Haploview: analysis and visualization of LD and haplotype maps

Research over the last few years has revealed significant haplotype structure in the human genome. The characterization of these patterns, particularly in the context of medical genetic association studies, is becoming a routine research activity. Haploview is a software package that provides computation of linkage disequilibrium statistics and population haplotype patterns from primary genotype data in a visually appealing and interactive interface.

AVAILABILITY

http://www.broad.mit.edu/mpg/haploview/

CONTACT

jcbarret@broad.mit.edu

Positive natural selection in the human lineage

Positive natural selection is the force that drives the increase in prevalence of advantageous traits, and it has played a central role in our development as a species. Until recently, the study of natural selection in humans has largely been restricted to comparing individual candidate genes to theoretical expectations. The advent of genome-wide sequence and polymorphism data brings fundamental new tools to the study of natural selection. It is now possible to identify new candidates for selection and to reevaluate previous claims by comparison with empirical distributions of DNA sequence variation across the human genome and among populations. The flood of data and analytical methods, however, raises many new challenges. Here, we review approaches to detect positive natural selection, describe results from recent analyses of genome-wide data, and discuss the prospects and challenges ahead as we expand our understanding of the role of natural selection in shaping the human genome.

Resource-based niches provide a basis for plant species diversity and dominance in arctic tundra

Ecologists have long been intrigued by the ways co-occurring species divide limiting resources. Such resource partitioning, or niche differentiation, may promote species diversity by reducing competition. Although resource partitioning is an important determinant of species diversity and composition in animal communities, its importance in structuring plant communities has been difficult to resolve. This is due mainly to difficulties in studying how plants compete for below-ground resources. Here we provide evidence from a 15N-tracer field experiment showing that plant species in a nitrogen-limited, arctic tundra community were differentiated in timing, depth and chemical form of nitrogen uptake, and that species dominance was strongly correlated with uptake of the most available soil nitrogen forms. That is, the most productive species used the most abundant nitrogen forms, and less productive species used less abundant forms. To our knowledge, this is the first documentation that the composition of a plant community is related to partitioning of differentially available forms of a single limiting resource.

Association of Opioid Prescribing With Opioid Consumption After Surgery in Michigan

Importance

There is growing evidence that opioids are overprescribed following surgery. Improving prescribing requires understanding factors associated with opioid consumption.

Objective

To describe opioid prescribing and consumption for a variety of surgical procedures and determine factors associated with opioid consumption after surgery.

Design, Setting, and Participants

A retrospective, population-based analysis of the quantity of opioids prescribed and patient-reported opioid consumption across 33 health systems in Michigan, using a sample of adults 18 years and older undergoing surgery. Patients were included if they were prescribed an opioid after surgery. Surgical procedures took place between January 1, 2017, and September 30, 2017, and were included if they were performed in at least 25 patients.

Exposures

Opioid prescription size in the initial postoperative prescription.

Main Outcomes and Measures

Patient-reported opioid consumption in oral morphine equivalents. Linear regression analysis was used to calculate risk-adjusted opioid consumption with robust standard errors.

Results

In this study, 2392 patients (mean age, 55 years; 1353 women [57%]) underwent 1 of 12 surgical procedures. Overall, the quantity of opioid prescribed was significantly higher than patient-reported opioid consumption (median, 30 pills; IQR, 27-45 pills of hydrocodone/acetaminophen, 5/325 mg, vs 9 pills; IQR, 1-25 pills; P < .001). The quantity of opioid prescribed had the strongest association with patient-reported opioid consumption, with patients using 0.53 more pills (95% CI, 0.40-0.65; P < .001) for every additional pill prescribed. Patient-reported pain in the week after surgery was also significantly associated with consumption but not as strongly as prescription size. Compared with patients reporting no pain, patients used a mean (SD) 9 (1) more pills if they reported moderate pain and 16 (2) more pills if they reported severe pain (P < .001). Other significant risk factors included history of tobacco use, American Society of Anesthesiologists class, age, procedure type, and inpatient surgery status. After adjusting for these risk factors, patients in the lowest quintile of opioid prescribing had significantly lower mean (SD) opioid consumption compared with those in the highest quintile (5 [2] pills vs 37 [3] pills; P < .001).

Conclusions and Relevance

The quantity of opioid prescribed is associated with higher patient-reported opioid consumption. Using patient-reported opioid consumption to develop better prescribing practices is an important step in combating the opioid epidemic.

Rapid 13C/12C turnover during growth of brown shrimp (Penaeus aztecus)

Using natural-abundance ¹³C/¹²C ratios as tracers, carbon turnover rates were determined for postlarval brown shrimp, Penaeus aztecus, in five laboratory growth experiments. Although tissue turnover in adult animals generally occurs during maintenance metabolism and is a function of time, turnover for young postlarval shrimp was accelerated during growth, and was primarily a function of weight gained rather than time. Metabolic loss of tissue carbon during growth was usually approximated by the function, Fraction lost=1-(initial weight/final weight). For shrimp that switch diets in the sea, model calculations show that this high turnover rate coupled with a four-fold weight increase suffices for shrimp to achieve a close isotopic resemblance of 1‰ or less (δ¹³C units) to the new diet.In accordance with these predictive calculations, shrimp which had increased in weight by a factor of four or more in the culture experiments showed essentially constant isotopic values reflecting their new diets. For these larger animals, the average animal-diet difference varied across three diets from-0.9 to +11‰, and the δ¹³C range among individuals was ≦1.4‰ in each experiment.

Assessing clinicopathological correlation in chronic traumatic encephalopathy: rationale and methods for the UNITE study

INTRODUCTION

Chronic traumatic encephalopathy (CTE) is a progressive neurodegeneration associated with repetitive head impacts. Understanding Neurologic Injury and Traumatic Encephalopathy (UNITE) is a U01 project recently funded by the National Institute of Neurological Disorders and Stroke and the National Institute of Biomedical Imaging and Bioengineering. The goal of the UNITE project is to examine the neuropathology and clinical presentation of brain donors designated as "at risk" for the development of CTE based on prior athletic or military exposure. Here, we present the rationale and methodology for UNITE.

METHODS

Over the course of 4 years, we will analyze the brains and spinal cords of 300 deceased subjects who had a history of repetitive head impacts sustained during participation in contact sports at the professional or collegiate level or during military service. Clinical data are collected through medical record review and retrospective structured and unstructured family interviews conducted by a behavioral neurologist or neuropsychologist. Blinded to the clinical data, a neuropathologist conducts a comprehensive assessment for neurodegenerative disease, including CTE, using published criteria. At a clinicopathological conference, a panel of physicians and neuropsychologists, blinded to the neuropathological data, reaches a clinical consensus diagnosis using published criteria, including proposed clinical research criteria for CTE.

RESULTS

We will investigate the validity of these clinical criteria and sources of error by using recently validated neuropathological criteria as a gold standard for CTE diagnosis. We also will use statistical modeling to identify diagnostic features that best predict CTE pathology.

CONCLUSIONS

The UNITE study is a novel and methodologically rigorous means of assessing clinicopathological correlation in CTE. Our findings will be critical for developing future iterations of CTE clinical diagnostic criteria.

Sulfur isotope effects associated with oxidation of sulfide by O2 in aqueous solution

Normal sulfur isotope effects averaging epsilon = -5.2 +/- 1.4% (s.d.) were consistently observed for the oxidation of sulfide in aqueous solution. Reaction products were sulfate, thiosulfate and sulfite at pH 10.8-11 in distilled water; S0 was formed in two experiments with synthetic seawater at pH 8-9.5. Because the -5.2% normal isotope effect differs significantly from the previously measured +2% inverse effect associated with anaerobic oxidation of sulfide by photosynthetic bacteria, stable sulfur isotopic measurements are potentially useful for distinguishing aerobic vs. anaerobic sulfide oxidation in marine and freshwater sulfureta.

Tracing Mississippi River influences in estuarine food webs of coastal Louisiana

The Breton Sound estuary in southern Louisiana receives large amounts of Mississippi River water via a controlled diversion structure at the upstream end of the estuary. We used stable isotopes to trace spatial and seasonal responses of the downstream food web to winter and spring introductions of river water. Analysis of delta13C, delta15N, and delta34S in the common local consumers such as grass shrimp (Palaemonetes sp.), barnacles (Balanus sp.), and small plankton-feeding fish (bay anchovies, Anchoa mitchilli) showed that the diversion was associated with two of the five major source regimes that were supporting food webs: a river regime near the diversion and a river-influenced productive marsh regime farther away from the diversion. Mixing models identified a third river-influenced source regime at the marine end of the estuary where major natural discharge from the Bird's Foot Delta wraps around into estuarine waters. The remaining two source regimes represented typical estuarine conditions: local freshwater sources especially from precipitation and a brackish source regime representing higher salinity marine influences. Overall, the Mississippi River diversion accounted for 75% of food web support in the upper estuary and 25% in the middle estuary, with influence strongest along known flow pathways and closest to the diversion. Isotopes also traced seasonal changes in river contributions, and indicated increased plant community productivity along the major flow path of diversion water. In the Breton Sound estuary, bottom-up forcing of food webs is strongly linked to river introductions and discharge, occurring in spatial and temporal patterns predictable from known river input regimes and known hydrologic circulation patterns.

Forest- and pasture-derived carbon contributions to carbon stocks and microbial respiration of tropical pasture soils

The clearing of tropical forest for pasture leads to important changes in soil organic carbon (C) stocks and cycling patterns. We used the naturally occurring distribution of¹³C in soil organic matter (SOM) to examine the roles of forest- and pasture-derived organic matter in the carbon balance in the soils of 3- to 81-year-old pastures created following deforestation in the western Brazilian Amazon Basin state of Rondônia. Different δ¹³C values of C3 forest-derived C (-28‰) and C4 pasture-derived C (-13‰) allowed determination of the origin of total soil C and soil respiration. The δ¹³C of total soil increased steadily across ecosystems from -27.8‰ in the forest to -15.8‰ in the 81-year-old pasture and indicated a replacement of forest-derived C with pasture-derived C. The δ¹³C of respired CO₂ increased more rapidly from -26.5‰ in the forest to -17‰ in the 3- to 13-year-old pastures and indicated a faster shift in the origin of more labile SOM. In 3-year-old pasture, soil C derived from pasture grasses made up 69% of respired C but only 17% of total soil C in the top 10 cm. Soils of pastures 5 years old and older had higher total C stocks to 30 cm than the original forest. This occurred because pasture-derived C in soil organic matter increased more rapidly than forest-derived C was lost. The increase of pasture-derived C in soils of young pastures suggests that C inputs derived from pasture grasses play a critical role in development of soil C stocks in addition to fueling microbial respiration. Management practices that promote high grass production will likely result in greater inputs of grass-derived C to pasture soils and will be important for maintaining tropical pasture soil C stocks.

Food web structure in exotic and native mangroves: a Hawaii–Puerto Rico comparison

Plant invasions can fundamentally alter detrital inputs and the structure of detritus-based food webs. We examined the detrital pathways in mangrove food webs in native (Puerto Rican) and introduced (Hawaiian) Rhizophora mangle forests using a dual isotope approach and a mixing model. Based on trophic-level fractionation of 0-1 per thousand for delta(13)C and 2-3 per thousand for delta(15)N, among the invertebrates, only nematodes, oligochaetes, and nereid polychaetes from native mangroves exhibited stable isotopes consistent with a mangrove-derived diet. Certain fauna, in particular tubificid oligochaetes, had delta(13)C values consistent with the consumption of mangrove leaves, but they were depleted in (15)N, suggesting their primary nitrogen source was low in (15)N, and was possibly N(2)-fixing bacteria. In introduced mangroves, all feeding groups appeared to rely heavily on non-mangrove sources, especially phytoplankton inputs. Mixing model results and discriminant analysis showed clear separation of introduced and native mangrove sites based on differential food source utilization within feeding groups, with stronger and more diverse use of benthic foods observed in native forests. Observed differences between native and invasive mangrove food webs may be due to Hawaiian detritivores being poorly adapted to utilizing the tannin-rich, nitrogen-poor mangrove detritus. In addition, differential utilization of mangrove detritus between native and introduced mangroves may be a consequence of forest age. We postulate that increasing mangrove forest age may promote diversification of bacterial food webs important in N and S cycling. Our results also suggest a potentially important role for sulfur bacteria in supporting the most abundant infaunal consumers, nematodes, in the most mature systems.

Human effects on ecological connectivity in aquatic ecosystems: Integrating scientific approaches to support management and mitigation

Understanding the drivers and implications of anthropogenic disturbance of ecological connectivity is a key concern for the conservation of biodiversity and ecosystem processes. Here, we review human activities that affect the movements and dispersal of aquatic organisms, including damming of rivers, river regulation, habitat loss and alteration, human-assisted dispersal of organisms and climate change. Using a series of case studies, we show that the insight needed to understand the nature and implications of connectivity, and to underpin conservation and management, is best achieved via data synthesis from multiple analytical approaches. We identify four key knowledge requirements for progressing our understanding of the effects of anthropogenic impacts on ecological connectivity: autecology; population structure; movement characteristics; and environmental tolerance/phenotypic plasticity. Structuring empirical research around these four broad data requirements, and using this information to parameterise appropriate models and develop management approaches, will allow for mitigation of the effects of anthropogenic disturbance on ecological connectivity in aquatic ecosystems.

34S/32S fractionation in sulfur cycles catalyzed by anaerobic bacteria

Stable isotopic distributions in the sulfur cycle were studied with pure and mixed cultures of the anaerobic bacteria, Chlorobium vibrioforme and Desulfovibrio vulgaris. D. vulgaris and C. vibrioforme can catalyze three reactions constituting a complete anaerobic sulfur cycle: reduction of sulfate to sulfide (D. vulgaris), oxidation of sulfide to elemental sulfur (C. vibrioforme), and oxidation of sulfur to sulfate (C. vibrioforme). In all experiments, the first and last reactions favored concentration of the light 32S isotope in products (isotopic fractionation factor epsilon = -7.2 and -1.7%, respectively), whereas oxidation of sulfide favored concentration of the heavy 34S isotope in products (epsilon = +1.7%). Experimental results and model calculations suggest that elemental sulfur enriched in 34S versus sulfide may be a biogeochemical marker for the presence of sulfide-oxidizing bacteria in modern and ancient environments.