Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples.

BACKGROUND: Next-generation sequencing (NGS) of tumour samples is a critical component of personalised cancer treatment, but it requires high-quality DNA samples. Routine neutral-buffered formalin (NBF) fixation has detrimental effects on nucleic acids, causing low yields, as well as fragmentation and DNA base changes, leading to significant artefacts. PATIENTS AND METHODS: We have carried out a detailed comparison of DNA quality from matched samples isolated from high-grade serous ovarian cancers from 16 patients fixed in methanol and NBF. These experiments use tumour fragments and mock biopsies to simulate routine practice, ensuring that results are applicable to standard clinical biopsies. RESULTS: Using matched snap-frozen tissue as gold standard comparator, we show that methanol-based fixation has significant benefits over NBF, with greater DNA yield, longer fragment size and more accurate copy-number calling using shallow whole-genome sequencing (WGS). These data also provide a new approach to understand and quantify artefactual effects of fixation using non-negative matrix factorisation to analyse mutational spectra from targeted and WGS data. CONCLUSION: We strongly recommend the adoption of methanol fixation for sample collection strategies in new clinical trials. This approach is immediately available, is logistically simple and can offer cheaper and more reliable mutation calling than traditional NBF fixation.

Aspiration removal of orbitofrontal cortex disrupts cholinergic fibers of passage to anterior cingulate cortex in rhesus macaques.

The study of anthropoid nonhuman primates has provided valuable insights into frontal cortex function in humans, as these primates share similar frontal anatomical subdivisions (Murray et al. 2011). Causal manipulation studies have been instrumental in advancing our understanding of this area. One puzzling finding is that macaques with bilateral aspiration removals of orbitofrontal cortex (OFC) are impaired on tests of cognitive flexibility and emotion regulation, whereas those with bilateral excitotoxic lesions of OFC are not (Rudebeck et al. 2013). This discrepancy is attributed to the inadvertent disruption of fibers of passage by aspiration lesions but not by excitotoxic lesions. Which fibers of passage are responsible for the impairments observed? One candidate is cholinergic fibers originating in the nucleus basalis magnocellularis (NBM) and passing nearby or through OFC on their way to other frontal cortex regions (Kitt et al. 1987). To investigate this possibility, we performed unilateral aspiration lesions of OFC in three macaques, and then compared cholinergic innervation of the anterior cingulate cortex (ACC) between hemispheres. Histological assessment revealed diminished cholinergic innervation in the ACC of hemispheres with OFC lesions relative to intact hemispheres. This finding indicates that aspiration lesions of the OFC disrupt cholinergic fibers of passage, and suggests the possibility that loss of cholinergic inputs to ACC contributes to the impairments in cognitive flexibility and emotion regulation observed after aspiration but not excitotoxic lesions of OFC.

Effect of an initial specimen diversion device on blood-culture contamination rates and vancomycin usage: A quasi-experimental study.

Initial specimen diversion devices (ISDDs) are a potential solution for reducing blood-culture contamination rates. We report the implementation of an ISDD associated with a sustained reduction in blood-culture contamination rates for >18 months after implementation. We did not observe a clinically significant reduction in inpatient vancomycin usage.

Factitious hand disorders: review of 29 years of multidisciplinary care.

PURPOSE: To improve our understanding of factitious hand disorders with a review of our experience over 29 years in a multidisciplinary hand center. METHODS: A retrospective chart review was performed to identify workers' compensation patients treated for factitious hand disorders in the multidisciplinary hand center between January 1981 and September 2010. Multidisciplinary evaluation at this center involved evaluation by hand surgeons, occupational therapists, and psychologists. Data collected include age, sex, race, educational level, clinical presentation, number of diagnostic tests, number of surgeries, time to referral to the multidisciplinary center, direct cost of care, psychological diagnosis, Minnesota Multiphasic Personality Inventory, treatment modalities, and work status. RESULTS: We identified 174 workers' compensation patients with factitious hand disorders. Presentation was used to classify patients into 1 of 4 categories: psychopathological dystonia, factitious edema, psychopathological complex regional pain syndrome, and factitious wound creation and manipulation. There were statistically significant differences between the 4 categories in demographics, utilization of medical resources, psychopathology, treatment modalities, and return-to-work status. Patients with factitious wounds were more educated, used more medical resources, demonstrated an angry or hostile profile, and experienced a lower return-to-work rate. Patients with dystonia were less educated, used less medical resources, demonstrated a hypochondriasis or depressed profile, and experienced a higher return-to-work rate. CONCLUSIONS: Treatment of factitious hand disorders remains frustrating and costly due to failure or recurrence after traditional approaches. This review is a large-scale examination of the factitious hand disorder population that demonstrates the unique pathology involved in each of the 4 categories. There is a specific association between the category of hand disorder and the underlying pathology and prognosis. TYPE OF STUDY/LEVEL OF EVIDENCE: Prognostic IV.

Nematode community structure in the brush-tailed rock-wallaby, Petrogale penicillata: implications of captive breeding and the translocation of wildlife.

Despite an increasing appreciation of the disease risks associated with wild-life translocations, the effects which captive breeding programs exert on parasite communities remain understudied. This may be attributed, in part, to the current lack of rapid and cost-effective techniques for comparing parasite assemblages between host populations. Terminal restriction fragment length polymorphism (T-RFLP) analysis of the rDNA region encompassing the internal transcribed spacers (ITS-1 and ITS-2) and 5.8S rRNA gene was used to characterise bursate nematode communities (suborder Strongylida) across two captive and two non-captive colonies of the threatened brush-tailed rock-wallaby, Petrogale penicillata. A clone library was constructed and a restriction enzyme selected to differentiate the predominant operational taxonomic units (OTUs) by the unique peak profiles they generated. The prevalence, intensity of infection and comparative structure of strongylid assemblages was evaluated for each of the host colonies. Compared to wild conspecifics, captive wallabies exhibited a reduced prevalence of infection and significantly lower faecal egg counts. T-RFLP revealed that a high proportion of the OTUs co-occurred across three of the four study locations. Despite this, the composition of strongylid assemblages was significantly different between the colonies, even when host translocation events had occurred. These results suggest that captive breeding programs may exert a profound impact on parasitic helminth assemblages. Developing efficient techniques for characterising community dynamics in potentially pathogenic organisms is critical to the long term success of species recovery efforts worldwide.

Molecular detection of hybridization between sympatric kangaroo species in south-eastern Australia.

Introgressive hybridization has traditionally been regarded as rare in many vertebrate groups, including mammals. Despite a propensity to hybridize in captivity, introgression has rarely been reported between wild sympatric macropodid marsupials. Here we investigate sympatric populations of western (Macropus fuliginosus) and eastern (Macropus giganteus) grey kangaroos through 12 autosomal microsatellite loci and 626 bp of the hypervariable mitochondrial DNA (mtDNA) control region. M. fuliginosus and M. giganteus within the region of sympatry corresponded, both genetically and morphologically, to their respective species elsewhere in their distributions. Of the 223 grey kangaroos examined, 7.6% displayed evidence of introgression, although no F1 hybrids were detected. In contrast to captive studies, there was no evidence for unidirectional hybridization in sympatric grey kangaroos. However, a higher portion of M. giganteus backcrosses existed within the sample compared with M. fuliginosus. Hybridization in grey kangaroos is reflective of occasional breakdowns in species boundaries, occurring throughout the region and potentially associated with variable conditions and dramatic reductions in densities. Such rare hybridization events allow populations to incorporate novel diversity while still retaining species integrity.

Susceptibility to high-altitude pulmonary edema is associated with increased pulmonary arterial stiffness during exercise.

High-altitude pulmonary edema (HAPE), a reversible form of capillary leak, is a common consequence of rapid ascension to high altitude and a major cause of death related to high-altitude exposure. Individuals with a prior history of HAPE are more susceptible to future episodes, but the underlying risk factors remain uncertain. Previous studies have shown that HAPE-susceptible subjects have an exaggerated pulmonary vasoreactivity to acute hypoxia, but incomplete data are available regarding their vascular response to exercise. To examine this, seven HAPE-susceptible subjects and nine control subjects (HAPE-resistant) were studied at rest and during incremental exercise at sea level and at 3,810 m altitude. Studies were conducted in both normoxic (inspired Po2 = 148 Torr) and hypoxic (inspired Po2 = 91 Torr) conditions at each location. Here, we report an expanded analysis of previously published data, including a distensible vessel model that showed that HAPE-susceptible subjects had significantly reduced small distal artery distensibility at sea level compared with HAPE-resistant control subjects [0.011 ± 0.001 vs. 0.021 ± 0.002 mmHg-1; P < 0.001). Moreover, HAPE-susceptible subjects demonstrated constant distensibility over all conditions, suggesting that distal arteries are maximally distended at rest. Consistent with having increased distal artery stiffness, HAPE-susceptible subjects had greater increases in pulmonary artery pulse pressure with exercise, which suggests increased proximal artery stiffness. In summary, HAPE-susceptible subjects have exercise-induced increases in proximal artery stiffness and baseline increases in distal artery stiffness, suggesting increased pulsatile load on the right ventricle.NEW & NOTEWORTHY In comparison to subjects who appear resistant to high-altitude pulmonary edema, those previously symptomatic show greater increases in large and small artery stiffness in response to exercise. These differences in arterial stiffness may be a risk factor for the development of high-altitude pulmonary edema or evidence that consequences of high-altitude pulmonary edema are long-lasting after return to sea level.

Radiation of chromosome shuffles.

Rock wallabies, Petrogale, exhibit chromosome diversity that is exceptional in marsupials, with 20 distinct chromosome races being recognized. Many of the karyotypic changes identified within Petrogale appear to be recent, although the rate of chromosome evolution varies between taxa. While the patchy distribution of Petrogale and their social structure would facilitate the fixation of novel rearrangements, these factors alone do not explain the pattern of chromosome evolution shown in this group. The chromosome changes that have come to characterize each taxon may offer selective advantages in the particular areas occupied, or it may be that these rearrangements play an important role in reproductive isolation. In Petrogale, the taxa with the largest number of chromosome rearrangements are those that are sympatric, or have multiple zones of parapatry, with other members of the genus. Male hybrids from a variety of chromosomal admixtures were found to be sterile, but with those heterozygous for the least complex rearrangements being least affected. As expected, equivalent female hybrids were less severely affected. Chromosomal and genic changes both appear important in these processes.

Mapping the distribution of the telomeric sequence (T2AG3)n in the Macropodoidea (Marsupialia) by fluorescence in situ hybridization. II. The ancestral 2n = 22 macropodid karyotype.

In marsupial karyotypes with little heterochromatin, the telomeric sequence (T(2)AG(3))(n), is involved in chromosome rearrangements. Here we compare the distribution of the (T(2)AG(3))(n) sequence in chromosomes recently derived by fusions and other rearrangements (7-0.5 MYBP) with its distribution in chromosomes derived earlier (24-9 MYBP). We have previously shown that the (T(2)AG(3))(n) sequence is consistently retained during chromosome rearrangements that are recent (7-0.5 MYBP). We suggest that in less recent rearrangements (24-9 MYBP) the pattern observed is initial retention followed by loss or amplification. We also suggest that the presence of interstitial (T(2)AG(3))(n) sequence is related to the evolutionary status of single chromosomes rather than entire karyotypes.

Gas exchange during exercise in habitually active asthmatic subjects.

We determined the relations among gas exchange, breathing mechanics, and airway inflammation during moderate- to maximum-intensity exercise in asthmatic subjects. Twenty-one habitually active (48.2 +/- 7.0 ml.kg(-1).min(-1) maximal O2 uptake) mildly to moderately asthmatic subjects (94 +/- 13% predicted forced expiratory volume in 1.0 s) performed treadmill exercise to exhaustion (11.2 +/- 0.15 min) at approximately 90% of maximal O2 uptake. Arterial O2 saturation decreased to < or =94% during the exercise in 8 of 21 subjects, in large part as a result of a decrease in arterial Po2 (PaO2): from 93.0 +/- 7.7 to 79.7 +/- 4.0 Torr. A widened alveolar-to-arterial Po2 difference and the magnitude of the ventilatory response contributed approximately equally to the decrease in PaO2 during exercise. Airflow limitation and airway inflammation at baseline did not correlate with exercise gas exchange, but an exercise-induced increase in sputum histamine levels correlated with exercise Pa(O2) (negatively) and alveolar-to-arterial Po2 difference (positively). Mean pulmonary resistance was high during exercise (3.4 +/- 1.2 cmH2O.l(-1).s) and did not increase throughout exercise. Expiratory flow limitation occurred in 19 of 21 subjects, averaging 43 +/- 35% of tidal volume near end exercise, and end-expiratory lung volume rose progressively to 0.25 +/- 0.47 liter greater than resting end-expiratory lung volume at exhaustion. These mechanical constraints to ventilation contributed to a heterogeneous and frequently insufficient ventilatory response; arterial Pco2 was 30-47 Torr at end exercise. Thus pulmonary gas exchange is impaired during high-intensity exercise in a significant number of habitually active asthmatic subjects because of high airway resistance and, possibly, a deleterious effect of exercise-induced airway inflammation on gas exchange efficiency.

Repeat exercise normalizes the gas-exchange impairment induced by a previous exercise bout in asthmatic subjects.

Twenty-one subjects with asthma underwent treadmill exercise to exhaustion at a workload that elicited approximately 90% of each subject's maximal O2 uptake (EX1). After EX1, 12 subjects experienced significant exercise-induced bronchospasm [(EIB+), %decrease in forced expiratory volume in 1.0 s = -24.0 +/- 11.5%; pulmonary resistance at rest vs. postexercise = 3.2 +/- 1.5 vs. 8.1 +/- 4.5 cmH2O.l(-1).s(-1)] and nine did not (EIB-). The alveolar-to-arterial Po2 difference (A-aDo2) was widened from rest (9.1 +/- 6.7 Torr) to 23.1 +/- 10.4 and 18.1 +/- 9.1 Torr at 35 min after EX1 in subjects with and without EIB, respectively (P < 0.05). Arterial Po2 (PaO2) was reduced in both groups during recovery (EIB+, -16.0 +/- -13.0 Torr vs. baseline; EIB-, -11.0 +/- 9.4 Torr vs. baseline, P < or = 0.05). Forty minutes after EX1, a second exercise bout was completed at maximal O2 uptake. During the second exercise bout, pulmonary resistance decreased to baseline levels in the EIB+ group and the A-aDo2 and PaO2 returned to match the values seen during EX1 in both groups. Sputum histamine (34.6 +/- 25.9 vs. 61.2 +/- 42.0 ng/ml, pre- vs. postexercise) and urinary 9alpha,11beta-prostaglandin F2 (74.5 +/- 38.6 vs. 164.6 +/- 84.2 ng/mmol creatinine, pre- vs. postexercise) were increased after exercise only in the EIB+ group (P < 0.05), and postexercise sputum histamine was significantly correlated with the exercise PaO2 and A-aDo2 in the EIB+ subjects. Thus exercise causes gas-exchange impairment during the postexercise period in asthmatic subjects independent of decreases in forced expiratory flow rates after the exercise; however, a subsequent exercise bout normalizes this impairment secondary in part to a fast acting, robust exercise-induced bronchodilatory response.

Yeast ferrochelatase: expression in a baculovirus system and purification of the expression protein.

The terminal step of the heme biosynthetic pathway is catalyzed by the enzyme ferrochelatase (EC 4.99.1.1). In eukaryotes this enzyme is bound to the inner mitochondrial membrane with its active site facing the matrix side of the membrane. Previously this laboratory has characterized this enzyme via kinetic and protein chemical modification techniques, and with the recent cloning of the enzyme from yeast, mouse, and human sources it now becomes possible to approach structure-function questions by using site-directed mutagenesis. Of primary significance to this is the development of an efficient expression vector. This is of particular significance for ferrochelatase, as it is a low-abundance protein whose DNA coding sequence has a very low codon bias. In the current work we describe the production of yeast ferrochelatase in a baculovirus system. This system is shown to be an excellent one in which to produce large quantities of active ferrochelatase. The expressed enzyme is membrane associated and is not released into the growth medium either during or after virus development and cell lysis. The expressed protein can be purified in a procedure that requires only 1 day and makes use of a Pharmacia Hi Trap blue affinity column. The measured Km's for the substrates mesoporphyrin and iron are the same as those reported previously for the yeast enzyme. To our knowledge this is the first example of a mitochondrial membrane protein that has been expressed in a baculovirus system.

Molecular mechanisms of neurotropic herpesvirus invasion and spread in the CNS.

Pseudorabies virus (PRV) is a herpesvirus in the subfamily alphaherpesvirinae (the alpha herpesviruses). After primary infection at mucosal surfaces, PRV infects the peripheral nervous system in its natural host (swine) with occasional invasion of the central nervous system. When other hosts (including cows and rodents) are infected, the infection almost always gives rise to fatal disease in the CNS as a result of infection of peripheral neurons and subsequent spread to the brain. Part of the ability to cause fatal CNS disease can be attributed to a viral glycoprotein called gE. Viruses lacking gE are thought to be less virulent because they do not spread efficiently from cell to cell. Based on a set of gE mutations we have constructed, we suggest that these two phenotypes of cell-cell spread and virulence reflect separate functions of the gE protein. In this report, we show that viruses carrying these new gE mutations have marked reduction in virulence, yet spread efficiently in defined neural circuits in the rat brain. As such, they offer new insight and opportunities for understanding of viral disease and host response to injury, as well as in the construction of viral tracers of neuronal connections.

Serum-free, defined medium for the growth and differentiation of murine erythroleukemia cells.

Murine erythroleukemia (MEL) cells are frequently employed to study both cell growth and erythroid differentiation. Although these cells are easily cultured and induced to differentiate, they are routinely maintained in a medium that contains 10%-15% fetal bovine serum. Because of the variability between different lots and the cost of serum, it was desirable to define a serum-free medium in which to culture MEL cells. In the present work, a totally serum-free, defined medium is described that supports both normal cell growth and dimethyl sulfoxide induced differentiation in the two MEL cell lines examined (DS-19 and 270). A variety of hormones and biological compounds are examined in this medium to determine their effects on growth and differentiation. This medium does not support the growth of the mouse hepatoma cell line.

Multiple organ failure after ingestion of pennyroyal oil from herbal tea in two infants.

BACKGROUND: Hepatic and neurologic injury developed in two infants after ingestion of mint tea. Examination of the mint plants, from which the teas were brewed, indicated that they contained the toxic agent pennyroyal oil. METHODS: Sera from each infant were analyzed for the toxic constituents of pennyroyal oil, including pulegone and its metabolite menthofuran. RESULTS: Fulminant liver failure with cerebral edema and necrosis developed in the first infant, who died. This infant was positive only for menthofuran (10 ng/mL). In the other infant, who was positive for both pulegone (25 ng/mL) and menthofuran (41 ng/mL), hepatic dysfunction and a severe epileptic encephalopathy developed. CONCLUSION: Pennyroyal oil is a highly toxic agent that may cause both hepatic and neurologic injury if ingested. A potential source of pennyroyal oil is certain mint teas mistakenly used as home remedies to treat minor ailments and colic in infants. Physicians should consider pennyroyal oil poisoning as a possible cause of hepatic and neurologic injury in infants, particularly if the infants may have been given home-brewed mint teas.

Abnormal cerebrovascular responses to CO2 in sleep apnea patients.

The responses of common carotid blood flow (CCF), pressure (BP), and resistance (R) to variations in respiratory gases were compared during waking periods in 10 sleep apnea patients (SA) and 10 healthy controls (N) of similar age. Respiratory gases were altered by 3-min CO2 rebreathing (RB), 3-min hyperventilation (HV), and 4-min hypoxia (HYP) procedures. CCF was measured continuously by a 5-MHz pulsed Doppler duplex scanner and R was calculated using brachial BP. During RB, which increased end-tidal PCO2 (PACO2) by 15 mm Hg, SA had a lower CCF and greater BP response and therefore a significantly different (positive) change in R compared with N. The ventilatory responses to CO2 were not significantly different. With HV the PACO2 fell by 13 mm Hg in both groups and CCF fell more markedly in SA than N with the same change in BP; therefore, R was increased significantly more in SA. The HYP results did not demonstrate a difference between groups. These results suggest that abnormal cerebrovascular responses to PACO2, initiated either by unusual vasoactive properties of cerebral resistance vessels or peculiar venous outlow patterns, may initiate or potentiate periodic breathing in SA by prolonging lung-to-brain circulation time.

Sleep apnea and autonomic cerebrovascular dysfunction.

Changes in common carotid blood flow (CCF) and resistance index (RI), calculated from velocity waveforms by a noninvasive pulsed Doppler technique, were measured during apneic episodes and voluntary breath holding in five sleep apnea patients (SA) and during breath holding in five normal subjects (N). During apneic episodes averaging 27 s, CCF was reduced by 9% and RI increased by 4%, both trends being related to apneic duration. Internal carotid artery measurements in one SA indicated more dramatic changes in blood flow and RI than noted in CCF. During breath holding, CCF decreased significantly in SA but not in N, and RI showed a smaller reduction in SA. These changes in CCF and RI during sleep apnea are similar to those noted in anesthetized dogs where vasomotor waves and associated apneas were induced by elevating intracranial pressure. Previously reported recordings of ventilatory and systemic cardiovascular responses in SA are similar to these recordings in dogs, and it is therefore proposed that vasomotor responses to intermittent cerebral ischemia and hypercapnia may be the principle event in SA and periodic breathing only a secondary consequence of the prevailing autonomic dysfunction.

Aerosol deposition in the airway model with excessive mucus secretions.

Aerosol deposition in the airways with excessive mucus secretions was investigated utilizing an in vitro airway model lined with various mucus simulants of differing rheological properties. The airway model was made with a straight glass tube (1.0 cm ID and 20 cm in length) and positioned vertically. The mucus simulants were supplied into the tube at a constant rate and made to move upward through the tube as a thin layer (0.6-1.7 mm) undergoing a random wave motion by means of upward airflow. Aerosols (3.0 and 5.0-micron diam) were passed through the mucus-lined tube at flow rates of 0.33-1.17 l/s, and the deposition of the aerosols in the tube was determined by sampling the aerosols at the inlet and the outlet of the tube on filters. During the sampling, pressure drop across the tube model was also measured. Deposition efficiency in the 20-cm-long mucus-lined tube ranged from 13 to 92% with 3.0-micron-diam particles and from 66 to 98% with 5.0-micron-diam particles. This deposition was 25-300 times higher than that in the dry tube. The deposition was higher with increasing viscosity of mucus but was lower with increasing elasticity of mucus. Pressure drop across the mucus-lined tube was much higher than that in the dry tube, and the increase was more prominent with mucous layers with higher viscosity but lower elasticity values. Therefore, aerosol deposition showed a good positive relationship with pressure drop. However, percent increase of aerosol deposition in the mucus-lined tube was 2-5 times higher than that of pressure drop.(ABSTRACT TRUNCATED AT 250 WORDS)

Airway responsiveness to inhaled and intravenous carbachol in sheep: effect of airway mucus.

Excessive airway mucus can alter both the mass and site of aerosol deposition, which, in turn, may affect airway responsiveness to inhaled materials. In six prone sheep, we therefore measured pulmonary airflow resistance (RL) and cumulative aerosol deposition during five standard breaths (AD5) at base line and 3 min after inhalation challenge with 2% carbachol in buffered saline (10 breaths, tidal volume = 500 ml) or after an intravenous loading dose of carbachol (3 micrograms/kg) followed by a constant infusion of 0.3 micrograms.kg-1.min-1 with and without instillation of 20 ml of a mucus simulant (MS) into the distal end of each of the main bronchi or 30 ml of MS into the right main bronchus only by means of a flexible fiber-optic bronchoscope. Before carbachol challenge, RL did not change with MS into either both lungs or one lung only. AD5 increased from 36 +/- 2% (SE) before to 42 +/- 2% after MS instillation into both lungs (P less than 0.05) but remained unchanged after MS into one lung. After carbachol inhalation, RL increased significantly by 154 +/- 20 before and 126 +/- 25% after MS into both lungs and 162 +/- 24 before and 178 +/- 31% after MS into one lung (P less than 0.05). When the percent increase in RL was normalized for total aerosol deposition (% delta RL/AD5), the normalized values were lower after MS (3.0 +/- 0.5) than before MS (4.4 +/- 0.3) into both lungs (P less than 0.05) but were not significantly different before and after MS into the right lung only.(ABSTRACT TRUNCATED AT 250 WORDS)