sample genotypes, inheritance patterns, and both pre-installed and custom genome annotations. GEMINI also provides methods for ad hoc queries and data exploration, a simple programming interface for custom analyses that leverage the underlying database, and both command line and graphical tools for common analyses. We demonstrate GEMINI's utility for exploring variation in personal genomes and family based genetic studies, and illustrate its ability to scale to studies involving thousands of human samples. GEMINI is designed for reproducibility and flexibility and our goal is to provide researchers with a standard framework for medical genomics.
Objective To evaluate the value of free-run electromyography (f-EMG) monitoring of extraocular cranial nerves (EOCN) III, IV, and VI during expanded endonasal surgery (EES) of the skull base in reducing iatrogenic cranial nerve (CN) deficits.
Design We retrospectively identified 200 patients out of 990 who had at least one EOCN monitored during EES. We further separated patients into groups according to the specific CN monitored. In each CN group, we classified patients who had significant (SG) f-EMG activity as Group I and those who did not as Group II.
Results A total of 696 EOCNs were monitored. The number of muscles supplied by EOCNs that had SG f-EMG activity was 88, including CN III = 46, CN IV = 21, and CN VI = 21. There were two deficits involving CN VI in patients who had SG f-EMG activity during surgery. There were 14 deficits observed, including CN III = 3, CN IV = 2, and CN VI = 9 in patients who did not have SG f-EMG activity during surgery.
Conclusions f-EMG monitoring of EOCN during EES can be useful in identifying the location of the nerve. It seems to have limited value in predicting postoperative neurological deficits. Future studies to evaluate the EMG of EOCN during EES need to be done with both f-EMG and triggered EMG.
electromyography; lower cranial nerves; expanded endonasal surgery
Salmonella Typhi and Typhimurium diverged only ∼50 000 years ago, yet have very different host ranges and pathogenicity. Despite the availability of multiple whole-genome sequences, the genetic differences that have driven these changes in phenotype are only beginning to be understood. In this study, we use transposon-directed insertion-site sequencing to probe differences in gene requirements for competitive growth in rich media between these two closely related serovars. We identify a conserved core of 281 genes that are required for growth in both serovars, 228 of which are essential in Escherichia coli. We are able to identify active prophage elements through the requirement for their repressors. We also find distinct differences in requirements for genes involved in cell surface structure biogenesis and iron utilization. Finally, we demonstrate that transposon-directed insertion-site sequencing is not only applicable to the protein-coding content of the cell but also has sufficient resolution to generate hypotheses regarding the functions of non-coding RNAs (ncRNAs) as well. We are able to assign probable functions to a number of cis-regulatory ncRNA elements, as well as to infer likely differences in trans-acting ncRNA regulatory networks.
To describe the clinical presentation, pathophysiology and treatment of spontaneous cerebrospinal fluid (CSF) leaks of the sphenoid bone, with an emphasis on a previously undescribed form in this location, in which CSF is trapped under the mucosa of the sinonasal cavity or in the soft tissue of the skull base.
Case series and literature review. Level of evidence 4.
Analysis of cases through medical records and literature review.
Four examples of unusual spontaneous CSF leaks of the skull base are presented. In each case, a CSF collection was contained behind the sinonasal mucosa of the sphenoid sinus, resembling a nasal polyp or mucocele on exam or imaging. In one case, the fluid collection was also associated with significant bone resorption and extravasation into the soft tissue of the infratemporal fossa. In each case, small defects of the ventral skull base (sphenoid bone) were the source of the CSF leaks. Successful treatment was achieved after transnasal endoscopic repair of the skull base defects using a combination of free abdominal fat grafts, free fascial grafts and pedicled nasoseptal flaps. Postoperatively, a ventriculoperitoneal shunt was placed if the intracranial pressure was elevated.
Spontaneous CSF leaks arising in the sphenoid sinus may not always present with overt CSF rhinorrhea but with a submucosal fluid collection (pseudomeningocele) that may mimic a mucocoele or nasal polyp. These bona fide pseudomeningoceles of the skull base may be associated with elevated intracranial pressure and can be managed using endoscopic endonasal surgery.
CSF leak; mucocele; meningocele; skull base; sinus
The Rfam database (available via the website at http://rfam.sanger.ac.uk and through our mirror at http://rfam.janelia.org) is a collection of non-coding RNA families, primarily RNAs with a conserved RNA secondary structure, including both RNA genes and mRNA cis-regulatory elements. Each family is represented by a multiple sequence alignment, predicted secondary structure and covariance model. Here we discuss updates to the database in the latest release, Rfam 11.0, including the introduction of genome-based alignments for large families, the introduction of the Rfam Biomart as well as other user interface improvements. Rfam is available under the Creative Commons Zero license.
The largest family of toxin-antitoxin (TA) modules are encoded by the vapBC operons, but their roles in bacterial physiology remain enigmatic. Microarray analysis in Mycobacterium smegmatis overexpressing VapC/VapBC revealed a high percentage of downregulated genes with annotated roles in carbon transport and metabolism, suggesting that VapC was targeting specific metabolic mRNA transcripts. To validate this hypothesis, purified VapC was used to identify the RNA cleavage site in vitro. VapC had RNase activity that was sequence specific, cleaving single-stranded RNA substrates at AUAU and AUAA in vitro and in vivo (viz., MSMEG_2121 to MSMEG_2124). A bioinformatic analysis of these regions suggested that an RNA hairpin 3′ of the AUA(U/A) motif is also required for efficient cleavage. VapC-mediated regulation in vivo was demonstrated by showing that MSMEG_2124 (dhaF) and MSMEG_2121 (dhaM) were upregulated in a ΔvapBC mutant growing on glycerol. The ΔvapBC mutant had a specific rate of glycerol consumption that was 2.4-fold higher than that of the wild type during exponential growth. This increased rate of glycerol consumption was not used for generating bacterial biomass, suggesting that metabolism by the ΔvapBC mutant was uncoupled from growth. These data suggest a model in which VapC regulates the rate of glycerol utilization to match the anabolic demands of the cell, allowing for fine-tuning of the catabolic rate at a posttranscriptional level.
The RNA world hypothesis, that RNA genomes and catalysts preceded DNA genomes and genetically-encoded protein catalysts, has been central to models for the early evolution of life on Earth. A key part of such models is continuity between the earliest stages in the evolution of life and the RNA repertoires of extant lineages. Some assessments seem consistent with a diverse RNA world, yet direct continuity between modern RNAs and an RNA world has not been demonstrated for the majority of RNA families, and, anecdotally, many RNA functions appear restricted in their distribution. Despite much discussion of the possible antiquity of RNA families, no systematic analyses of RNA family distribution have been performed. To chart the broad evolutionary history of known RNA families, we performed comparative genomic analysis of over 3 million RNA annotations spanning 1446 families from the Rfam 10 database. We report that 99% of known RNA families are restricted to a single domain of life, revealing discrete repertoires for each domain. For the 1% of RNA families/clans present in more than one domain, over half show evidence of horizontal gene transfer (HGT), and the rest show a vertical trace, indicating the presence of a complex protein synthesis machinery in the Last Universal Common Ancestor (LUCA) and consistent with the evolutionary history of the most ancient protein-coding genes. However, with limited interdomain transfer and few RNA families exhibiting demonstrable antiquity as predicted under RNA world continuity, our results indicate that the majority of modern cellular RNA repertoires have primarily evolved in a domain-specific manner.
In cells, DNA carries recipes for making proteins, and proteins perform chemical reactions, including replication of DNA. This interdependency raises questions for early evolution, since one molecule seemingly cannot exist without the other. A resolution to this problem is the RNA world, where RNA is postulated to have been both genetic material and primary catalyst. While artificially selected catalytic RNAs strengthen the chemical plausibility of an RNA world, a biological prediction is that some RNAs should date back to this period. In this study, we ask to what degree RNAs in extant organisms trace back to the common ancestor of cellular life. Using the Rfam RNA families database, we systematically screened genomes spanning the three domains of life (Archaea, Bacteria, Eukarya) for RNA genes, and examined how far back in evolution known RNA families can be traced. We find that 99% of RNA families are restricted to a single domain. Limited conservation within domains implies ongoing emergence of RNA functions during evolution. Of the remaining 1%, half show evidence of horizontal transfer (movement of genes between organisms), and half show an evolutionary history consistent with an RNA world. The oldest RNAs are primarily associated with protein synthesis and export.
Background Access to the intraorbital optic nerve segment can be facilitated via a transcranial approach that allows access to the entire orbital cavity. The endoscopic endonasal approach (EEA) combined with a transconjunctival-medial orbitotomy represents an alternative technique to achieve the same goal.
Objective Report a surgical technique that allows total resection of the intraorbital optic nerve with minimal trauma and excellent results. Further extend and define the limits and indications of the EEA to orbital surgery.
Methods A patient with rapidly progressive, but asymmetric, vision loss underwent EEA for optic nerve biopsy. Due to the undetermined histopathological diagnosis and complete unilateral vision loss, diagnostic total optic nerve resection was indicated. The entire intraorbital length of the nerve was resected via an endoscopic endonasal transorbital approach combined with transconjunctival-medial orbitotomy.
Results A 2-cm intraorbital nerve segment was sent for pathological examination. The patient maintained normal extraocular movements and experienced no complications. The postoperative course was uneventful and the patient was discharged the next day.
Conclusion The EEA provides another option for access to the entire optic nerve. It is a safe and effective technique lacking cosmetic defects and providing an alternative corridor to traditional transcranial approaches to the orbit.
endoscopic endonasal approach; optic nerve resection; orbital surgery; transconjunctival-medial orbitotomy
Nicotine activation of nicotinic acetylcholine receptors (nAChRs) within the dopaminergic (DAergic) neuron-rich ventral tegmental area (VTA) is necessary and sufficient for nicotine reinforcement. In this study, we show that rewarding doses of nicotine activated VTA DAergic neurons in a region-selective manner, preferentially activating neurons in the posterior VTA (pVTA) but not in the anterior VTA (aVTA) or in the tail VTA (tVTA). Nicotine (1 μM) directly activated pVTA DAergic neurons in adult mouse midbrain slices, but had little effect on DAergic neurons within the aVTA. Quantification of nAChR subunit gene expression revealed that pVTA DAergic neurons expressed higher levels of α4, α6, and β3 transcripts than did aVTA DAergic neurons. Activation of nAChRs containing the α4 subunit (α4* nAChRs) was necessary and sufficient for activation of pVTA DAergic neurons: nicotine failed to activate pVTA DAergic neurons in α4 knockout animals; in contrast, pVTA α4* nAChRs were selectively activated by nicotine in mutant mice expressing agonist-hypersensitive α4* nAChRs (Leu9′Ala mice). In addition, whole-cell currents induced by nicotine in DAergic neurons were mediated by α4* nAChRs and were significantly larger in pVTA neurons than in aVTA neurons. Infusion of an α6* nAChR antagonist into the VTA blocked activation of pVTA DAergic neurons in WT mice and in Leu9′Ala mice at nicotine doses, which only activate the mutant receptor indicating that α4 and α6 subunits coassemble to form functional receptors in these neurons. Thus, nicotine selectively activates DAergic neurons within the pVTA through α4α6* nAChRs. These receptors represent novel targets for smoking-cessation therapies.
dopamine; acetylcholine; nicotine; smoking; ventral tegmental area; mice; acetylcholine; dopamine; addiction & substance abuse; neurophysiology; nicotine; smoking; ventral tegmental area; mice
Recently, we investigated the molecular mechanisms of the smoking cessation drug varenicline, a nicotinic acetylcholine receptor (nAChR) partial agonist, in its ability to decrease voluntary ethanol intake in mice. Previous to our study, other labs had shown that this drug can decrease ethanol consumption and seeking in rat models of ethanol intake. Although varenicline was designed to be a high affinity partial agonist of nAChRs containing the α4 and β2 subunits (designated as α4β2*), at higher concentrations it can also act upon α3β2*, α6*, α3β4* and α7 nAChRs. Therefore, to further elucidate the nAChR subtype responsible for varenicline-induced reduction of ethanol consumption, we utilized a pharmacological approach in combination with two complimentary nAChR genetic mouse models, a knock-out line that does not express the α4 subunit (α4 KO) and another line that expresses α4* nAChRs hypersensitive to agonist (the Leu9′Ala line). We found that activation of α4* nAChRs was necessary and sufficient for varenicline-induced reduction of alcohol consumption. Consistent with this result, here we show that a more efficacious nAChR agonist, nicotine, also decreased voluntary ethanol intake, and that α4* nAChRs are critical for this reduction.
alcoholism; ethanol; nicotine; varenicline; nicotinic acetylcholine receptors; mice
We report a technical variation of the endoscopic endonasal approach to the sellar and suprasellar regions which relies on the use of a 45-degree angled endoscope. The so-called “infrasellar approach” aims at excising lesions situated within the intermediate and posterior lobes of the pituitary gland without damaging the anterior lobe, thus potentially minimizing endocrinological morbidity. In this regard the endoscopic infrasellar approach might be advantageous in selected cases when compared with the traditional transsphenoidal approach with the microscope. We describe the technique and illustrate it with representative clinical cases.
Endoscopic endonasal approach; infrasellar approach; 45-degrees angled endoscope; Rathke's cleft cysts; Cushing disease; hypothalamic pilocytic astrocytoma
Wikipedia, the online encyclopedia, is the most famous wiki in use today. It contains over 3.7 million pages of content; with many pages written on scientific subject matters that include peer-reviewed citations, yet are written in an accessible manner and generally reflect the consensus opinion of the community. In this, the 19th Annual Database Issue of Nucleic Acids Research, there are 11 articles that describe the use of a wiki in relation to a biological database. In this commentary, we discuss how biological databases can be integrated with Wikipedia, thereby utilising the pre-existing infrastructure, tools and above all, large community of authors (or Wikipedians). The limitations to the content that can be included in Wikipedia are highlighted, with examples drawn from articles found in this issue and other wiki-based resources, indicating why other wiki solutions are necessary. We discuss the merits of using open wikis, like Wikipedia, versus other models, with particular reference to potential vandalism. Finally, we raise the question about the future role of dedicated database biocurators in context of the thousands of crowdsourced, community annotations that are now being stored in wikis.
Cerebral aneurysm rupture can lead to devastating neurological complications and present a complex problem to treat. We report a unique case of a ruptured posterior communicating artery (PCoA) aneurysm presenting with sudden and complete vision loss.
A 39-year-old man presented with the acute onset of severe headache and complete bilateral vision loss. The patient described headaches for several months prior to presentation. However, prior to the day of presentation, he had no visual disturbance. A CT angiogram (CTA) and magnetic resonance imaging (MRI) of the brain revealed a 1.6-cm, non-contrast enhancing suprasellar mass, eccentric to the left side, consistent with hemorrhagic mass. There was no obvious aneurysm or vascular malformation. The sella tursica was normal in appearance. The patient was taken for an immediate endoscopic endonasal transtuberculum approach for optic nerve decompression. Hematoma without an associated tumor was encountered and partially evacuated before aborting with resultant partial improvement in vision. A subsequent cerebral angiogram revealed an irregularly shaped, postero-laterally pointing, 2.5-mm left PCoA aneurysm. The patient was then taken for open clipping of the ruptured aneurysm. A large, fibrinous capsule was found over the superolateral aspect of the aneurysm. The ruptured aneurysm was secured with clips and the surrounding hematoma was evacuated.
In the immediate postoperative period, the patient regained vision in the nasal field of his right eye. This case illustrates a unique presentation of a ruptured PCoA aneurysm, and thus must be considered in the differential diagnosis of a suprasellar hemorrhage resulting in visual loss in absence of a recognizable associated tumor.
Apoplexy; posterior communicating artery aneurysm; ruptured cerebral aneurysm
Genome-wide association studies have underscored the importance of the clustered neuronal nicotinic acetylcholine receptor subunit genes with respect to nicotine dependence as well as lung cancer susceptibility. CHRNB4, which encodes the nicotinic acetylcholine receptor β4 subunit, plays a major role in the molecular mechanisms that govern nicotine withdrawal. Thus, elucidating how expression of the β4 gene is regulated is critical for understanding the pathophysiology of nicotine addiction. We previously identified a CA box regulatory element, (5′ – CCACCCCT –3′) critical for β4 promoter activity in vitro. We further demonstrated that a 2.3-kb fragment of the β4 promoter region containing the CA box is capable of directing cell-type specific expression of a reporter gene to a myriad of brain regions that endogenously express the β4 gene. To test the hypothesis that the CA box is critical for β4 promoter activity in vivo, transgenic animals expressing a mutant form of the β4 promoter were generated. Reporter gene expression was not detected in any tissue or cell type at embryonic day 18.5. Similarly, we observed drastically reduced reporter gene expression at postnatal day 30 when compared to wild type transgenic animals. Finally, we demonstrated that CA box mutation results in decreased interaction of the transcription factor Sp1 with the mutant β4 promoter. Taken together these results demonstrate that the CA box is critical for β4 promoter activity in vivo.
Nicotinic Acetylcholine Receptors; CHRNB4; Sp1; CACCC; Transgenic Mice
More than 1 billion people around the world smoke, with 10 million cigarettes sold every minute. Cigarettes contain thousands of harmful chemicals including the psychoactive compound, nicotine. Nicotine addiction is initiated by the binding of nicotine to nicotinic acetylcholine receptors, ligand-gated cation channels activated by the endogenous neurotransmitter, acetylcholine. These receptors serve as prototypes for all ligand-gated ion channels and have been extensively studied in an attempt to elucidate their role in nicotine addiction. Many of these studies have focused on heteromeric nicotinic acetylcholine receptors containing α4 and β2 subunits and homomeric nicotinic acetylcholine receptors containing the α7 subunit, two of the most abundant subtypes expressed in the brain. Recently however, a series of linkage analyses, candidate-gene analyses and genome-wide association studies have brought attention to three other members of the nicotinic acetylcholine receptor family: the α5, α3 and β4 subunits. The genes encoding these subunits lie in a genomic cluster that contains variants associated with increased risk for several diseases including nicotine dependence and lung cancer. The underlying mechanisms for these associations have not yet been elucidated but decades of research on the nicotinic receptor gene family as well as emerging data provide insight on how these receptors may function in pathological states. Here, we review this body of work, focusing on the clustered nicotinic acetylcholine receptor genes and evaluating their role in nicotine addiction and lung cancer.
Nicotinic acetylcholine receptors; CHRNA5/A3/B4 gene cluster; Nicotine addiction; Lung cancer; Genome-wide association studies
Nicotine activation of nicotinic acetylcholine receptors (nAChRs) within the dopaminergic (DAergic) neuron-rich ventral tegmental area (VTA) is necessary and sufficient for nicotine reinforcement. Here we show that rewarding doses of nicotine activated VTA DAergic neurons in a region-selective manner, preferentially activating neurons in the posterior VTA (pVTA) but not the anterior VTA (aVTA) or tail VTA (tVTA). Nicotine (1µM) directly activated pVTA DAergic neurons in adult mouse midbrain slices but had little effect on DAergic neurons within the aVTA. Quantification of nAChR subunit gene expression revealed that pVTA DAergic neurons expressed higher levels of α4, α6, and β3 transcripts, compared to aVTA DAergic neurons. Activation of nAChRs containing the α4 subunit (α4* nAChRs) was necessary and sufficient for activation of pVTA DAergic neurons: Nicotine failed to activate pVTA DAergic neurons in α4 knock-out animals; in contrast pVTA α4* nAChRs were selectively activated by nicotine, in mutant mice expressing agonist hypersensitive α4* nAChRs (Leu9’Ala mice). In addition, whole-cell currents induced by nicotine in DAergic neurons were mediated by α4* nAChRs and were significantly larger in pVTA neurons compared to aVTA neurons. Infusion of an α6* nAChR antagonist into the VTA blocked activation of pVTA DAergic neurons in WT mice and Leu9’Ala mice at nicotine doses that only activate the mutant receptor indicating that α4 and α6 subunits coassemble to form functional receptors in these neurons. Thus, nicotine selectively activates DAergic neurons within the pVTA via α4α6* nAChRs. These receptors represent novel targets for smoking cessation therapies.
Dopamine; Acetylcholine; Nicotine; Smoking; Ventral Tegmental Area; Mice
Campylobacter jejuni is the most common bacterial cause of foodborne disease in the developed world. Its general physiology and biochemistry, as well as the mechanisms enabling it to colonize and cause disease in various hosts, are not well understood, and new approaches are required to understand its basic biology. High-throughput sequencing technologies provide unprecedented opportunities for functional genomic research. Recent studies have shown that direct Illumina sequencing of cDNA (RNA-seq) is a useful technique for the quantitative and qualitative examination of transcriptomes. In this study we report RNA-seq analyses of the transcriptomes of C. jejuni (NCTC11168) and its rpoN mutant. This has allowed the identification of hitherto unknown transcriptional units, and further defines the regulon that is dependent on rpoN for expression. The analysis of the NCTC11168 transcriptome was supplemented by additional proteomic analysis using liquid chromatography-MS. The transcriptomic and proteomic datasets represent an important resource for the Campylobacter research community.
Frontline treatment of small cell lung carcinoma (SCLC) relies heavily on chemotherapeutic agents and radiation therapy. Though SCLC patients respond well to initial cycles of chemotherapy, they eventually develop resistance. Identification of novel therapies against SCLC is therefore imperative.
Methods and Findings
We have designed a bioluminescence-based cell viability assay for high-throughput screening of anti-SCLC agents. The assay was first validated via standard pharmacological agents and RNA interference using two human SCLC cell lines. We then utilized the assay in a high-throughput screen using the LOPAC1280 compound library. The screening identified several drugs that target classic cancer signaling pathways as well as neuroendocrine markers in SCLC. In particular, perturbation of dopaminergic and serotonergic signaling inhibits SCLC cell viability.
The convergence of our pharmacological data with key SCLC pathway components reiterates the importance of neurotransmitter signaling in SCLC etiology and points to possible leads for drug development.
As endoscopic skull base resections have advanced, appropriate reconstruction has become paramount. The reconstructive options for the skull base include both avascular and vascular grafts. We review these and provide an algorithm for endoscopic skull base reconstruction. One hundred and sixty-six skull base dural defects, reconstructed with an endonasal vascular flap, were examined. As an adjunct, avascular reconstruction techniques are discussed to illustrate all options for endonasal skull base reconstruction. Cerebrospinal fluid (CSF) leak rates are also discussed. Small CSF leaks may be successfully repaired with various avascular grafting techniques. Endoscopic endonasal approaches (EEAs) to the skull base often have larger dural defects with high-flow CSF leaks. Success rates for some EEA procedures utilizing avascular grafts approach 90%, yet in high-flow leak situations, success rates are much lower (50 to 70%). Defect location and complexity guides vascularized flap choice. When nasoseptal flaps are unavailable, anterior/sellar defects are best managed with an endoscopically harvested pericranial flap, whereas clival/posterior defects may be reconstructed with an inferior turbinate or temporoparietal flap. An endonasal skull base reconstruction algorithm was constructed and points to increased use of various vascularized reconstructions for more complex skull base defects.
Skull base reconstruction; nasoseptal flap; AlloDerm; CSF leak rate; algorithm; skull base; pericranial flap; vascular reconstruction
Bacterial Rho-independent terminators (RITs) are important genomic landmarks involved in gene regulation and terminating gene expression. In this investigation we present RNIE, a probabilistic approach for predicting RITs. The method is based upon covariance models which have been known for many years to be the most accurate computational tools for predicting homology in structural non-coding RNAs. We show that RNIE has superior performance in model species from a spectrum of bacterial phyla. Further analysis of species where a low number of RITs were predicted revealed a highly conserved structural sequence motif enriched near the genic termini of the pathogenic Actinobacteria, Mycobacterium tuberculosis. This motif, together with classical RITs, account for up to 90% of all the significantly structured regions from the termini of M. tuberculosis genic elements. The software, predictions and alignments described below are available from http://github.com/ppgardne/RNIE.