Plasticity and environment-specific relationships between gene expression and fitness in Saccharomyces cerevisiae

Phenotypic evolution is shaped by interactions between organisms and their environments. The environment influences how an organism's genotype determines its phenotype and how this phenotype affects its fitness. To better understand this dual role of the environment in the production and selection of phenotypic variation, we empirically determined and compared the genotype-phenotype-fitness relationship for mutant strains of the budding yeast Saccharomyces cerevisiae in four environments. Specifically, we measured how mutations in the promoter of the metabolic gene TDH3 modified its expression level and affected its growth on media with four different carbon sources. In each environment, we observed a clear relationship between TDH3 expression level and fitness, but this relationship differed among environments. Genetic variants with similar effects on TDH3 expression in different environments often had different effects on fitness and vice versa. Such environment-specific relationships between phenotype and fitness can shape the evolution of phenotypic plasticity. The set of mutants we examined also allowed us to compare the effects of mutations disrupting binding sites for key transcriptional regulators and the TATA box, which is part of the core promoter sequence. Mutations disrupting the binding sites for the transcription factors had more variable effects on expression among environments than mutations disrupting the TATA box, yet mutations with the most environmentally variable effects on fitness were located in the TATA box. This observation suggests that mutations affecting different molecular mechanisms are likely to contribute unequally to regulatory sequence evolution in changing environments.

Divergence of Grainy head affects chromatin accessibility, gene expression, and embryonic viability in Drosophila melanogaster

Pioneer factors are critical for gene regulation and development because they bind chromatin and make DNA more accessible for binding by other transcription factors. The pioneer factor Grainy head (Grh) is present across metazoans and has been shown to retain a role in epithelium development in fruit flies, nematodes, and mice despite extensive divergence in both amino acid sequence and length. Here, we investigate the evolution of Grh function by comparing the effects of the fly ( Drosophila melanogaster ) and worm ( Caenorhabditis elegans ) Grh orthologs on chromatin accessibility, gene expression, embryonic development, and viability in transgenic D. melanogaster . We found that the Caenorhabditis elegans ortholog rescued cuticle development but not full embryonic viability in Drosophila melanogaster grh null mutants. At the molecular level, the C. elegans ortholog only partially rescued chromatin accessibility and gene expression. Divergence in the disordered N-terminus of the Grh protein contributes to these differences in embryonic viability and molecular phenotypes. These data show how pioneer factors can diverge in sequence and function at the molecular level while retaining conserved developmental functions at the organismal level.

SUMMARY STATEMENT

Despite divergence in a disordered region that affects function at both molecular and organismal levels, the Caenorhabditis elegans Grainy head (Grh) protein rescued cuticle morphology in D. melanogaster embryos.

Active compensation for changes in TDH3 expression mediated by direct regulators of TDH3 in Saccharomyces cerevisiae

Genetic networks are surprisingly robust to perturbations caused by new mutations. This robustness is conferred in part by compensation for loss of a gene's activity by genes with overlapping functions, such as paralogs. Compensation occurs passively when the normal activity of one paralog can compensate for the loss of the other, or actively when a change in one paralog's expression, localization, or activity is required to compensate for loss of the other. The mechanisms of active compensation remain poorly understood in most cases. Here we investigate active compensation for the loss or reduction in expression of the Saccharomyces cerevisiae gene TDH3 by its paralog TDH2. TDH2 is upregulated in a dose-dependent manner in response to reductions in TDH3 by a mechanism requiring the shared transcriptional regulators Gcr1p and Rap1p. TDH1, a second and more distantly related paralog of TDH3, has diverged in its regulation and is upregulated by another mechanism. Other glycolytic genes regulated by Rap1p and Gcr1p show changes in expression similar to TDH2, suggesting that the active compensation by TDH3 paralogs is part of a broader homeostatic response mediated by shared transcriptional regulators.

Mutational sources of trans-regulatory variation affecting gene expression in Saccharomyces cerevisiae

Heritable variation in a gene’s expression arises from mutations impacting cis- and trans-acting components of its regulatory network. Here, we investigate how trans-regulatory mutations are distributed within the genome and within a gene regulatory network by identifying and characterizing 69 mutations with trans-regulatory effects on expression of the same focal gene in Saccharomyces cerevisiae. Relative to 1766 mutations without effects on expression of this focal gene, we found that these trans-regulatory mutations were enriched in coding sequences of transcription factors previously predicted to regulate expression of the focal gene. However, over 90% of the trans-regulatory mutations identified mapped to other types of genes involved in diverse biological processes including chromatin state, metabolism, and signal transduction. These data show how genetic changes in diverse types of genes can impact a gene’s expression in trans, revealing properties of trans-regulatory mutations that provide the raw material for trans-regulatory variation segregating within natural populations.

Evolution of protein specificity: insights from ancestral protein reconstruction

Specific interactions between proteins and their molecular partners drive most biological processes, so understanding how these interactions evolve is an important question for biochemists and evolutionary biologists alike. It is often thought that ancestral proteins were systematically more promiscuous than modern proteins and that specificity usually evolves after gene duplication by partitioning and refining the activities of multifunctional ancestors. However, recent studies using ancestral protein reconstruction (APR) have found that ligand-specific functions in some modern protein families evolved de novo from ancestors that did not already have those functions. Further, the new specific interactions evolved by simple mechanisms, with just a few mutations changing classically recognized biochemical determinants of specificity, such as steric and electrostatic complementarity. Acquiring new specific interactions during evolution therefore appears to be neither difficult nor rare. Rather, it is likely that proteins continually gain and lose new activities over evolutionary time as mutations cause subtle but consequential changes in the shape and electrostatics of interaction interfaces. Only a few of these activities, however, are incorporated into the biological processes that contribute to fitness before they are lost to the ravages of further mutation.

Current understanding of the pathogenesis of autoimmune inner ear disease: a review

BACKGROUND

Autoimmune inner ear disease (AIED) is a poorly understood form of sensorineural hearing loss that causes bilateral, asymmetric, progressive hearing loss, sometimes with vestibular symptoms, often associated with a systemic autoimmune disease, which is noteworthy as the only sensorineural loss responsive to medical therapy. Despite much research interest of the past 25 years, its aetiopathogenesis is still unproven.

OBJECTIVE OF REVIEW

To succinctly consolidate research and opinion regarding the pathogenesis of autoimmune inner ear disease, in ongoing efforts to elucidate the molecular and intracellular pathways that lead to inner ear damage, which may identify new targets for pharmacotherapy.

TYPE OF REVIEW

Systematic review

SEARCH STRATEGY

PubMed/MEDLINE search using key terms to identify articles published between January 1980 and Apr 2014. Additionally, any landmark works discussed in this body of literature were obtained and relevant information extracted as necessary.

EVALUATION METHOD

Inclusion criterion was any information from animal or human studies with information relevant to possible aetiopathogenesis of AIED. Studies that focused on diagnosis, ameliorating symptoms or treatment, without specific information relevant to mechanisms of immune-mediated injury were excluded from this work. Articles meeting the inclusion criteria were digested and summarised.

RESULTS

A proposed pathogenic mechanism of AIED involves inflammation and immune-mediated attack of specific inner ear structures, leading to an excessive Th1 immune response with vascular changes and tissue damage in the cochlea. Studies have identified self-reactive T cells and immunoglobulins, and have variously implicated immune-complex deposition, microthrombosis and electrochemical disturbances causing impaired neurosignalling in the pathogenesis of AIED. Research has also demonstrated abnormalities in the cytokine milieu in subjects with AIED, which may prove a target for therapy in the future.

CONCLUSION

Ongoing research is needed to further elucidate the aetiopathogenesis of AIED and discern between various mechanisms of tissue injury. Large-cohort clinical studies employing IL-1 receptor blockade are warranted to determine its potential for future therapy.

Pleiotropic effects of a mitochondrial-nuclear incompatibility depend upon the accelerating effect of temperature in Drosophila

Interactions between mitochondrial and nuclear gene products that underlie eukaryotic energy metabolism can cause the fitness effects of mutations in one genome to be conditional on variation in the other genome. In ectotherms, the effects of these interactions are likely to depend upon the thermal environment, because increasing temperature accelerates molecular rates. We find that temperature strongly modifies the pleiotropic phenotypic effects of an incompatible interaction between a Drosophila melanogaster polymorphism in the nuclear-encoded, mitochondrial tyrosyl-transfer (t)RNA synthetase and a D. simulans polymorphism in the mitochondrially encoded tRNA(Tyr). The incompatible mitochondrial-nuclear genotype extends development time, decreases larval survivorship, and reduces pupation height, indicative of decreased energetic performance. These deleterious effects are ameliorated when larvae develop at 16° and exacerbated at warmer temperatures, leading to complete sterility in both sexes at 28°. The incompatible genotype has a normal metabolic rate at 16° but a significantly elevated rate at 25°, consistent with the hypothesis that inefficient energy metabolism extends development in this genotype at warmer temperatures. Furthermore, the incompatibility decreases metabolic plasticity of larvae developed at 16°, indicating that cooler development temperatures do not completely mitigate the deleterious effects of this genetic interaction. Our results suggest that the epistatic fitness effects of metabolic mutations may generally be conditional on the thermal environment. The expression of epistatic interactions in some environments, but not others, weakens the efficacy of selection in removing deleterious epistatic variants from populations and may promote the accumulation of incompatibilities whose fitness effects will depend upon the environment in which hybrids occur.

Empty sella syndrome associated with a hyperfunctioning microadenoma invading the clivus

The empty sella syndrome is usually associated with normal pituitary function. If dysfunction is present, this is commonly hypofunction. Hyperfunctioning microadenomas have been described in the presence of the empty sella syndrome. We present the first reported cases of a microadenoma invading the clivus associated with an empty sella.

Early results of titanium ossiculoplasty using the Kurz titanium prosthesis – a UK perspective

Titanium has been shown to be a highly biocompatible material and recently interest has been raised by its use as a prosthetic material in the ear. Our objective was to prospectively assess the early results of titanium partial and total ossicular replacement prostheses in chronic ear disease. Thirty-three consecutive patients (20 titanium partials and 13 total ossicular replacement prostheses) were analysed and data from pre and post-operative pure tone audiograms were collected and compared at six months over a four frequency range (0.5–4 kHz) as well as using the American Academy of Otolaryngology–Head and Neck Surgery criteria (0.5–3 kHz). Closure of the air-bone gap and improvement in air conduction at six months was also calculated. 69% of patients obtained an air-bone gap of ≤20 dB, with titanium partial ossicular replacement prostheses (85 per cent) doing better than total ossicular replacement prostheses (46 per cent). There have been no cases of sensorineural hearing loss or extrusion. In conclusion, titanium prostheses are easy to use, allow good visibility and have shown good short-term results in our hands.

Facial palsy secondary to cholesteatoma: analysis of outcome following surgery

Facial palsy is a rare presenting feature of cholesteatoma. Prompt treatment usually results in a good outcome, but if treatment is delayed the prognosis can be difficult to predict. We retrospectively reviewed 326 consecutive patients who had undergone temporal bone surgery for cholesteatoma. Eleven patients had presented with facial palsy, of whom eight had petrous apex involvement and three had disease confined to the middle-ear cleft. All patients with middle-ear disease were operated upon within two months of presentation, and all showed some recovery in facial function. The diagnosis had been delayed in all eight cases of apical disease, with four cases having had a long-standing total weakness. One case treated after seven months' partial weakness achieved a full recovery. In three cases of long-standing partial weakness, pre-operative facial function was preserved by maintaining the facial nerve in its normal anatomical location.

Facial palsy associated with cholesteatoma should be treated as early as possible. Recovery can occur even if treatment is delayed for up to seven months. After this time, recovery is increasingly unlikely, but any residual function can be maintained and further deterioration prevented.

Otosclerosis: a review of aetiology, management and outcomes

Otosdcerosis is an autosomal dominant condition affecting the temporal bone. It presents predominantly with deafness in a young population. This review looks at the aetiological theories, present treatment strategies and surgical outcomes of this condition.

Otosclerosis: a review of aetiology, management and outcomes

Otosclerosis is an autosomal dominant condition affecting the temporal bone. It presents predominantly with deafness in a young population. This review looks at the aetiological theories, present treatment strategies and surgical outcomes of this condition.

Cerebellopontine angle arachnoid cysts in adult patients: what is the appropriate management?

Arachnoid cysts can occur at different intracranial sites, including the cerebellopontine angle (CPA). The incidence of arachnoid cysts is 1 per cent of all intracranial lesions. Recent advances in MRI (magnetic resonance imaging) scan techniques have led to CPA arachnoid cysts being more frequently diagnosed and with a higher degree of certainty. The need for further understanding of their natural history as well as for the development of a management rationale has been highlighted with this increased rate of diagnosis.

We present a series of five adult patients with different clinical presentations attributed to CPA arachnoid cysts. These lesions have a characteristic location in the posterior-inferior aspect of the CPA below the facial and vestibulocochlear nerves. These cysts did not show change in size on repeated MRI scan and the patients’ symptoms did not progress over the period of follow up. Our findings would support a conservative management approach to the majority of these cysts.

Current management in pharyngeal pouch surgery by UK otorhinolaryngologists

INTRODUCTION

Many surgical techniques have been described for the treatment of pharyngeal pouches but there is no single treatment of choice. The aim of this study was to determine current practice in pharyngeal pouch surgery by UK otolaryngologists.

METHODS

A postal questionnaire was sent to all UK-based consultant members of the British Association of Otolaryngologists - Head and Neck Surgeons (BAO-HNS).

RESULTS

Endoscopic stapling diverticulotomy is the most commonly performed procedure, performed by 89% of surgeons, followed by excision. Of those consultants that considered there to be a treatment of choice, 83% stated endoscopic stapling as their preference. Practices differ regarding the insertion of nasogastric tubes after endoscopic procedures and the need for postoperative barium studies. The length of in-patient stay tends to be short with 80% of surgeons discharging patients by day 2.

CONCLUSIONS

Endoscopic stapling diverticulotomy is now the most commonly performed procedure for the management of pharyngeal pouches by UK otolaryngologists and is now considered by many to be the treatment of choice.

Long-term hearing results of incus transposition

Incus transposition is an option for reconstructing an ossicular discontinuity. We looked at the long-term outcome (average 9.2 years) in terms of hearing results in patients who had undergone incus transposition. Patients were requested to attend for a pure tone audiogram. Details of their preoperative audiograms were obtained from the patients' case notes. A postoperative air-bone gap of 20 dB or less averaged over four frequencies (0.5, 1, 2, 4 kHz) was considered to be an acceptable result. We found that 70% of patients had an air-bone gap of 20 dB or less and 54% had had cholesteatoma surgery at the time of the incus transposition. This study represents the longest follow-up of patients having undergone incus transposition from our search of the literature. Incus transposition, we feel, offers good long-term hearing results.

Gastrointestinal stromal tumour of the pharynx

This documents the case of a 55-year-old female presenting with a solitary polypoidal tumour of the pharynx. Histological examination revealed features consistent with a gastrointestinal stromal tumour. Although well described elsewhere in the gastrointestinal tract, from our literature search, this is the first reported case of such a tumour occurring in the pharynx

Persistent otorrhoea after ventilation tube insertion: a treatment protocol

Otorrhoea is the commonest complication of ventilation tube (grommet) insertion. In some cases it may be unresponsive to short courses of topical antibiotic/steroid drops and/or systemic antibiotics. This study investigated whether a five-day course of inpatient treatment with intravenous antibiotics, topical medication and daily microsuction was effective in treating persistent otorrhoea. Eleven subjects were included, of whom nine responded to the proposed treatment regimen. We recommend that patients with persistent otorrhoea after ventilation tube insertion should be managed according to these guidelines before considering an examination under anaesthetic or a ventilation tube removal.

First branchial cleft anomaly presenting as a recurrent post-auricular abscess

Embryological anomalies of the first branchial cleft are uncommonly encountered. They usually present as cysts, swellings, or fistulas in the pre-auricular or post-auricular area or high in the neck, which may become infected. Failure to recognise these unusual cases may result in misdiagnosis, inadequate treatment, and subsequent recurrence. Further definitive surgery may thus be complicated. A case is reported of a patient who attended accident and emergency on three occasions with an infected post-auricular cyst, which was treated by incision and drainage. It was subsequently found to be a first branchial cleft anomaly.

Pharyngeal pouch (Zenker's diverticulum)

Pharyngeal pouches occur most commonly in elderly patients (over 70 years) and typical symptoms include dysphagia, regurgitation, chronic cough, aspiration, and weight loss. The aetiology remains unknown but theories centre upon a structural or physiological abnormality of the cricopharyngeus. A diagnosis is easily established on barium studies. Treatment is surgical via an endoscopic or external cervical approach and should include a cricopharyngeal myotomy. Unfortunately pharyngeal pouch surgery has long been associated with significant morbidity, partly due to the surgery itself and also to the fact that the majority of patients are elderly and often have general medical problems. External approaches are associated with higher complication rates than endoscopic procedures. Recently, treatment by endoscopic stapling diverticulotomy has becoming increasingly popular as it has distinct advantages, although long term results are not yet available. The small risk of developing carcinoma within a pouch that is not excised remains a contentious issue and is an argument for long term follow up or treating the condition by external excision, particularly in younger patients.

Pharyngeal pouch surgery: a five year review

The treatment of pharyngeal pouch varies widely. Our aim was to establish current and recent practice in pharyngeal pouch surgery in our department and set guidelines for future management. A retrospective audit over a 5-year period was performed with all data derived from patient notes. 28 procedures were performed on 24 patients with a mean age of 72 years. Over two thirds of these patients (68%) underwent an endoscopic procedure (stapling or diathermy) and the remainder underwent excision (14%), inversion (10%), cricopharyngeal myotomy (4%) or dilatation (4%). The primary diagnostic investigation performed was a barium swallow in 17 cases, but in 7 cases, referred by gastroenterologists, an oesophagogastroscopy was performed despite characteristic presenting features in all cases. The average inpatient stay was similar for endoscopic and excision procedures (5.5 and 5 days respectively), but longer for inversion procedures (9 days). This was influenced mainly by operative complications. 2 endoscopic stapling procedures were complicated by perforations and 1 patient developed hoarseness after an inversion procedure. The mean follow up time was one month at which stage all asymptomatic patients were discharged. 2 patients treated by endoscopic stapling and 1 patient treated by inversion complained of persistent symptoms and required further surgery. We conclude that endoscopic stapling was the commonest procedure used. Concerning future management, the use of nasogastric tubes after uncomplicated stapling procedures was abandoned. Also it was felt that large pouches should be treated by excision, small pouches by cricopharyngeal myotomy and the remainder by endoscopic stapling. The long-term evaluation of results was also deemed necessary.

Metastatic endometrial carcinoma of the neck

We report a case of metastatic endometrial carcinoma of the neck. A patient with a past medical history of squamous cell carcinoma of the larynx, breast carcinoma and endometrial carcinoma presented with a neck mass. Fine needle aspiration cytology (FNAC) showed this to be a poorly differentiated carcinoma with squamoid features and thus a potentially curative neck dissection was performed. Histology of the mass showed a clear cell endometrial carcinoma. Metastatic gynacecological malignancies to the head and neck are rare and this is the first reported case of metastatic endometrial carcinoma in the neck.

Nasal non-Hodgkin's lymphoma causing mucocele of the maxillary antrum

The authors report a case of an antral mucocele secondary to obstruction of the antral ostium by a non-Hodgkin's lymphoma. Antral mucoceles are rare, and this is the first report of one such caused by a nasal lymphoma.

Erythema multiforme after application of aural Gentisone HC drops

Erythema multiforme is an uncommon acute self-limiting condition characterized by mucocutaneous lesions of varying severity with a variable pattern of recurrence. This is a case of a four-year-old girl who developed erythema multiforme secondary to topical aural application of Gentisone HC drops (hydrocortisone acetate one per cent, gentamicin 0.3 per cent (as sulphate)) prescribed as a treatment for otorrhoea following grommet insertion. The clinical features are described and the literature reviewed. To my knowledge, this is the first reported case in the literature, of erythema multiforme secondary to a topical aminoglycoside/steroid preparation.

Subcutaneous cervical emphysema after self-induced vomiting

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