DNA from soil mirrors plant taxonomic and growth form diversity.

Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughput and simultaneous taxa identification based on a very short (usually <100 base pairs) but informative DNA fragment. Short DNA fragments allow the use of degraded DNA from environmental samples. All analyses included amplification using plant-specific versatile primers, sequencing and estimation of taxonomic diversity. We tested in three steps whether degraded DNA from dead material in soil has the potential of efficiently assessing biodiversity in different biomes. First, soil DNA from eight boreal plant communities located in two different vegetation types (meadow and heath) was amplified. Plant diversity detected from boreal soil was highly consistent with plant taxonomic and growth form diversity estimated from conventional above-ground surveys. Second, we assessed DNA persistence using samples from formerly cultivated soils in temperate environments. We found that the number of crop DNA sequences retrieved strongly varied with years since last cultivation, and crop sequences were absent from nearby, uncultivated plots. Third, we assessed the universal applicability of DNA metabarcoding using soil samples from tropical environments: a large proportion of species and families from the study site were efficiently recovered. The results open unprecedented opportunities for large-scale DNA-based biodiversity studies across a range of taxonomic groups using standardized metabarcoding approaches.

Using next-generation sequencing for molecular reconstruction of past Arctic vegetation and climate.

Palaeoenvironments and former climates are typically inferred from pollen and macrofossil records. This approach is time-consuming and suffers from low taxonomic resolution and biased taxon sampling. Here, we test an alternative DNA-based approach utilizing the P6 loop in the chloroplast trnL (UAA) intron; a short (13-158 bp) and variable region with highly conserved flanking sequences. For taxonomic reference, a whole trnL intron sequence database was constructed from recently collected material of 842 species, representing all widespread and/or ecologically important taxa of the species-poor arctic flora. The P6 loop alone allowed identification of all families, most genera (>75%) and one-third of the species, thus providing much higher taxonomic resolution than pollen records. The suitability of the P6 loop for analysis of samples containing degraded ancient DNA from a mixture of species is demonstrated by high-throughput parallel pyrosequencing of permafrost-preserved DNA and reconstruction of two plant communities from the last glacial period. Our approach opens new possibilities for DNA-based assessment of ancient as well as modern biodiversity of many groups of organisms using environmental samples.

The evolutionary history of the extinct ratite moa and New Zealand Neogene paleogeography.

The ratite moa (Aves: Dinornithiformes) were a speciose group of massive graviportal avian herbivores that dominated the New Zealand (NZ) ecosystem until their extinction approximately 600 years ago. The phylogeny and evolutionary history of this morphologically diverse order has remained controversial since their initial description in 1839. We synthesize mitochondrial phylogenetic information from 263 subfossil moa specimens from across NZ with morphological, ecological, and new geological data to create the first comprehensive phylogeny, taxonomy, and evolutionary timeframe for all of the species of an extinct order. We also present an important new geological/paleogeographical model of late Cenozoic NZ, which suggests that terrestrial biota on the North and South Island landmasses were isolated for most of the past 20-30 Ma. The data reveal that the patterns of genetic diversity within and between different moa clades reflect a complex history following a major marine transgression in the Oligocene, affected by marine barriers, tectonic activity, and glacial cycles. Surprisingly, the remarkable morphological radiation of moa appears to have occurred much more recently than previous early Miocene (ca. 15 Ma) estimates, and was coincident with the accelerated uplift of the Southern Alps just ca. 5-8.5 Ma. Together with recent fossil evidence, these data suggest that the recent evolutionary history of nearly all of the iconic NZ terrestrial biota occurred principally on just the South Island.

Gastroesophageal reflux-induced bronchoconstriction. An intraesophageal acid infusion study using state-of-the-art technology.

STUDY OBJECTIVE: To study mechanisms of gastroesophageal reflux-induced bronchoconstriction during intraesophageal infusions. DESIGN: Prospective study blinded to the subject. SETTING: Outpatient pulmonary function laboratory at a 908-bed university hospital. PARTICIPANTS: Forty-seven adult subjects divided into four groups: asthmatics with reflux, 20; asthmatics, 7; gastroesophageal refluxers, 10; and normal controls, 10. Asthmatics were defined by American Thoracic Society criteria, and refluxers were defined by symptoms and 24-hour pH monitoring. INTERVENTIONS: Dual antimony esophageal pH probe placed just below the upper esophageal sphincter and 5 cm above the lower esophageal sphincter. Intraesophageal infusions of normal saline solution followed by 0.1N hydrochloric acid then normal saline solution were given for 15 to 18 min. Spirometry and specific airway resistance (SRaw) were performed after placement of pH probes, insertion of esophageal infusion tube, and after each infusion. Bernstein tests were assessed during esophageal infusions. MEASUREMENTS AND RESULTS: Peak expiratory flow rate (PEF) decreased with intraesophageal acid in all four groups (p < 0.014). Esophageal acid clearance improved PEF in all groups except the asthmatics with reflux group that had a further decrease in PEF. These effects were not dependent on a positive Bernstein test or evidence of proximal reflux. The asthmatics with reflux group also had an increase in SRaw with intraesophageal acid, which continued to increase despite acid clearance. CONCLUSIONS: Intraesophageal acid infusions caused a decrease in PEF in all groups without evidence of microaspiration, implying a vagally mediated reflex may be involved. Esophageal mucosal inflammation, assessed by a positive Bernstein test, was not required. Asthmatics with reflux also had further decline in PEF despite acid clearance.

Altered pain perception and psychosocial features among women with gastrointestinal disorders and history of abuse: a preliminary model.

OBJECTIVES: To evaluate the relationships between sexual/physical abuse, pain perception, environmental events, coping strategies, and psychiatric morbidity in a sample of female patients with painful gastrointestinal disorders. PATIENTS: Fifty paid volunteers from a tertiary care center including 13 patients with gastroesophageal reflux disease (GERD), 26 with noncardiac chest pain (NCCP), and 11 with irritable bowel syndrome (IBS). MEASUREMENTS: (1) Sexual and physical abuse interview questions; (2) Structured psychiatric interview; (3) Self-report questionnaires: demographics, clinical pain measurement, Millon Behavioral Health Inventory, Hassles and Uplifts Scales, Sickness Impact Profile, Life Experiences Survey, Pain Beliefs and Perceptions Inventory, and Coping Strategies Questionnaire; (4) Pain Perception and Sensory Decision Theory tasks. RESULTS: Fifty-six percent of the sample reported a history of sexual/physical abuse. Abuse was significantly more prevalent among patients with GERD (92%) and IBS (82%) compared with those with NCCP (27%). Abused patients, relative to nonabused patients, had significantly lower pain threshold levels in response to finger pressure stimuli and significantly lower cognitive standards for judging stimuli as noxious. Abused patients reported significantly higher levels of functional disability and a significantly greater number of psychiatric disorders, minor daily hassles, and pain syndromes unrelated to gastrointestinal disorders. In addition, abused patients more frequently blamed themselves for their pain and reported significantly greater use of maladaptive pain coping strategies than nonabused patients. CONCLUSION: These data suggest that the relationships between abuse, disability, multiple pain syndromes, and health care seeking behavior are mediated by abnormal pain perception, psychiatric disorders, disruption of physical function, and environmental stressors.

Relaxation training reduces symptom reports and acid exposure in patients with gastroesophageal reflux disease.

BACKGROUND/AIMS: Previous studies have shown that psychological factors play a role in symptom perception among patients with gastroesophageal reflux disease. This report describes the first controlled study showing the effects of relaxation training on symptom reports and esophageal acid exposure in patients with reflux disease. METHODS: Twenty subjects with documented reflux disease were studied during psychologically neutral and stressful tasks, followed immediately by either a relaxation or attention-placebo control intervention. RESULTS: Stressful tasks, relative to neutral tasks, produced significant increases in blood pressure, subjective ratings of anxiety, and reports of reflux symptoms. Despite increased symptom reports, stressful tasks did not significantly increase objective measures of esophageal acid exposure. Subjects who received a relaxation intervention after the stressful task had significantly lower heart rate values and subjective ratings of anxiety compared with subjects who received the attention-placebo control intervention. Subjects who received relaxation training also had significantly lower reflux symptom ratings and total esophageal acid exposure than subjects who received the attention-placebo control intervention. CONCLUSIONS: Relaxation may be a useful adjunct to traditional antireflux therapy in patients who experience increased symptoms during stress.

The symptom index. Differential usefulness in suspected acid-related complaints of heartburn and chest pain.

The symptom index is a quantitative measure developed for assessing the relationship between gastroesophageal reflux and symptoms. Controversy exists, however, over its accuracy and the appropriate threshold for defining acid-related symptoms of heartburn and chest pain. Therefore, a retrospective review was done of 153 consecutive patients referred to our esophageal laboratory. Three groups were identified: patients with normal 24-hr pH tests and no esophagitis, patients with abnormal 24-hr pH tests and no esophagitis, and patients with abnormal 24 hr pH values and endoscopic esophagitis. If symptoms occurred during the pH study, a symptom index (number of acid related symptoms/total number of symptoms x 100%) was calculated separately for heartburn and chest pain. Heartburn and chest pain episodes were similar among the three groups. However, the mean symptom index for heartburn was significantly (P < 0.001) higher in the patient groups with abnormal pH values [abnormal pH/no esophagitis: 70 +/- 7.1% (+/- SE); abnormal pH/esophagitis: 85 +/- 4.6%] as compared to those with normal studies, ie, functional heartburn (26 +/- 10.7%). The mean symptom index for chest pain was similar for all three groups. Using receiver operating characteristic curves, a heartburn symptom index > or = 50% had excellent sensitivity (93%) and good specificity (71%) for acid reflux disease, especially if patients complain of multiple episodes of heartburn. In contrast, an optimal symptom index threshold for defining acid-related chest pain episodes could not be defined.

The relationship between stress and symptoms of gastroesophageal reflux: the influence of psychological factors.

This paper describes the first controlled study of the relationships among stress, psychological traits associated with chronic anxiety, acid reflux parameters, and perceptions of reflux symptoms. Seventeen subjects with symptomatic reflux disease were studied using a 2 (high vs. low gastrointestinal susceptibility score) x 2 (stress vs. neutral tasks) x 3 (periods 1, 2, or 3) experimental design. It was found that the stress tasks produced significant increases in systolic and diastolic blood pressure, pulse rates, and subjective ratings of anxiety and reflux symptoms. The stress tasks, however, did not influence objective parameters of acid reflux (total acid exposure, number of reflux episodes, duration of longest reflux episode). Moreover, the effect of stress on reflux ratings was due primarily to the responses of the subjects with high gastrointestinal susceptibility scale scores. These subjects' reflux ratings remained at high levels during all stress periods, whereas subjects in all other experimental conditions reported decreased reflux symptoms across periods. These results suggest that reflux patients who are chronically anxious and exposed to prolonged stress may perceive low intensity esophageal stimuli as painful reflux symptoms. Future effort should be devoted to examining the efficacy of anxiolytic and behavioral therapies with these reflux patients.

Psychosocial and psychophysical assessments of patients with unexplained chest pain.

It is imperative to assess the psychosocial factors that may influence the subjective experiences and pain behavior of persons with chronic unexplained chest pain. Both psychologists and physicians tend to rely on self-report measures of psychological distress, which provide little unique information about patients with chronic chest pain to differentiate them from patients with other painful disorders such as irritable bowel syndrome, gastroesophageal reflux disease, or coronary artery disease. However, assessment of pain-coping strategies, spouse responses to the patient's pain behaviors, and pain thresholds for esophageal balloon distention do differentiate patients with chronic chest pain from healthy controls and patients with various other chronic pain disorders. Specifically, chronic chest pain patients tend to use relatively passive pain-coping strategies such as praying and hoping, and to report relatively high levels of spouse reinforcement of pain behaviors. Finally, in response to esophageal balloon distention, chronic chest pain patients display low pain thresholds that do not generalize to stimulation by mechanical finger pressure. Preliminary evidence suggests these low thresholds are due primarily to a tendency to set low standards for making pain judgments regarding esophageal stimuli of moderate-to-high intensity levels.