bluuebunny/crossref_metadata_2025 huggingface dataset:
Cartilage oligomeric matrix protein neoepitope in the synovial fluid of horses with acute lameness: A new biomarker for the early stages of osteoarthritis
Authors: Skiöldebrand E. , Ekman S. , Mattsson Hultén L. , Svala E. , Björkman K. , Lindahl A. , Lundqvist A. , Önnerfjord P. , Sihlbom C. , Rüetschi U.
Published: January 2017

Background

Clinical tools to diagnose the early changes of osteoarthritis (OA) that occur in the articular cartilage are lacking.

Objectives

We sought to identify and quantify a novel cartilage oligomeric matrix protein (COMP) neoepitope in the synovial fluid from the joints of healthy horses and those with different stages of OA.

Study design

In vitro quantitative proteomics and assay development with application in synovial fluids samples obtained from biobanks of well‐characterised horses.

Methods

Articular cartilage explants were incubated with or without interleukin‐1β for 25 days. Media were analysed via quantitative proteomics. Synovial fluid was obtained from either normal joints (n = 15) or joints causing lameness (n = 17) or with structural OA lesions (n = 7) and analysed for concentrations of the COMP neoepitope using a custom‐developed inhibition enzyme‐linked immunosorbent assay (ELISA). Explants were immunostained with polyclonal antibodies against COMP and the COMP neoepitopes.

Results

Semitryptic COMP peptides were identified and quantified in cell culture media from cartilage explants. A rabbit polyclonal antibody was raised against the neoepitope of the N‐terminal portion of one COMP fragment (sequence SGPTHEGVC). An inhibition ELISA was developed to quantify the COMP neoepitope in synovial fluid. The mean concentration of the COMP neoepitope significantly increased in the synovial fluid from the joints responsible for acute lameness compared with normal joints and the joints of chronically lame horses and in joints with chronic structural OA. Immunolabelling for the COMP neoepitope revealed a pericellular staining in the interleukin‐1β‐stimulated explants.

Main limitations

The ELISA is based on polyclonal antisera rather than a monoclonal antibody.

Conclusions

The increase in the COMP neoepitope in the synovial fluid from horses with acute lameness suggests that this neoepitope has the potential to be a unique candidate biomarker for the early molecular changes in articular cartilage associated with OA.
In situ electrical monitoring of cancer cells invading vascular endothelial cells with semiconductor‐based biosensor
Authors: Sakata Toshiya , Matsuse Yusuke
Published: January 2017

Cellular dynamics is very closely related to ionic behaviors, most of which have been hardly monitored in real time, whereas semiconductor‐based biosensors have the unique advantage of direct detection of ionic charges in a real‐time and noninvasive manner. In this study, we monitored the invasion process of cancer cells into the vascular endothelial layer in real time by a label‐free method using a field‐effect transistor (FET) biosensor. Endothelial cells were cultured on the sensing surface of the FET gate, to form a basement membrane between the endothelial cells and the sensing surface. When invasive cancer cells (HeLa cells) approached the endothelial cell‐coated gate FET biosensor, a change in the surface potential was clearly detected using the FET biosensor. This is because HeLa cells, which invaded the endothelial cell layer, reduced the molecular charge density in the basement membrane by decomposing it. A platform based on the cell‐coated gate FET biosensor is suitable for real‐time and noninvasive monitoring of cellular dynamics based on intrinsic ionic charges.
Antibiotic resistance of Helicobacter pylori in Chinese children: A multicenter retrospective study over 7 years
Authors: Li Lan , Ke Yini , Yu Chaohui , Li Guogang , Yang Ningmin , Zhang Jianzhong , Li Youming
Published: January 2017

Background

To determine the prevalence of resistance to metronidazole, clarithromycin, levofloxacin, amoxicillin, and furazolidone in Helicobacter pylori isolated from Chinese children.

Materials and Methods

This multicenter retrospective study was conducted from January 2009 to December 2015. A total of 1746 isolates of H. pylori were collected from nine areas of Zhejiang province in the southeast coastal region of China. H. pylori strains were examined for antibiotics susceptibility by agar dilution method.

Results

The resistance rates were 75.20% for metronidazole, 16.38% for clarithromycin, 6.70% for levofloxacin, 0.06% for amoxicillin, and 0.06% for furazolidone. The pattern of H. pylori antibiotic resistance demonstrated no significant changes in the rates of resistance to clarithromycin, amoxicillin, furazolidone, and metronidazole over 7 years. A significant trend of increasing resistance to metronidazole was observed as children aged, but a downward trend in clarithromycin resistance was observed as children aged. No difference in the resistance to other antibiotics was observed among different age groups. Also, there was no significant difference between male and female subjects in rates of resistance to these five types of antibiotics. The predominant dual resistance to metronidazole and clarithromycin was presented in 10.65% of the isolates.

Conclusions

The resistance rates of H. pylori in children from southeast coastal region of China were very high to metronidazole, moderate to clarithromycin and levofloxacin, and low to amoxicillin and furazolidone. It is important to continue monitoring the resistance profiles of H. pylori isolated in this region.
Pharmacist–industry relationships
Authors: Saavedra Keene , O'Connor Bonnie , Fugh-Berman Adriane
Published: January 2017

Objectives

The purpose of this study was to document, in their own words, beliefs and attitudes that American pharmacists have towards the pharmaceutical industry and pharmacists’ interactions with industry.

Methods

An ethnographic-style qualitative study was conducted utilizing open-ended interviews with four hospital pharmacists, two independent pharmacists, two retail pharmacists and one administrative pharmacist in the Washington, DC, metropolitan area to elicit descriptions of and attitudes towards pharmacists’ relationships with industry. Analysis of the qualitative material followed established ethnographic conventions of narrative thematic analysis.

Key Findings

All pharmacists reported interactions with pharmaceutical company representatives. Most had received free resources or services from industry, including educational courses. Respondents uniformly believed that industry promotional efforts are primarily directed towards physicians. Although respondents felt strongly that drug prices were excessive and that ‘me-too’ drugs were of limited use, they generally had a neutral-to-positive view of industry-funded adherence/compliance programmes, coupons, vouchers, and copay payment programmes. Interviewees viewed direct-to-consumer advertising negatively, but had a generally positive view of industry-funded drug information.

Conclusions

Pharmacists may represent a hitherto under-identified cohort of health professionals who are targeted for industry influence; expanding roles for pharmacists may make them even more attractive targets for future industry attention. Pharmacy schools should ensure that students learn to rely on unbiased information sources and should teach students about conflicts of interest and the risks of interacting with industry. Further research should be conducted on the extent to which pharmacists’ attitudes towards their duties and towards drug assessment and recommendation are influenced by the pharmaceutical industry.
Geographical variation in reproductive investment across avian assemblages in Europe: effects of environmental drivers differ between altricial and precocial species
Authors: Kopsová‐Storchová Lenka , Storch David , Brotons Lluís , Hořák David
Published: January 2017

Reproductive traits provide information about the ways by which available resources are allocated during breeding. We tested for environmental drivers of large scale geographical patterns in assemblage mean clutch size, number of broods and overall reproductive investment per breeding season in European birds. We combined data about geographical distribution with published information about reproductive traits, and calculated mean trait values for avian assemblages occurring in 50 × 50 km grid cells. In total, we employed data from 499 species and 2059 assemblages. As the time available for breeding and the amount of food limit the reproductive effort, we related the geographical variation in reproductive traits to the length of breeding season, normalized difference vegetation index (NDVI) as a surrogate of resource availability, and its seasonality. Geographical patterns in traits may differ between reproductive modes, thus we performed the analyses separately for altricial Passerines (n = 203) and precocial non‐passerine species (n = 164) and controlled for the effect of taxonomy. Large clutches dominated in areas with high NDVI and, in precocial birds, also in areas with high annual seasonality and a long breeding season. High number of broods and high overall reproductive investment dominated in areas with a long breeding season, and high number of broods was found also in areas with low annual seasonality, but only in precocial species. High overall reproductive investment dominated in highly productive areas and also in areas with low annual seasonality in both groups. The increase in reproductive investment is caused mostly by an increase in the number of broods related to the length of season and partly by increase in clutch size related to NDVI. We found a negative correlation between clutch size and the number of broods in Passerines, which might suggest a trade‐off between these traits. Processes behind trait patterns differ between altricial and precocial species.
Hermaphroditism in the dash‐and‐dot goatfish Parupeneus barberinus
Authors: Longenecker K. , Langston R. , Crane M.
Published: January 2017

Presence of bisexual individuals and a sex‐specific bimodal size distribution are suggestive of protogyny in the dash‐and‐dot goatfish Parupeneus barberinus, but the most parsimonious interpretation of histological analysis is juvenile hermaphroditism. This is the first report of hermaphroditism in the Mullidae.
Survival and partitioning of male‐specific coliphage (MS2) as a surrogate for enteric viruses in the production process of traditional butter
Authors: Fatemizadeh Saeedeh Sadat , Yavarmanesh Masoud , Habibi Najafi Mohammad B.
Published: January 2017

Dairy products are potentially considered as important sources of enteric viruses transmission. Currently, there is a lack of appropriate methods for sampling and study of enteric viruses in food products. Therefore, the design of modeling experiments can lead to accurate and precise estimation of viral pathogenic agents. To achieve this aim, the effects of thermal treatment of raw milk, traditional butter storage time, and the bacteriophage spiked levels on survival of the male‐specific MS2 coliphage in traditional butter were studied. MS2 spiking concentrations in three levels of 102, 104, and 106 pfu/ml, traditional butter storage time in four levels (after 1, 2, 3, and 4 weeks), and pasteurization process (85°C for 30 min) of raw milk were chosen as treatments. MS2 coliphage survival, as well as chemical and microbial tests were conducted on pasteurized and unpasteurized butter. The results revealed that pasteurization of raw milk used in the production process of traditional butter led to the reduction of MS2 coliphage survival. Also, acidity and pH affected MS2 bacteriophage recovery in a way that increase in acidity and reduction of pH caused a decrease in bacteriophage recovery. pH was measured at 1‐week intervals until 4 weeks of storage; the highest pH was indicated in the butter samples after the first week, and the lowest pH was observed in the Doogh samples after the fourth week. Therefore, we ascribed the lowest and highest MS2 recovery rates to butter and Doogh, respectively.

Practical applications

Traditional dairy products, including traditional butter and Doogh, are gaining economic and nutritional significance in Iran and worldwide. Little research has been conducted on the survival of enteric viruses in traditional dairy products. However, Safety evaluation of these products is essential as enteric viruses can cause severe health issues in consumers. The results from this study demonstrate that pasteurization could serve as a promising treatment for inactivation of enteric viruses in traditional Iranian butter and Doogh. Additionally, such a treatment might potentially be used to control viral propagation in other dairy products.
Behavior of thirteen foodborne bacteria on whole Hass avocado and potential of roselle calyx extracts as alternative disinfectant agents of avocado
Authors: Gómez‐Aldapa Carlos A. , Refugio Torres‐Viela Ma. , Amaya‐Acosta Mariel A. , Rangel‐Vargas Esmeralda , Villaruel‐López Angélica , Castro‐Rosas Javier
Published: January 2017

The behavior of thirteen foodborne bacteria onto whole Hass avocado and the antibacterial effect of Hibiscus sabdariffa calyx extracts, sodium hypochlorite, acetic acid, and colloidal silver against foodborne bacteria on contaminated avocado were investigated. Avocados were inoculated with foodborne bacteria: Listeria monocytogenes, Shigella flexneri, Staphylococcus aureus, Salmonella Typhimurium, S. Typhi, S. Montevideo, Escherichia coli O157:H7, non‐O157:H7‐Shiga toxin‐producing E. coli, enteropathogenic E. coli, enterotoxigenic E. coli, enteroinvasive E. coli, enteroaggregative E. coli, and Vibrio cholerae O1. The antibacterial effect of four roselle calyx extracts (water, methanol, acetone, and ethyl acetate), sodium hypochlorite, colloidal silver, and acetic acid against all foodborne bacteria were examined onto avocados. All foodborne bacteria successfully attached and survived onto avocado at least 20 days. The acetonic and methanolic roselle extracts caused a greater reduction (until 4‐log10 in some cases) in the concentration of all foodborne bacteria than sodium hypochlorite, colloidal silver, and acetic acid on contaminated avocados.

Practical applications

Hass avocado have been associated with foodborne disease caused by Salmonella. The sodium hypochlorite and colloidal silver solution are widely used to disinfect fruit and vegetables in restaurants and home in Mexico. Even, the Health Secretariat of Mexico promotes their use as disinfectants of fruit and vegetables. However, a number of studies have shown that chemical agents used to eliminate pathogenic bacteria on fruits have a limited antimicrobial effect. Roselle calyx extracts are reported to have an antimicrobial effect. This study provides information on the significant impact of acetone and methanol roselle calyx extracts may be a potentially useful addition to disinfection procedures of avocado in the field and processing plants.
Effects of a dietary ketone ester on hippocampal glycolytic and tricarboxylic acid cycle intermediates and amino acids in a 3xTgAD mouse model of Alzheimer's disease
Authors: Pawlosky Robert J. , Kemper Martin F. , Kashiwaya Yoshihero , King Michael Todd , Mattson Mark P. , Veech Richard L.
Published: January 2017

In patients with Alzheimer's disease (AD) and in a triple transgenic (3xTgAD) mouse model of AD low glucose metabolism in the brain precedes loss of memory and cognitive decline. The metabolism of ketones in the brain by‐passes glycolysis and therefore may correct several deficiencies that are associated with glucose hypometabolism. A dietary supplement composed of an ester of D‐β‐hydroxybutyrate and R‐1,3 butane diol referred to as ketone ester (KE) was incorporated into a rodent diet and fed to 3xTgAD mice for 8 months. At 16.5 months of age animals were killed and brains dissected. Analyses were carried out on the hippocampus and frontal cortex for glycolytic and TCA (Tricarboxylic Acid) cycle intermediates, amino acids, oxidized lipids and proteins, and enzymes. There were higher concentrations of d‐β‐hydroxybutyrate in the hippocampus of KE‐fed mice where there were also higher concentrations of TCA cycle and glycolytic intermediates and the energy‐linked biomarker, N‐acetyl aspartate compared to controls. In the hippocampi of control‐fed animals the free mitochondrial [NAD+]/[NADH] ratio were highly oxidized, whereas, in KE‐fed animals the mitochondria were reduced. Also, the levels of oxidized protein and lipids were lower and the energy of ATP hydrolysis was greater compared to controls. 3xTgAD mice maintained on a KE‐supplemented diet had higher concentrations of glycolytic and TCA cycle metabolites, a more reduced mitochondrial redox potential, and lower amounts of oxidized lipids and proteins in their hippocampi compared to controls. The KE offers a potential therapy to counter fundamental metabolic deficits common to patients and transgenic models.

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Read the Editorial Highlight for this article on page 162.
The fatal affinity of the ‘Sonderweg’ revisited: The diffusion of emergency powers in Germany, Japan and Korea (1871–1987)
Authors: Kim Hak Jae
Published: January 2017

Many authoritarian regimes in Asia have utilized emergency powers to legitimize their measures of suppressing political opponents and maintaining power. In opposition to previous interpretations that categorize Asian experiences as ‘exceptional cases’ when compared to ‘normal’ Western liberal democracies, this article suggests that this issue should be viewed within the context of the broader ‘affinity’ of the ‘Sonderweg’ phenomenon. The paper compares Germany, Japan and Korea by examining the complex ‘diffusion’ processes of constitutional emergency powers and also by illuminating systemic affinities and fundamental differences. It argues that elites and technocrats in Germany, Japan and Korea exhibited diverging patterns in adopting, filtering and utilizing these constitutional powers.
Human transporters, PEPT1/2, facilitate melatonin transportation into mitochondria of cancer cells: An implication of the therapeutic potential
Authors: Huo Xiaokui , Wang Chao , Yu Zhenlong , Peng Yulin , Wang Shumei , Feng Shengnan , Zhang Shouji , Tian Xiangge , Sun Chengpeng , Liu Kexin , Deng Sa , Ma Xiaochi
Published: January 2017

Melatonin is present in virtually all organisms from bacteria to mammals, and it exhibits a broad spectrum of biological functions, including synchronization of circadian rhythms and oncostatic activity. Several functions of melatonin are mediated by its membrane receptors, but others are receptor‐independent. For the latter, melatonin is required to penetrate membrane and enters intracellular compartments. However, the mechanism by which melatonin enters cells remains debatable. In this study, it was identified that melatonin and its sulfation metabolites were the substrates of oligopeptide transporter (PEPT) 1/2 and organic anion transporter (OAT) 3, respectively. The docking analysis showed that the binding of melatonin to PEPT1/2 was attributed to their low binding energy and suitable binding conformation in which melatonin was embedded in the active site of PEPT1/2 and fitted well with the cavity in three‐dimensional space. PEPT1/2 transporters play a pivotal role in melatonin uptake in cells. Melatonin's membrane transportation via PEPT1/2 renders its oncostatic effect in malignant cells. For the first time, PEPT1/2 were identified to localize in the mitochondrial membrane of human cancer cell lines of PC3 and U118. PEPT1/2 facilitated the transportation of melatonin into mitochondria. Melatonin accumulation in mitochondria induced apoptosis of PC3 and U118 cells. Thus, PEPT1/2 can potentially be used as a cancer cell‐targeted melatonin delivery system to improve the therapeutic effects of melatonin in cancer treatment.
Modern state of the Small (Northern) Aral Sea fauna
Authors: Plotnikov Igor S. , Ermakhanov Zaualkhan K. , Aladin Nikolai V. , Micklin Philip
Published: January 2017

The Aral Sea is a terminal lake lying within the deserts of Central Asia in Kazakhstan and Uzbekistan, draining the Amu Darya and Syr Darya rivers. Before the 1960s, it was a large brackish water lake with an average salinity of 10.3 g L−1. The anthropogenic regression and salinization of the Aral Sea at that time resulted from increasing water withdrawals from the Amu Darya and Syr Darya for irrigation purposes. The salinization resulted in the disappearance of most of its invertebrates and all freshwater fish. As a result of the water level decrease, the Aral Sea divided into a northern Small Aral and a southern Large Aral at the end of the 1980s, with the two having different hydrological regimes. After construction the first Kokaral Dam in 1992, the water level of the Small Aral Sea increased by >1 m, with a gradual decline in the salinity beginning. To date, the Small Aral has again become brackish. Its average salinity reached 5.3 g L−1 by April–May 2013, with the highest salinity of 9.9 g L−1 in Butakov Bay, whereas the salinity was very low at 1.2–2.0 g L−1 in the estuary zone of the Syr Darya. There is an ongoing process of restoration of the former biodiversity, with many fresh water and brackish water invertebrate species reappearing due to the decreasing salinity. Freshwater fish species (bream, roach, carp, asp, zander, wels, etc.) returned into the Small Aral from the Syr Darya River and lakes in its lower reaches where they survived. Fisheries are recovering and catches are growing. Continuing salinity decreases, however, may cause decreases in the numbers, or even disappearance, of marine and halophilic invertebrate species. This study summarizes the results of studies of the Small Aral zooplankton, zoobenthos and ichthyofauna carried out in the spring of 2013. An historical review of changes in the Aral Sea and its fauna also is presented.
Mean hydroclimatic and hydrological conditions during two climatic modes in the Devils Lake Basin, North Dakota (USA)
Authors: Todhunter Paul E.
Published: January 2017

Proxy variables from palaeolimnological studies of lakes in the Prairie Pothole Region of North America have been used to infer large oscillations during the late Holocene between longer periods of high‐salinity–dry conditions and shorter periods of low‐salinity–wet conditions producing a normative pattern marked by the absence of hydrological stability. Studies of the historical rise in lake level at Devils Lake have identified 1980 as a transition point between two such hydroclimatic modes. This study uses multiple datasets to characterize the mean hydroclimatological and hydrological conditions of these two climatic modes. Mode 1 is a cool and dry phase, and mode 2 is a warmer and wetter phase. Precipitation onto the lake increased by 24% from mode 1 to mode 2. This small, but sustained, increase produced significant changes in the mean hydroclimatic and hydrological states for the basin, including a 383% increase in surface run‐off to the lake, and a 282% increase in the basin run‐off ratio. Devils Lake Basin is located along a hydrotone (region of strong hydroclimatic gradients) where small changes in hydrological drivers are amplified into large changes in regional moisture. The effects of the fluctuating climatic modes and strong hydroclimatic gradients are probably further amplified by the unique fill–spill hydrology of the northern glaciated plains, which can result in nonlinear precipitation–run‐off relationships. This natural pattern of extreme hydrological variations for Devils Lake produces enormous challenges for lake management.
Growth and population parameters of Nile tilapia, Oreochromis niloticus (L.) in the open waters of Lake Victoria, Kenya
Authors: Yongo Edwine , Outa Nicholas
Published: January 2017

The Nile tilapia (Oreochromis niloticus) was introduced into Lake Victoria in the early 1950s and 1960s and has since become the dominant tilapiine in the lake. This study investigated the growth and population parameters of O. niloticus in Lake Victoria on the basis of length–frequency data collected during the period June 2014 and June 2015. The asymptotic length (L∞) had a mean (±SE) value of 46.24 ± 0.04 cm TL, growth curvature (K) of 0.69 ± 0.25 year−1, total mortality (Z) of 2.18 ± 0.80 year−1, a natural mortality (M) of 1.14 ± 0.28 year−1, a fishing mortality (F) of 1.05 ± 0.53 year−1, an exploitation rate (E) of 0.46 ± 0.08, a growth performance index (∅) of 3.14 ± 0.17 and a length at first capture (LC50) of 20.31 ± 0.40 cm TL. Comparing the results of this study with previous studies indicates the parameters K, Z and M have increased, whereas ∅, F, E and LC50 have decreased. Changes in these parameters could be attributed to the existing high fishing capacity, and changing lake conditions. Thus, management measures should include continued restriction on illegal fishing methods and gears, such as the use of undersized gillnets (<5 in. mesh size) and beach seines. More attention also should be directed to the implementation of measures to control pollution of the lake from its various sources.
Parent‐adolescent influences on everyday dietary practices: Perceptions of adolescent females with obesity and their mothers
Authors: Winkler Megan R. , Moore Elizabeth D. , Bennett Gary G. , Armstrong Sarah C. , Brandon Debra H.
Published: January 2017

Parents demonstrate an important influence on adolescent obesity and dietary behavior; yet, family‐based obesity interventions continue to exhibit limited success among adolescents. To further inform family‐based approaches for adolescent obesity treatment, we examined the perceptions of adolescent females with obesity and their mothers of the influences experienced within the parent‐adolescent relationship that affect everyday dietary practices. We conducted six focus group interviews (three adolescent female and three mother) among 15 adolescent (12–17 years old) females with obesity and 12 of their mothers. Content analysis techniques were used to analyze the transcribed interviews. Adolescent females with obesity discussed a diverse set of parental influences (controlling, supporting and cultivating, overlooking and tempting, acquiescing, providing, attending, and not providing and avoiding) on their daily dietary practices. Among mother focus groups, mothers discussed specific intentional and unintentional types of influences from children that affected the food and drink they consumed, prepared, and acquired. Findings provide a fuller view of the varied social influences on everyday dietary practices within the parent‐adolescent relationship. They indicate the importance of examining both parent‐to‐child and child‐to‐parent influences and begin to illuminate the value of attending to the social circumstances surrounding dietary behaviors to strengthen family‐based obesity treatment approaches.
Association mapping of morphological traits in wild and captive zebra finches: reliable within, but not between populations
Authors: Knief Ulrich , Schielzeth Holger , Backström Niclas , Hemmrich‐Stanisak Georg , Wittig Michael , Franke Andre , Griffith Simon C. , Ellegren Hans , Kempenaers Bart , Forstmeier Wolfgang
Published: January 2017

Identifying causal genetic variants underlying heritable phenotypic variation is a long‐standing goal in evolutionary genetics. We previously identified several quantitative trait loci (QTL) for five morphological traits in a captive population of zebra finches (Taeniopygia guttata) by whole‐genome linkage mapping. We here follow up on these studies with the aim to narrow down on the quantitative trait variants (QTN) in one wild and three captive populations. First, we performed an association study using 672 single nucleotide polymorphisms (SNPs) within candidate genes located in the previously identifiedQTLregions in a sample of 939 wild‐caught zebra finches. Then, we validated the most promisingSNP–phenotype associations (n = 25SNPs) in 5228 birds from four populations. Genotype–phenotype associations were generally weak in the wild population, where linkage disequilibrium (LD) spans only short genomic distances. In contrast, in captive populations, whereLDblocks are large, apparentSNPeffects on morphological traits (i.e. associations) were highly repeatable with independent data from the same population. Most of thoseSNPs also showed significant associations with the same trait in other captive populations, but the direction and magnitude of these effects varied among populations. This suggests that the testedSNPs are not the causalQTNbut rather physically linked to them, and thatLDbetweenSNPs and causal variants differs between populations due to founder effects. While the identification ofQTNremains challenging in nonmodel organisms, we illustrate that it is indeed possible to confirm the location and magnitude ofQTLin a population with stable linkage between markers and causal variants.
Conversion of Amazon rainforest to agriculture alters community traits of methane‐cycling organisms
Authors: Meyer Kyle M. , Klein Ann M. , Rodrigues Jorge L. M. , Nüsslein Klaus , Tringe Susannah G. , Mirza Babur S. , Tiedje James M. , Bohannan Brendan J. M.
Published: January 2017

Land use change is one of the greatest environmental impacts worldwide, especially to tropical forests. The Amazon rainforest has been subject to particularly high rates of land use change, primarily to cattle pasture. A commonly observed response to cattle pasture establishment in the Amazon is the conversion of soil from a methane sink in rainforest, to a methane source in pasture. However, it is not known how the microorganisms that mediate methane flux are altered by land use change. Here, we use the deepest metagenomic sequencing of Amazonian soil to date to investigate differences in methane‐cycling microorganisms and their traits across rainforest and cattle pasture soils. We found that methane‐cycling microorganisms responded to land use change, with the strongest responses exhibited by methane‐consuming, rather than methane‐producing, microorganisms. These responses included a reduction in the relative abundance of methanotrophs and a significant decrease in the abundance of genes encoding particulate methane monooxygenase. We also observed compositional changes to methanotroph and methanogen communities as well as changes to methanotroph life history strategies. Our observations suggest that methane‐cycling microorganisms are vulnerable to land use change, and this vulnerability may underlie the response of methane flux to land use change in Amazon soils.
Independent evolution of sexual dimorphism and female‐limited mimicry in swallowtail butterflies (Papilio dardanus and Papilio phorcas)
Authors: Timmermans M. J. T. N. , Thompson M. J. , Collins S. , Vogler A. P.
Published: January 2017

Several species of swallowtail butterflies (genus Papilio) are Batesian mimics that express multiple mimetic female forms, while the males are monomorphic and nonmimetic. The evolution of such sex‐limited mimicry may involve sexual dimorphism arising first and mimicry subsequently. Such a stepwise scenario through a nonmimetic, sexually dimorphic stage has been proposed for two closely related sexually dimorphic species: Papilio phorcas, a nonmimetic species with two female forms, and Papilio dardanus, a female‐limited polymorphic mimetic species. Their close relationship indicates that female‐limited polymorphism could be a shared derived character of the two species. Here, we present a phylogenomic analysis of the dardanus group using 3964 nuclear loci and whole mitochondrial genomes, showing that they are not sister species and thus that the sexually dimorphic state has arisen independently in the two species. Nonhomology of the female polymorphism in both species is supported by population genetic analysis of engrailed, the presumed mimicry switch locus in P. dardanus. McDonald–Kreitman tests performed on SNPs in engrailed showed the signature of balancing selection in a polymorphic population of P. dardanus, but not in monomorphic populations, nor in the nonmimetic P. phorcas. Hence, the wing polymorphism does not balance polymorphisms in engrailed in P. phorcas. Equally, unlike in P. dardanus, none of the SNPs in P. phorcas engrailed were associated with either female morph. We conclude that sexual dimorphism due to female polymorphism evolved independently in both species from monomorphic, nonmimetic states. While sexual selection may drive male–female dimorphism in nonmimetic species, in mimetic Papilios, natural selection for protection from predators in females is an alternative route to sexual dimorphism.
Isolation with asymmetric gene flow during the nonsynchronous divergence of dry forest birds
Authors: Oswald Jessica A. , Overcast Isaac , Mauck William M. , Andersen Michael J. , Smith Brian Tilston
Published: January 2017

Dry forest bird communities in South America are often fragmented by intervening mountains and rainforests, generating high local endemism. The historical assembly of dry forest communities likely results from dynamic processes linked to numerous population histories among codistributed species. Nevertheless, species may diversify in the same way through time if landscape and environmental features, or species ecologies, similarly structure populations. Here we tested whether six co‐distributed taxon pairs that occur in the dry forests of the Tumbes and Marañón Valley of northwestern South America show concordant patterns and modes of diversification. We employed a genome reduction technique, double‐digest restriction site‐associated DNA sequencing, and obtained 4407–7186 genomewide SNPs. We estimated demographic history in each taxon pair and inferred that all pairs had the same best‐fit demographic model: isolation with asymmetric gene flow from the Tumbes into the Marañón Valley, suggesting a common diversification mode. Overall, we also observed congruence in effective population size (Ne) patterns where ancestral Ne were 2.9–11.0× larger than present‐day Marañón Valley populations and 0.3–2.0× larger than Tumbesian populations. Present‐day Marañón Valley Ne was smaller than Tumbes. In contrast, we found simultaneous population isolation due to a single event to be unlikely as taxon pairs diverged over an extended period of time (0.1–2.9 Ma) with multiple nonoverlapping divergence periods. Our results show that even when populations of codistributed species asynchronously diverge, the mode of their differentiation can remain conserved over millions of years. Divergence by allopatric isolation due to barrier formation does not explain the mode of differentiation between these two bird assemblages; rather, migration of individuals occurred before and after geographic isolation.
Positive selection on sperm ion channels in a brooding brittle star: consequence of life‐history traits evolution
Authors: Weber A. A.‐T. , Abi‐Rached L. , Galtier N. , Bernard A. , Montoya‐Burgos J. I. , Chenuil A.
Published: January 2017

Closely related species are key models to investigate mechanisms leading to reproductive isolation and early stages of diversification, also at the genomic level. The brittle star cryptic species complex Ophioderma longicauda encompasses the sympatric broadcast‐spawning species C3 and the internal brooding species C5. Here, we used de novo transcriptome sequencing and assembly in two closely related species displaying contrasting reproductive modes to compare their genetic diversity and to investigate the role of natural selection in reproductive isolation. We reconstructed 20 146 and 22 123 genes for C3 and C5, respectively, and characterized a set of 12 229 orthologs. Genetic diversity was 1.5‐2 times higher in C3 compared to C5, confirming that species with low parental investment display higher levels of genetic diversity. Forty‐eight genes were the targets of positive diversifying selection during the evolution of the two species. Notably, two genes (NHE and TetraKCNG) are sperm‐specific ion channels involved in sperm motility. Ancestral sequence reconstructions show that natural selection targeted the two genes in the brooding species. This may result from an adaptation to the novel environmental conditions surrounding sperm in the brooding species, either directly affecting sperm or via an increase in male/female conflict. This phenomenon could have promoted prezygotic reproductive isolation between C3 and C5. Finally, the sperm receptors to egg chemoattractants differed between C3 and C5 in the ligand‐binding region. We propose that mechanisms of species‐specific gamete recognition in brittle stars occur during sperm chemotaxis (sperm attraction towards the eggs), contrary to other marine invertebrates where prezygotic barriers to interspecific hybridization typically occur before sperm–egg fusion.
Back to basics: using colour polymorphisms to study evolutionary processes
Authors: Svensson Erik I.
Published: January 2017

Here, I suggest that colour polymorphic study systems have been underutilized to answer general questions about evolutionary processes, such as morph frequency dynamics between generations and population divergence in morph frequencies. Colour polymorphisms can be used to study fundamental evolutionary processes like frequency‐dependent selection, gene flow, recombination and correlational selection for adaptive character combinations. However, many previous studies of colour polymorphism often suffer from weak connections to population genetic theory. I argue that too much focus has been directed towards noticeable visual traits (colour) at the expense of understanding the evolutionary processes shaping genetic variation and covariation associated with polymorphisms in general. There is thus no need for a specific evolutionary theory for colour polymorphisms beyond the general theory of the maintenance of polymorphisms in spatially or temporally variable environments or through positive or negative frequency‐dependent selection. I outline an integrative research programme incorporating these processes and suggest some fruitful avenues in future investigations of colour polymorphisms.
Temptation and the efficient taxation of education and labor
Authors: Bethencourt Carlos , Kunze Lars
Published: January 2017

This paper studies efficient tax policies in Ramsey's tradition when consumers face temptation and self control problems in intertemporal decision making. We embed the class of preferences developed by Gul and Pesendorfer into a simple two‐period life‐cycle model and show that education should be effectively subsidized if the elasticity of the earnings function is increasing in education and if temptation problems are sufficiently severe. By contrast, if temptation problems are not sufficiently severe, efficient education policy calls for taxing education. Moreover, efficient labor taxation calls for subsidizing qualified labor if the strength of temptation is sufficiently large.
What is ‘needed’ to keep remembering? War‐specific communication, parental exemplar behaviour and participation in national commemorations
Authors: Coopmans Manja , Van der Lippe Tanja , Lubbers Marcel
Published: January 2017

Given the abundance of literature on collective memory practices, there is relatively little empirical research on the socialization processes explaining the transmission of such practices. This article examines to what extent war‐specific communication and parental exemplar behaviour function as a link between the collected memories of individuals and society's collective memory. Utilizing data from an online survey conducted in 2014, we focus on participation in the activities organized on Remembrance Day and Liberation Day in the Netherlands in remembrance of the Second World War. We distinguish between public and private practices. Our findings highlight that different forms of socialization substitute for one another. Whereas communication with non‐relatives is particularly relevant for those communicating less frequently with parents about past war experiences, parental exemplar behaviour, such as participating in the two‐minute silence on Remembrance Day, plays a bigger role amongst those with lower levels of communication with either relatives or non‐relatives.
Living with cardiac resynchronization therapy: Challenges for people with heart failure
Authors: Dehghanzadeh Shadi , Dehghan Nayeri Nahid , Varaei Shokoh , Kheirkhah Jalal
Published: January 2017

Abstract

The number of people with heart failure requiring implantation of a cardiac resynchronization device is increasing in Iran. Although this intervention is an effective life‐saving treatment, several challenges are associated with patients’ lifestyle after insertion. This study identified the challenges and coping mechanisms of Iranians with heart failure living with cardiac resynchronization therapy. A qualitative approach using conventional content analysis was adopted. Seventeen people with heart failure and three nurses were recruited between December 2014 and November 2015 from a teaching hospital and a private clinic in Rasht, Iran. Participants were interviewed using semi‐structured interviews lasting 30–60 min. Five themes emerged: (i) fear of implantation, (ii) the panic of receiving a shock from the device, (iii) lack of control over life, (iv) inadequacies of the healthcare system, and (v) psychosocial coping. A heightened understanding of these challenges and coping strategies could prepare healthcare professionals to provide better routine care, education, and support to the recipients of cardiac resynchronization therapy prior to implantation, during the recovery period, and for long‐term management.
Methods of anorectal manometry vary widely in clinical practice: Results from an international survey
Authors: Carrington E. V. , Heinrich H. , Knowles C. H. , Rao S. S. , Fox M. , Scott S. M. ,   The International Anorectal Physiology Working Party Group (IAPWG)
Published: January 2017

Background

Ano‐rectal manometry (ARM) is the most commonly performed investigation for assessment of anorectal dysfunction. Its use is supported by expert consensus documents and international guidelines. Variation in technology, data acquisition, and analysis affect results and clinical interpretation. This study examined variation in ARM between institutions to establish the status of current practice.

Methods

A 50‐item web‐based questionnaire assessing analysis and interpretation of ARM was distributed by the International Anorectal Physiology Working Group via societies representing practitioners that perform ARM. Study methodology and performance characteristics between institutions were compared.

Key Results

One hundred and seven complete responses were included from 30 countries. Seventy‐nine (74%) institutions performed at least two studies per week. Forty‐nine centers (47%) applied conventional ARM (≤8 pressure sensors) and 57 (53%) high‐resolution ARM (HR‐ARM). Specialist centers were most likely to use HR‐ARM compared to regional hospitals and office‐based practice (63% vs 37%). Most conventional ARM systems used water‐perfused technology (34/49); solid‐state hardware was more frequently used in centers performing HR‐ARM (44/57). All centers evaluated rest and squeeze. There was marked variation in the methods used to report results of maneuvers. No two centers had identical protocols for patient preparation, setup, study, and data interpretation, and no center fully complied with published guidelines.

Conclusions & Inferences

There is significant discrepancy in methods for data acquisition, analysis, and interpretation of ARM. This is likely to impact clinical interpretation, transfer of data between institutions, and research collaboration. There is a need for expert international co‐operation to standardize ARM.
Conservation vs divergence in LEAFY and APETALA1 functions between Arabidopsis thaliana and Cardamine hirsuta
Authors: Monniaux Marie , McKim Sarah M. , Cartolano Maria , Thévenon Emmanuel , Parcy François , Tsiantis Miltos , Hay Angela
Published: January 2017

A conserved genetic toolkit underlies the development of diverse floral forms among angiosperms. However, the degree of conservation vs divergence in the configuration of these gene regulatory networks is less clear.

We addressed this question in a parallel genetic study between the closely related species Arabidopsis thaliana and Cardamine hirsuta.

We identified leafy (lfy) and apetala1 (ap1) alleles in a mutant screen for floral regulators in C. hirsuta. C. hirsuta lfy mutants showed a complete homeotic conversion of flowers to leafy shoots, mimicking lfy ap1 double mutants in A. thaliana. Through genetic and molecular experiments, we showed that AP1 activation is fully dependent on LFY in C. hirsuta, by contrast to A. thaliana. Additionally, we found that LFY influences heteroblasty in C. hirsuta, such that loss or gain of LFY function affects its progression. Overexpression of UNUSUAL FLORAL ORGANS also alters C. hirsuta leaf shape in an LFY‐dependent manner.

We found that LFY and AP1 are conserved floral regulators that act nonredundantly in C. hirsuta, such that LFY has more obvious roles in floral and leaf development in C. hirsuta than in A. thaliana.
Fine nurse variations explain discrepancies in the stress‐interaction relationship in alpine regions
Authors: Anthelme Fabien , Meneses Rosa I. , Valero Nerida N. Huaman , Pozo Paola , Dangles Olivier
Published: January 2017

Despite a large consensus on increasing facilitation among plants with increasing stress in alpine regions, a number of different outcomes of interaction have been observed, which impedes the generalisation of the ‘stress‐gradient hypothesis’ (SGH). With the aim to reconcile the different viewpoints on the stress‐interaction relationship in alpine environments we hypothesized that fine nurse variations within a single life form (cushion) may explain this pattern variability. To test this hypothesis, we compared the magnitude of the stress‐interaction relationship in a single study area with that observed in existing studies involving cushions, worldwide. We characterized the nurse effects of cushions on the whole plant community at inter‐specific, intra‐specific and intra‐individual levels along a stress gradient in the dry, alpine tropics of Bolivia (4400 m, 4700 m and 4900 m a.s.l). Using a relative index of interaction (RII) we included our data in a meta‐analysis on the nurse effects of cushions along alpine gradients, worldwide. At inter‐specific level, the loose cushion Pycnophyllum was a better nurse than the compact Azorella compacta. However, at intra‐individual level facilitation was higher at the periphery than at the centre of cushions, exceeding in magnitude the variation observed at inter‐specific level. This pattern was associated with higher minimum temperature and lower mortality at the periphery of cushions. The net effects of cushions on plant communities became more positive at higher elevation, corroborating the SGH. Within our single site in Bolivia, fine morphological nurse variations captured a similar variability in the stress‐interaction relationship as that observed in a subset of studies on cushions on a worldwide scale. This suggests that fine variations in nurse traits, in general those not considered in protocols dealing with facilitation or in restoration/conservation management plans, explain in part the current discrepancies among SGH studies in alpine regions.