Predicting patterns of long-term adaptation and extinction with population genetics.

Population genetics struggles to model extinction; standard models track the relative rather than absolute fitness of genotypes, while the exceptions describe only the short-term transition from imminent doom to evolutionary rescue. But extinction can result from failure to adapt not only to catastrophes, but also to a backlog of environmental challenges. We model long-term adaptation to long series of small challenges, where fitter populations reach higher population sizes. The population's long-term fitness dynamic is well approximated by a simple stochastic Markov chain model. Long-term persistence occurs when the rate of adaptation exceeds the rate of environmental deterioration for some genotypes. Long-term persistence times are consistent with typical fossil species persistence times of several million years. Immediately preceding extinction, fitness declines rapidly, appearing as though a catastrophe disrupted a stably established population, even though gradual evolutionary processes are responsible. New populations go through an establishment phase where, despite being demographically viable, their extinction risk is elevated. Should the population survive long enough, extinction risk later becomes constant over time.

Evidence-Based Medicine as a Tool for Undergraduate Probability and Statistics Education.

Most students have difficulty reasoning about chance events, and misconceptions regarding probability can persist or even strengthen following traditional instruction. Many biostatistics classes sidestep this problem by prioritizing exploratory data analysis over probability. However, probability itself, in addition to statistics, is essential both to the biology curriculum and to informed decision making in daily life. One area in which probability is particularly important is medicine. Given the preponderance of pre health students, in addition to more general interest in medicine, we capitalized on students' intrinsic motivation in this area to teach both probability and statistics. We use the randomized controlled trial as the centerpiece of the course, because it exemplifies the most salient features of the scientific method, and the application of critical thinking to medicine. The other two pillars of the course are biomedical applications of Bayes' theorem and science and society content. Backward design from these three overarching aims was used to select appropriate probability and statistics content, with a focus on eliciting and countering previously documented misconceptions in their medical context. Pretest/posttest assessments using the Quantitative Reasoning Quotient and Attitudes Toward Statistics instruments are positive, bucking several negative trends previously reported in statistics education.

Constraints on the evolution of phenotypic plasticity: limits and costs of phenotype and plasticity.

Phenotypic plasticity is ubiquitous and generally regarded as a key mechanism for enabling organisms to survive in the face of environmental change. Because no organism is infinitely or ideally plastic, theory suggests that there must be limits (for example, the lack of ability to produce an optimal trait) to the evolution of phenotypic plasticity, or that plasticity may have inherent significant costs. Yet numerous experimental studies have not detected widespread costs. Explicitly differentiating plasticity costs from phenotype costs, we re-evaluate fundamental questions of the limits to the evolution of plasticity and of generalists vs specialists. We advocate for the view that relaxed selection and variable selection intensities are likely more important constraints to the evolution of plasticity than the costs of plasticity. Some forms of plasticity, such as learning, may be inherently costly. In addition, we examine opportunities to offset costs of phenotypes through ontogeny, amelioration of phenotypic costs across environments, and the condition-dependent hypothesis. We propose avenues of further inquiry in the limits of plasticity using new and classic methods of ecological parameterization, phylogenetics and omics in the context of answering questions on the constraints of plasticity. Given plasticity's key role in coping with environmental change, approaches spanning the spectrum from applied to basic will greatly enrich our understanding of the evolution of plasticity and resolve our understanding of limits.

Transplantation of hNT neurons into the ischemic cortex: cell survival and effect on sensorimotor behavior.

Cell transplantation offers a potential new treatment for stroke. Animal studies using models that produce ischemic damage in both the striatum and the frontal cortex have shown beneficial effects when hNT cells (postmitotic immature neurons) were transplanted into the ischemic striatum. In this study, we investigated the effect of hNT cells in a model of stroke in which the striatum remains intact and damage is restricted to the cortex. hNT cells were transplanted into the ischemic cortex 1 week after stroke induced by distal middle cerebral artery occlusion (dMCAo). The cells exhibited robust survival at 4 weeks posttransplant even at the lesion border. hNT cells did not migrate, but they did extend long neurites into the surrounding parenchyma mainly through the white matter. Neurite extension was predominantly toward the lesion in ischemic animals but was bidirectional in uninjured animals. Extension of neurites through the cortex toward the lesion was also seen when there was some surviving cortical tissue between the graft and the infarct. Prolonged deficits were obtained in four tests of sensory-motor function. hNT-transplanted animals showed a significant improvement in functional recovery on one motor test, but there was no effect on the other three tests relative to control animals. Thus, despite clear evidence of graft survival and neurite extension, the functional benefit of hNT cells after ischemia is not guaranteed. Functional benefit could depend on other variables, such as infarct location, whether the cells mature, the behavioral tests employed, rehabilitation training, or as yet unidentified factors.

Genetic assimilation can occur in the absence of selection for the assimilating phenotype, suggesting a role for the canalization heuristic.

Genetic assimilation occurs when an acquired trait loses dependency on its environmental trigger and becomes an inherited trait. According to the standard quantitative genetic model for genetic assimilation, the trait is determined by the contributions of multiple genes. Trait expression occurs at a lower threshold with the trigger. Selection for the trait in the presence of the trigger increases the frequency of the trait-determining alleles. Eventually these alleles become frequent enough to breach the higher threshold for expression in the absence of the trigger. This loss of dependence on the trigger signifies genetic assimilation. Here I show that genetic assimilation can occur in the absence of selection for the trait in an evolutionary simulation of a gene network model. This contradicts the prediction of the standard quantitative genetic model, but is consistent with an explanation in terms of the canalization heuristic.

Transplanted human fetal neural stem cells survive, migrate, and differentiate in ischemic rat cerebral cortex.

We characterize the survival, migration, and differentiation of human neurospheres derived from CNS stem cells transplanted into the ischemic cortex of rats 7 days after distal middle cerebral artery occlusion. Transplanted neurospheres survived robustly in naive and ischemic brains 4 wk posttransplant. Survival was influenced by proximity of the graft to the stroke lesion and was negatively correlated with the number of IB4-positive inflammatory cells. Targeted migration of the human cells was seen in ischemic animals, with many human cells migrating long distances ( approximately 1.2 mm) predominantly toward the lesion; in naive rats, cells migrated radially from the injection site in smaller number and over shorter distances (0.2 mm). The majority of migrating cells in ischemic rats had a neuronal phenotype. Migrating cells between the graft and the lesion expressed the neuroblast marker doublecortin, whereas human cells at the lesion border expressed the immature neuronal marker beta-tubulin, although a small percentage of cells at the lesion border also expressed glial fibrillary acid protein (GFAP). Thus, transplanted human CNS (hCNS)-derived neurospheres survived robustly in naive and ischemic brains, and the microenvironment influenced their migration and fate.

Non-CF bronchiectasis: clinical and HRCT evaluation.

Childhood bronchiectasis not related to underlying disease is still common in some populations in affluent countries. The aims of the study were to: 1) describe demographics, 2) evaluate the effectiveness of routine investigations, and 3) determine the relationship between spirometry and radiology scoring systems, in children with chronic suppurative lung disease (CSLD) living in Central Australia. Data of children living in Central Australia aged 70%) and early hospitalisation for pneumonia were common (median age, 0.5 years). Previous admissions for pneumonia were almost universally present and significantly more common than bronchiolitis (95% CI for proportional difference, 0.4-0.51). Although the majority did not have a treatable underlying cause, investigations had significant impact on management in 12.3% of children. None of the chest HRCT scores related to any spirometry data. In conclusion, CSLD is unacceptably common in indigenous children of this region, commences early in life, and is associated with significant comorbidities. Spirometry data do not reflect the severity of lung disease in HRCT scans. While improvement in the living standards is of utmost importance, the medical management that includes thorough investigations of these children should not be neglected.

Bronchoscopic findings in children with non-cystic fibrosis chronic suppurative lung disease.

BACKGROUND: Published data on the frequency and types of flexible bronchoscopic airway appearances in children with non-cystic fibrosis bronchiectasis and chronic suppurative lung disease are unavailable. The aims of this study were to describe airway appearances and frequency of airway abnormalities and to relate these airway abnormalities to chest high resolution computed tomography (cHRCT) findings in a cohort of children with non-cystic fibrosis chronic suppurative lung disease (CSLD). METHODS: Indigenous children with non-cystic fibrosis CSLD (>4 months moist and/or productive cough) were prospectively identified and collected over a 2.5 year period at two paediatric centres. Their medical charts and bronchoscopic notes were retrospectively reviewed. RESULTS: In all but one child the aetiology of the bronchiectasis was presumed to be following a respiratory infection. Thirty three of the 65 children with CSLD underwent bronchoscopy and five major types of airway findings were identified (mucosal abnormality/inflammation only, bronchomalacia, obliterative-like lesion, malacia/obliterative-like combination, and no macroscopic abnormality). The obliterative-like lesion, previously undescribed, was present in 16.7% of bronchiectatic lobes. Structural airway lesions (bronchomalacia and/or obliterative-like lesion) were present in 39.7% of children. These lesions, when present, corresponded to the site of abnormality on the cHRCT scan. CONCLUSIONS: Structural airway abnormality is commonly found in children with post-infectious bronchiectasis and a new bronchoscopic finding has been described. Airway abnormalities, when present, related to the same lobe abnormality on the cHRCT scan. How these airway abnormalities relate to aetiology, management strategy, and prognosis is unknown.

Distinctive enchondromatosis with spine abnormality, regressive lesions, short stature, and coxa vara: importance of long-term follow-up.

We report a girl with a unique type of enchondromatosis observed from birth to puberty. Radiographic abnormalities documented at the age of 14 months included distinctive spondylometaphyseal enchondromatous types of lesions with minimal involvement of the short tubular and flat bones. Follow-up radiographic examinations documented progressive coxa vara and hypoplasia/dysplasia of the left ulna. At puberty, the short tubular bones appeared normal. There was marked regression of the flat bone, rib, and spinal lesions. This case shows the importance of long-term observation of unclassified forms of skeletal dysplasia.

Premature calvarial synostosis and epidermal hyperplasia (Beare-Stevenson syndrome-like anomalies) resulting from a P250R missense mutation in the gene encoding fibroblast growth factor receptor 3.

We report on a patient with a severe premature calvarial synostosis and epidermal hyperplasia. The phenotype was consistent with that of a mild presentation of Beare-Stevenson syndrome but molecular analysis of the IgIII-transmembrane linker region and the transmembrane domain of the gene encoding the FGFR2 receptor, revealed wild-type sequence only. Subsequently, molecular analysis of the FGFR3 receptor gene identified a heterozygous P250R missense mutation in both the proposita and her mildly affected father. This communication extends the clinical spectrum of the FGFR3 P250R mutation to encompass epidermal hyperplasia and documents the phenomenon of activated FGFR receptors stimulating common downstream developmental pathways, resulting in overlapping clinical outcomes.

The measured level of prion infectivity varies in a predictable way according to the aggregation state of the infectious agent.

Transmissible spongiform encephalopathies are believed to be caused by an infectious form of the prion protein, designated PrP(Sc). The concentration of PrP(Sc) is often poorly correlated to the level of infectivity. Infectivity can be measured in two ways, namely endpoint titration and the incubation time assay, but patterns of infectivity vary depending on which method is used. These discrepancies can be explained by variation in the aggregation state of PrP(Sc). Both methods of measuring infectivity are modelled mathematically, and the theoretical results are in agreement with published data. It was found to be theoretically impossible to characterise prion infectivity by a multiple of a single quantity representing 'one prion', no matter how it is measured. Infectivity is instead characterised by both the number and sizes of the PrP(Sc) aggregates. Apparent discrepancies arise when these complexities are reduced to a single number.

Application of chest high-resolution computer tomography in young children with cystic fibrosis.

SUMMARY. High-resolution computed tomography (HRCT) of the chest permits early detection of lung disease; two relevant scoring systems (Bhalla and Nathanson) have been developed to describe CF lung disease. Comparisons between the two scoring systems have not been made, and it is not known which system is more appropriate for young children, i.e., the age group where other objective markers are scarce. We reviewed the clinical findings, pulmonary function data, and HRCT of 16 children aged less than 12 years. The Bhalla scoring system had a better correlation with FEV(1) (r = -0.65, P = 0.012) than the Nathanson score (r = 0.53, P = 0.05). All children had bronchiectasis, including 5 with normal pulmonary function tests. The lower lobes were universally involved, and 5 children did not have any upper lobe disease. Four of these 5 children were aged less than 7 years. We conclude that the Bhalla scoring system is more applicable to young children than is the Nathanson system. Also, in this group of young children with CF, lower lobes are more commonly involved than upper lobes, which is in contrast to the classical teaching that CF lung disease begins in the upper lobes.

Clinical findings in a patient with FGFR1 P252R mutation and comparison with the literature.

We report on a patient with the skeletal findings of Jackson-Weiss syndrome, who manifests only mild craniofacial anomalies. Molecular analysis of her fibroblast growth factor receptor 1 gene (FGFR1) identified a heterozygous P252R missense mutation, previously only reported with FGFR1-Pfeiffer syndrome like manifestations. Mutations in the immunoglobulin-like, II-III (IgII-III) linker region of FGFR1 and FGFR3 molecules may present as a skeletal dysplasia affecting the appendicular skeleton including, brachydactyly, short broad middle phalanges, phalangeal epiphyseal coning and broad halluces. This communication is a further example of the phenomenon of an activated FGFR molecule resulting in overlapping manifestations in FGFR syndromes.

Fluctuations in HIV-1 viral load are correlated to CD4+ T-lymphocyte count during the natural course of infection.

Viral load fluctuates during the natural course of asymptomatic HIV-1 infection. It is often assumed that these fluctuations are random around a set point or underlying growth trend. Using longitudinal data, we tested whether fluctuations in viral load can be better explained by changes in CD4+ T-cell count than by a set point or trend of exponential growth. The correspondence between viral load and CD4+ T-cell count could be described by a simple mathematical relation. Using a bootstrapping approach, the hypothesis that viral load fluctuations are random around a set point was rejected with p < .00005. The hypothesis that viral load fluctuations are random around a trend of exponential growth was rejected with p < .005. Viral load data was explained better by changes in CD4+ T-cell counts than by a set point or by a trend of exponential growth. The implications of this finding for improved prognostication are discussed.

Evaluation and management of mechanical dysfunction in continent colonic urinary reservoirs.

PURPOSE: We analyze a group of patients who presented with mechanical dysfunction of the reservoir and/or efferent limb of a continent colonic urinary diversion, and establish an evaluation and management algorithm. MATERIALS AND METHODS: A total of 16 patients with a mean age of 58 years and 1 or more symptoms related to continent colonic urinary diversion were evaluated. Presenting symptomatology included difficult catheterization in 8 cases (50%), disabling incontinence in 8 (50%) and recurrent urinary tract infections in 6 (37.5%). All patients had normal, nonobstructed, nonrefluxing upper tracts and none presented with stone disease. Urological evaluation consisted of catheterization, fluoroscopy and urography of the pouch, retrograde urography of the external limb and urodynamics (enterocystometrogram and outlet pressure profilometry). RESULTS: Of the 8 patients with difficulty with catheterization 4 had stomal stenosis, 2 had an elongated and redundant external limb, and 2 had a false passage. Diagnosis was established by the inability to catheterize, fluoroscopy of the pouch and retrograde urography. Disabling incontinence occurred in 8 patients, including 7 who presented with an incompetent outlet and 2 with high pressure intestinal contractions of the reservoir. The aforementioned abnormalities were diagnosed by a combination of retrograde urography, urography of the pouch and urodynamics. Recurrent symptomatic urinary infections were observed in 5 patients of the previous groups and in another with an hourglass reservoir, which was primarily diagnosed by urography of the pouch. Surgical correction in 15 patients included outlet reinforcement, reservoir revision, stomal or external limb revision and conversion to a urinary conduit. Surgical treatment was successful in 14 of 15 patients (93%). CONCLUSIONS: Catheterization difficulty requires retrograde urography to define possible anatomical abnormalities (false passage, conduit elongation) if catheterization and fluoroscopy of the pouch do not demonstrate stomal stenosis. Urinary incontinence benefits from enterocystometry and outlet pressure measurement to determine reservoir and external limb function. Recurrent urinary tract infections not related to ureteral obstruction or reflux requires fluoroscopy of the pouch and external limb to determine abnormalities in patients with detubularization and localization of areas of urine pooling.

Designing drugs to stop the formation of prion aggregates and other amyloids.

Amyloid protein aggregates are implicated in many neurodegenerative diseases, including Alzheimer's disease and the prion diseases. Therapeutics to block amyloid formation are often tested in vitro, but it is not clear how to extrapolate from these experiments to a clinical setting, where the effective drug dose may be much lower. Here we address this question using a theoretical kinetic model to calculate the growth rate of protein aggregates as a function of the dose of each of three categories of drug. We find that therapeutics which block the growing ends of amyloids are the most promising, as alternative strategies may be ineffective or even accelerate amyloid formation at low drug concentrations. Our mathematical model can be used to identify and optimise an end-blocking drug in vitro. Our model also suggests an alternative explanation for data previously thought to prove the existence of an entity known as protein X.

The kinetics of proteinase K digestion of linear prion polymers.

Transmissible spongiform encephalopathies such as scrapie are caused by a protein-only infectious agent, known as a prion. It is not clear how a protein can be capable of replicating itself, and the mechanism remains controversial. One influential model hypothesizes that prions are nucleated, macroscopically linear polymers. We investigated the theoretical kinetics of this model and derived predictions which could be used to test the model. In the model, the polymerization and depolymerization rates are independent polymer size. This leads to an exponential size distribution at equilibrium. In agreement with a prediction stemming from this size distribution, the average size of PrP-res polymers was proportional to the square root of the concentration of PrP-res in a published study of in vitro conversion. Prion digestion by proteinase K (PK) is predicted to be biphasic. The second phase of digestion should be virtually independent of the PK concentration and should depend on the initial size distribution of prion polymers. For initially equilibrated polymers with an exponential size distribution, phase two digestion is exponential at a predicted rate. This rate varies in a defined way with the concentration used for equilibration and with other parameters which affect the average polymer size.

Phallic construction in a 65-year-old male pseudohermaphrodite.

The authors constructed a functional, sensate phallus for a 65-year-old male pseudohermaphrodite. Although their technique is employed frequently for gender reassignment and posttraumatic reconstruction, the opportunity to perform this procedure to aid an adult patient with ambiguous genitalia is unusual. Of course, having such a patient present for treatment in his seventh decade of life is also unique. After careful consideration of his history, previous failure of medical therapy, and overall excellent medical condition the authors determined that age alone should not be an impediment to phallic construction for this patient. Their decision not to construct a penile urethra, and therefore avoid potential urethral complications, helped to ensure an uneventful postoperative course. Their success in this case has clearly broadened the range of patients that can benefit from phallic construction.

alpha-Adrenergic blockade in children with neuropathic and nonneuropathic voiding dysfunction.

PURPOSE: Inadequate bladder emptying is a common urinary dysfunction in children. The role of alpha-blockers for managing bladder outlet obstruction remains relatively unexplored in children. Because of the well established impact of alpha-blocker therapy in men, we investigated its use for treating inadequate bladder emptying in the pediatric population. MATERIALS AND METHODS: We treated 17 children 3 to 15 years old with documented poor bladder emptying of various etiologies, including dysfunctional voiding, the Hinman syndrome, the lazy bladder syndrome, posterior urethral valves, myelomeningocele and the prune-belly syndrome, using the alpha-1 adrenergic receptor antagonist, doxazosin. The initial dose of 0.5 to 1.0 mg. nightly was increased according to patient response and as tolerated. Patients were followed weekly to monthly by symptomatic history, and urine flow and/or post-void residual urine volume measurement. Two patients with neurogenic bladder were also followed with cystometrography and leak point pressure determination. RESULTS: Bladder symptomatology and/or emptying improved in 14 patients (82%). Ten patients had decreased post-void residual urine during treatment and in 3 uroflowmetry showed increased maximum flow. Two patients with neuropathic bladder secondary to myelomeningocele had decreased leak point pressure on alpha-blocker therapy and in 2 with a history of posterior urethral valves new onset bilateral hydronephrosis completely resolved. Only 1 patient had mild postural hypotension, which resolved with dose reduction. CONCLUSIONS: Selective alpha-blocker therapy seems to be well tolerated in children and appears effective for improving bladder emptying in various pediatric voiding disorders at short-term followup. Long-term followup and further investigation are warranted to validate the potential role of alpha-blocker therapy in pediatric urinary dysfunction.

Variability in kyphomelic dysplasia.

Four infants with kyphomelic dysplasia ascertained from three families demonstrate variability within the syndrome. In the first family, sibling recurrence in female sibs was noted with atypical kyphomelic dysplasias, suggesting autosomal recessive inheritance. In the second family, with a male affected with the 'typical findings' of lethal kyphomelic dysplasia, diagnosis of a skeletal dysplasia was suspected at 29-30 weeks' gestation following US detection of short, bent femurs. In the third family, with a female affected, severe radiographic changes were documented at birth. The clinical course of the disease was mild with almost complete regression of the radiographic findings at the age of 7 years.