bluuebunny/crossref_metadata_2025 huggingface dataset:
Forward genetics by sequencing EMS variation induced inbred lines
Authors: Addo-Quaye Charles , Buescher Elizabeth , Best Norman , Chaikam Vijay , Baxter Ivan , Dilkes Brian P.
Published: March 2016

In order to leverage novel sequencing techniques for cloning genes in eukaryotic organisms with complex genomes, the false positive rate of variant discovery must be controlled for by experimental design and informatics. We sequenced five lines from three pedigrees of EMS mutagenized Sorghum bicolor, including a pedigree segregating a recessive dwarf mutant. Comparing the sequences of the lines, we were able to identify and eliminate error prone positions. One genomic region contained EMS mutant alleles in dwarfs that were homozygous reference sequence in wild-type siblings and heterozygous in segregating families. This region contained a single non-synonymous change that cosegregated with dwarfism in a validation population and caused a premature stop codon in the sorghum ortholog encoding the giberellic acid biosynthetic enzyme ent-kaurene oxidase. Application of exogenous giberillic acid rescued the mutant phenotype. Our method for mapping did not require outcrossing and introduced no segregation variance. This enables work when line crossing is complicated by life history, permitting gene discovery outside of genetic models.This inverts the historical approach of first using recombination to define a locus and then sequencing genes. Our formally identical approach first sequences all the genes and then seeks co-segregation with the trait. Mutagenized lines lacking obvious phenotypic alterations are available for an extention of this approach: mapping with a known marker set in a line that is phenotypically identical to starting material for EMS mutant generation.
Assessing the measurement transfer function of single-cell RNA sequencing
Authors: Dueck Hannah R. , Ai Rizi , Camarena Adrian , Ding Bo , Dominguez Reymundo , Evgrafov Oleg V. , Fan Jian-Bing , Fisher Stephen A. , Hernstein Jennifer S. , Kim Tae Kyung , Kim Jae Mun (Hugo) , Lin Ming-Yi , Liu Rui , Mack William J. , McGroty Sean , Nguyen Joseph , Salathia Neeraj , Shallcross Jamie , Souaiaia Tade , Spaethling Jennifer , Walker Chris P. , Wang Jinhui , Wang Kai , Wang Wei , Wilberg Andre , Zheng Lina , Chow Robert H. , Eberwine James , Knowles James A. , Zhang Kun , Kim Junhyoung
Published: March 2016

Recently, measurement of RNA at single cell resolution has yielded surprising insights. Methods for single-cell RNA sequencing (scRNA-seq) have received considerable attention, but the broad reliability of single cell methods and the factors governing their performance are still poorly known. Here, we conducted a large-scale control experiment to assess the transfer function of three scRNA-seq methods and factors modulating the function. All three methods detected greater than 70% of the expected number of genes and had a 50% probability of detecting genes with abundance greater than 2 to 4 molecules. Despite the small number of molecules, sequencing depth significantly affected gene detection. While biases in detection and quantification were qualitatively similar across methods, the degree of bias differed, consistent with differences in molecular protocol. Measurement reliability increased with expression level for all methods and we conservatively estimate the measurement transfer functions to be linear above ~5-10 molecules. Based on these extensive control studies, we propose that RNA-seq of single cells has come of age, yielding quantitative biological information.
The power and pitfalls of Dirichlet-multinomial mixture models for ecological count data
Authors: O’Brien John D. , Record Nicholas R. , Countway Peter
Published: March 2016

The Dirichlet-multinomial mixture model (DMM) and its extensions provide powerful new tools for interpreting the ecological dynamics underlying taxon abundance data. However, like many complex models, how effectively they capture the many features of empirical data is not well understood. In this work, we expand the DMM to an infinite mixture model (iDMM) and use posterior predictive distributions (PPDs) to explore the performance in three case studies, including two amplicon metagenomic time series. We avoid concentrating on fluctuations within individual taxa and instead focus on consortial-level dynamics, using straight-forward methods for visualizing this perspective. In each study, the iDMM appears to perform well in organizing the data as a framework for biological interpretation. Using the PPDs, we also observe several exceptions where the data appear to significantly depart from the model in ways that give useful ecological insight. We summarize the conclusions as a set of considerations for field researchers: problems with samples and taxa; relevant scales of ecological fluctuation; additional niches as outgroups; and possible violations of niche neutrality.
Mechanical signals inhibit growth of a grafted tumorin vivo: Proof of Concept
Authors: Brossel Rémy , Yahi Alexandre , David Stéphane , Moreno Velasquez Laura , Guinebretière Jean-Marc
Published: March 2016

In the past ten years, many studies have shown that malignant tissue has been “normalized”in vitrousing mechanical signals. We apply the principles of physical oncology (or mechanobiology)in vivoto show the effect of a “constraint field” on tumor growth. The human breast cancer cell line, MDA MB 231, admixed with ferric nanoparticles was grafted subcutaneously in Nude mice. The magnetizable particles rapidly surrounded the growing tumor. Two permanent magnets located on either side of the tumor created a gradient of magnetic field. Magnetic energy is transformed into mechanical energy by the particles acting as “bioactuators”, applying a constraint field and, by consequence, biomechanical stress to the tumor. This biomechanical treatment was applied 2 hours/day during 21 days, from Day 18 to Day 39 following tumor implantation. The study lasted 74 days. Palpable tumor was measured two times a week. There was a significantin vivodifference between the median volume of treated tumors and untreated controls in the mice measured up to D 74 (D 59 + population): (529 [346; 966] mm3vs 1334 [256; 2106] mm3; p=0.015), treated mice having smaller tumors. The difference was not statistically significant in the group of mice measured at least to D 59 (D 59 population). Onex vivoexamination, the surface of the tumor mass, measured on histologic sections, was less in the treated group, G1, than in the control groups: G2 (nanoparticles, no magnetic field), G3 (magnetic field, no nanoparticles), G4 (no nanoparticles, no magnetic field) in the D 59 population (Median left surface was significantly lower in G1 (5.6 [3.0; 42.4] mm2, p=0.005) than in G2 (20.8 [4.9; 34.3]), G3 (16.5 [13.2; 23.2]) and G4 (14.8 [1.8; 55.5]); Median right surface was significantly lower in G1 (4.7 [1.9; 29.2] mm2, p=0.015) than in G2 (25.0 [5.2; 55.0]), G3 (18.0 [14.6; 35.2]) and G4 (12.5 [1.5; 51.8]). There was no statistically significant difference in the day 59+ population. This is the first demonstration of the effect of stress on tumor growthin vivosuggesting that biomechanical intervention may have a high translational potential as a therapy in locally advanced tumors like pancreatic cancer or primary hepatic carcinoma for which no effective therapy is currently available.
Hormetic Shifting of Redox Environment by Pro-Oxidative Resveratrol Protects Cells Against Stress
Authors: Plauth Annabell , Geikowski Anne , Cichon Susanne , Wowro Silvia J. , Liedgens Linda , Rousseau Morten , Weidner Christopher , Fuhr Luise , Kliem Magdalena , Jenkins Gail , Lotito Silvina , Wainwright Linda J. , Sauer Sascha
Published: March 2016

Resveratrol has gained tremendous interest owing to multiple reported health-beneficial effects. However, the underlying key mechanism of action of resveratrol remained largely controversial. Here, we demonstrate that under physiologically relevant conditions major biological effects of resveratrol can be attributed to the generation of oxidation products such as reactive oxygen species (ROS). At low hormetic concentrations (< 50 μM), treatment with resveratrol increased cell viability in a set of representative cell models, whereas application of quenchers of ROS completely truncated these beneficial effects. Notably, application of resveratrol led to mild, Nrf2-specific cellular gene expression reprogramming. For example, in primary human epidermal keratinocytes this resulted in a 1.3-fold increase of endogenous metabolites such as gluthathione (GSH) and subsequently in a quantitative reduction of the cellular redox environment by 2.61 mV mmol GSH (g protein)-1. In particular in resveratrol pre-treated cells, after external application of oxidative stress by using 0.8 % ethanol, endogenous ROS generation was consequently reduced by 24 %. In contrast to the common perception that resveratrol acts mainly as a chemical antioxidant or as a target protein-specific ligand, we propose that effects from resveratrol treatment are essentially based on oxidative triggering of cells. In relevant physiological microenvironments this effect can lead to hormetic shifting of cellular defence towards a more reductive state to improve resilience to oxidative stress in a manner that can be exactly defined by the redox-environment of the cell.
Mapping and Inheritance analysis of a novel dominant rice male sterility mutant,OsDMS-1
Authors: Yang Kun , Chen Yun , Shi Min , Converse Richard , Chen Xin , Min Hengqi , Zhao Baimei , Zhang Yi , Lv Jun
Published: March 2016

We found a rice dominant genetic male sterile mutantOsDMS-1from the tissue culture regenerated offspring of Zhonghua 11 (japonicarice). Compared to wild Zhonghua 11,OsDMS-1mutant anthers were thinner and whiter, and could not release any pollen although the glume opened normally; most of the mutant pollen was small and malformed, and could not be stained by iodine treatment; a paraffin section assay showed the degradation ofOsDMS-1mutant tapetum was delayed, with no accumulation of starch in the mutant pollen, ultimately leading to pollen abortion. Classical genetic analysis indicated that only one dominant gene was controlling the sterility in theOsDMS-1mutant. However, molecular mapping suggested three loci simultaneously control male sterility in this mutant:OsDMS-1A,flanked by InDel markers C1D4 and C1D5 with a genetic distance of 0.15 and 0.30 cM, respectively;OsDMS-1B,flanked by InDel markers C2D3 and C2D10 with a genetic distance of 0.44 and 0.88 cM, respectively;OsDMS-1C,flanked by InDel markers 0315 and C3D3 with a genetic distance of 0.44 and 0.88 cM, respectively. Molecular mapping disagreed with classical genetic analysis about the number of controlling genes in theOsDMS-1mutant, indicating a novel mechanism underlying sterility inOsDMS-1. We present two hypotheses to explain this novel inheritance behavior: one is described as Parent-Originated Loci Tying Inheritance (POLTI); or the hypothesis is described as Loci Recombination Lethal (LRL).

Key message

Three loci, which were localized on the chromosomes 1, 2 and 3 respectively, simultaneously control a dominant rice male sterility in this mutant:OsDMS-1.
A Multidisciplinary Approach to Explain Biological Aging and Longevity
Authors: Augsburger Brett N.
Published: March 2016

Scientists have been unable to reach a consensus on why organisms age and why they live as long as they do. Here, a multidisciplinary approach was taken in an attempt to understand the root causes of aging. Nonequilibrium thermodynamics may play a previously unappreciated role in determining longevity by governing the dynamics of degradation and renewal within biomolecular ensembles and dictating the inevitability of fidelity loss. The proposed model offers explanations for species longevity trends that have been previously unexplained and for aging-related observations that are considered paradoxical within current paradigms—for example, the elevated damage levels found even in youth within many long-lived species, such as the naked mole-rat. This framework questions whether declining selective pressure is the primary driver of aging, and challenges major tenets of the disposable soma theory. Unifying pertinent principles from diverse disciplines leads to a theoretical framework of biological aging with fewer anomalies, and may be useful in predicting outcomes of experimental attempts to modulate the aging phenotype.
The LATS2 tumor suppressor inhibits SREBP and suppresses hepatic cholesterol accumulation
Authors: Aylon Yael , Gershoni Anat , Rotkopf Ron , Biton Inbal E. , Porat Ziv , Koh Anna P. , Sun Xiaochen , Lee Youngmin , Fiel Maria-Isabel , Hoshida Yujin , Friedman Scott L. , Johnson Randy L. , Oren Moshe
Published: March 2016

The Hippo signaling pathway is a major regulator of organ size. In the liver, Hippo pathway deregulation promotes hyperplasia and hepatocellular carcinoma primarily through hyperactivation of its downstream effector, YAP. The LATS2 tumor suppressor is a core member of the Hippo pathway. A screen for LATS2-interacting proteins in liver-derived cells identified the transcription factor SREBP2, master regulator of cholesterol homeostasis. LATS2 down-regulation caused SREBP activation and accumulation of excessive cholesterol. Likewise, mice harboring liver-specific Lats2 conditional knockout (Lats2-CKO) displayed constitutive SREBP activation and overexpressed SREBP target genes and developed spontaneous fatty liver disease. Interestingly, the impact of LATS2 depletion on SREBP-mediated transcription was clearly distinct from that of YAP overexpression. When challenged with excess dietary cholesterol, Lats2-CKO mice manifested more severe liver damage than wild-type mice. Surprisingly, apoptosis, inflammation, and fibrosis were actually attenuated relative to wild-type mice, in association with impaired p53 activation. Subsequently, Lats2-CKO mice failed to recover effectively from cholesterol-induced damage upon return to a normal diet. Additionally, decreased LATS2 mRNA in association with increased SREBP target gene expression was observed in a subset of human nonalcoholic fatty liver disease cases. Together, these findings further highlight the tight links between tumor suppressors and metabolic homeostasis.
The simultaneous inducibility of phytochemicals related to plant direct and indirect defences against herbivores is stronger at low elevation
Authors: Pellissier Loïc , Moreira Xoaquín , Danner Holger , Serrano Martha , Salamin Nicolas , van Dam Nicole M. , Rasmann Sergio
Published: March 2016

Ecological theory indicates that warmer and more stable climates should result in stronger biotic interactions. Therefore, plant species growing at lower elevations and experiencing greater herbivore pressure should invest in higher levels of defences than those at higher elevations. Nonetheless, there are a number of studies that have found no effect of elevational gradients on plant defensive traits. Several factors might explain the lack of consistency for the altitude–defence relationships, including (i) the reduction of all defensive traits into one measure of resistance; (ii) not considering plant defence as the simultaneous expression of several defensive traits; and (iii) not considering the relative influence of biotic (e.g. herbivory) and abiotic (e.g. climate and soil conditions) factors associated with the ecological gradient.

Here, we present a comprehensive test of the effects of elevation and its associated biotic and abiotic factors on the individual and simultaneous expression of constitutive direct and indirect defences and their inducibility (i.e. expression of defences after herbivore attack). Specifically, we estimated climatic and soil variables and measured herbivore damage and constitutive and jasmonic acid‐induced glucosinolate levels in the leaves as a proxy for direct defences, and volatile emission as a proxy for indirect defences in 16 Cardamine species naturally growing along the steep elevational gradient of the Alps.

Within a phylogenetic comparative framework, we found that species growing at lower elevations invested more in the simultaneous inducibility of both direct and indirect defences, whereas species growing at higher elevations invested more in constitutive direct defences. Although we found strong elevational gradients in herbivory and climatic and soil variables, these biotic and abiotic factors only partially explained elevational patterns in plant defences.

Synthesis. These results highlight that the complex regulation of multiple defence traits strongly vary across elevational gradients and build towards a better understanding of the multiple mechanisms underlying trait evolution and species interactions along ecological gradients.
Determination of Both Fetus’ and Mother's Blood Type from an Autopsy Case Immersed in Formalin for Over 50 Years
Authors: Uno Akari Takaya , Morita Satomu , Furukawa Satoshi , Nishi Katsuji , Hitosugi Masahito
Published: March 2016

A female fetus which had been immersed in formalin for more than 50 years was found in Japan. Because no liquid blood could be obtained, we tried to use immunohistochemistry (IHC) methods to tissue samples obtained at autopsy to identify both the fetal and mother's blood type. We detected B antigens on endothelial cells in paraffin sections of the fetal organs. Furthermore, we observed both anti‐A‐ and anti‐B‐positive red blood cells in the intervillous space, which is indicative of the mother's blood type. To our knowledge, this is the first case report on determining the blood type of both the fetus and the mother from tissue immersed in formalin for such a long time. The results suggest that IHC is valuable for the determination of ABO blood type in circumstances of long postmortem duration and unfavorable storage conditions.
Survival of Very High Blood Alcohol Concentration Without Consequential Damage in a Patient Without a Previous Substance Use Disorder
Authors: Malejko Kathrin , Graf Heiko , Gahr Maximilian
Published: March 2016

Intoxications with alcohol may lead to death depending on (maximum) blood alcohol concentration (BAC) and accompanying factors such as liver function, tolerance, and comedication. Death may occur due to ethanol‐induced respiratory depression and/or aspiration of gastric content (due to an impaired gag reflex); thus, securing of the airway and ventilation is occasionally necessary. A case of a 58‐year‐old female patient with depression who demonstrated a very high BAC of 8.68 gm/L (0.868%) following ingestion of large amounts of alcohol with suicidal intent is presented. Intubation and ventilation were life‐saving, and the patient did not develop any physical or consequential damage. As the patient had not regularly used alcohol or any other psychotropic agent, tolerance could be ruled out. This case emphasizes the necessity of rapid securing of the airway in patients with alcohol intoxication and respiratory depression and, furthermore, illustrates the large interindividual differences regarding ethanol susceptibility.
Alcohol Toxicity in Diabetes and Its Complications: A Double Trouble?
Authors: Munukutla Srikar , Pan Guodong , Deshpande Mandar , Thandavarayan Rajarajan A. , Krishnamurthy Prasanna , Palaniyandi Suresh S.
Published: March 2016

Background

Eight percent of the U.S. population has been diagnosed with diabetes mellitus (DM), while another large percentage has gone undiagnosed. As the epidemiology of this disease constitutes a larger percentage of the American population, another factor presents a dangerous dilemma that can exacerbate the hazardous effects imposed by DM. Excessive alcohol consumption concerns the health of more than 50% of all adults. When this heavy‐alcohol‐drinking population overlaps with DM and its complications, the effects can be dangerous. In this review, we term it as “double trouble.”

Methods

We provide evidence of alcohol‐induced exacerbation of organ damage in diabetic conditions. In certain cases, we have explained how diabetes and alcohol induce similar pathological effects.

Results

Known exacerbated complications include those related to heart diseases, liver damage, kidney dysfunction, as well as retinal and neurological impairment. Often, pathophysiological damage concludes with end‐stage disorders and even mortality. The metabolic, cell signaling, and pathophysiological changes associated with “double trouble” would lead to the identification of novel therapeutic targets.

Conclusions

This review summarizes the epidemiology, diagnosis, pathophysiology, metabolic, and cell signaling alterations and finally brushes upon issues and strategies to manage the “double trouble.”
Alcohol‐Induced Blackouts as Predictors of Other Drinking Related Harms Among Emerging Young Adults
Authors: Hingson Ralph , Zha Wenxing , Simons‐Morton Bruce , White Aaron
Published: March 2016

Background

Alcohol‐related blackouts are periods of amnesia that reflect the failure of the brain to record memories of what transpires while drinking. This paper examined the incidence, predictors, and behavioral correlates of blackouts among emerging adults and examined whether questions about blackouts could serve as better markers of risk for other alcohol related harms than questions about levels of consumption.

Methods

In 2012 to 2013, 1,463 (68%) of 2,140 respondents 1‐year past high school reported having consumed alcohol. They were asked whether, in the past 6 months because of drinking, they forgot where they were or what they did. The survey also explored demographics, substance use behaviors, and other alcohol‐related problems in the past 6 months. Chi‐square and logistic regression analyses explored bivariate and multivariate predictors of blackouts and other alcohol‐related problems.

Results

Twenty percent of respondents who ever drank alcohol reported a blackout in the past 6 months. Blackouts were more prevalent among females and those who, in the past 30 days, used multiple drugs, more frequently binged, were drunk, smoked, had lower body weight, and lived in college dorms. After controlling for drinking levels, having a blackout was the strongest independent predictor of most other alcohol problems examined, including in the past 6 months because of drinking, missing class or work, getting behind in work or school, doing something respondents later regretted, arguing with friends, experiencing an overdose, and total number of alcohol problems reported. It was also an independent predictor of hangovers, damaging property, getting hurt, and trouble with police.

Conclusions

Because blackouts indicate drinking at levels that result in significant cognitive and behavioral impairment, questions about blackouts could serve as important, simple screeners for the risk of experiencing other alcohol related harms. Additional work on this subject is warranted.
Testing the role of action and inaction anticipated regret on intentions and behaviour
Authors: Sandberg Tracy , Hutter Russell , Richetin Juliette , Conner Mark
Published: March 2016

Anticipated regret (AR) has been suggested as a useful addition to the theory of planned behaviour (TPB) that captures affective influences. However, previous research has generally (1) assessed the impact of AR in relation to one behaviour (action or inaction) when considering TPB variables in relation to the alternative behaviour, (2) not controlled for affective attitudes or past behaviour, and (3) examined only one or two behaviours. In two studies across several behaviours, the present research showed that even when controlling for affective attitudes, past behaviour, and other TPB variables towards action, action and inaction AR each added to the prediction of intentions across multiple behaviours. The two studies also showed that inaction regret was generally the stronger predictor, although action regret was important for some types of behaviour. Implications and issues for further research are discussed.
Negative influence of programmed death‐1‐ligands on the survival of esophageal cancer patients treated with chemotherapy
Authors: Tanaka Koji , Miyata Hiroshi , Sugimura Keijiro , Kanemura Takashi , Hamada‐Uematsu Mika , Mizote Yu , Yamasaki Makoto , Wada Hisashi , Nakajima Kiyokazu , Takiguchi Shuji , Mori Masaki , Doki Yuichiro , Tahara Hideaki
Published: March 2016

The programmed death‐1/programmed death‐1 ligands (PD‐1/PD‐L) pathway plays an important role in immunological tumor evasion. However, the clinical significance of the PD‐L (L1 and L2) expression in esophageal cancer treated with chemotherapy has not been fully investigated. We examined the expression of PD‐L of the primary tumors obtained from 180 esophageal cancer patients who underwent radical resection with or without neoadjuvant chemotherapy (NAC) using immunohistochemical staining. The relationship between the expression patterns and clinico‐pathological characteristics was examined. In the present study, 53 patients (29.4%) and 88 patients (48.3%) were classified into positive for PD‐L1 and PD‐L2 expression, respectively. In all the patients examined, overall survival rates of the patients with tumors positive for PD‐L1 or PD‐L2 were significantly worse than those with tumors negative for PD‐L1 or PD‐L2 (P = 0.0010 and P = 0.0237, respectively). However, subgroup analysis showed that these tendencies are only found in the patients treated with NAC, and not in those without NAC. The patients with positive PD‐L1 expression had a significantly higher rate of NAC history (P = 0.0139), but those with positive PD‐L2 expression did not have a significantly high rate of NAC history (P = 0.6127). There is no significant relationship between PD‐L1 expression and response to chemotherapy (P = 0.3118), but patients with positive PD‐L2 expression had significantly inferior responses to chemotherapy (P = 0.0034). The PD‐1/PD‐L pathway might be an immunological mechanism associated with the long‐term effectiveness of chemotherapy in esophageal cancer patients. Further investigation into the roles of PD‐1 pathway in chemotherapy could lead to the development of better treatment options for this disease.
CAMKK2, Regulated by Promoter Methylation, is a Prognostic Marker in Diffuse Gliomas
Authors: Liu Da‐Ming , Wang Hong‐Jun , Han Bo , Meng Xiang‐Qi , Chen Ming‐Hui , Yang Dong‐Bo , Sun Ying , Li Yong‐Li , Jiang Chuan‐Lu
Published: March 2016

Aims

To explore the expression, methylation pattern, the prognostic value, and the biological consequences of CAMKK2 in gliomas.

Methods

The expression and methylation pattern of CAMKK2 was inferred and validated from mRNA expression profile (N = 866) and methylation profile (N = 426) of glioma tissue samples, and independent samples were used for further validation by IHC and pyrosequencing. To explore the function of CAMKK2 in gliomas, in vitro studies, colony formation assays and migration and invasion assays were performed.

Results

We found the upregulation of CAMKK2 in high‐grade glioma samples was associated with promoter hypomethylation. An elevated expression of CAMKK2 was associated with worse prognosis. By in vitro assays, we demonstrated that CAMKK2 could promote cell migration, invasion, and proliferation.

Conclusions

The expression level of CAMKK2 could be regulated by promoter methylation. CAMKK2 serves as a prognostic marker in gliomas and could be a potential therapeutic target in gliomas.
Nurr1‐Based Therapies for Parkinson's Disease
Authors: Dong Jie , Li Song , Mo Jing‐Lin , Cai Huai‐Bin , Le Wei‐Dong
Published: March 2016

Previous studies have documented that orphan nuclear receptor Nurr1 (also known asNR4A2) plays important roles in the midbrain dopamine (DA) neuron development, differentiation, and survival. Furthermore, it has been reported that the defects in Nurr1 are associated with Parkinson's disease (PD). Thus, Nurr1 might be a potential therapeutic target forPD. Emerging evidence fromin vitroandin vivostudies has recently demonstrated that Nurr1‐activating compounds and Nurr1 gene therapy are able not only to enhanceDAneurotransmission but also to protectDAneurons from cell injury induced by environmental toxin or microglia‐mediated neuroinflammation. Moreover, modulators that interact with Nurr1 or regulate its function, such as retinoid X receptor, cyclicAMP‐responsive element‐binding protein, glial cell line‐derived neurotrophic factor, and Wnt/β‐catenin pathway, have the potential to enhance the effects of Nurr1‐based therapies inPD. This review highlights the recent progress in preclinical studies of Nurr1‐based therapies and discusses the outlook of this emerging therapy as a promising new generation ofPDmedication.
Daphnetin Alleviates Experimental Autoimmune Encephalomyelitis via Regulating Dendritic Cell Activity
Authors: Wang Dan , Lu Zhe , Zhang Hang , Jin Su‐Feng , Yang Hao , Li Yun‐Man , Shi Li‐Yun
Published: March 2016

Aims

Daphnetin, a coumarin derivative extracted from Daphne odora var. marginata, has been reported to have antiinflammatory and immunosuppressive properties. Our previous study indicated that it was able to remarkably suppress the neuroinflammation and suggested its potential application in treating neuroinflammatory diseases. Multiple sclerosis (MS), a Th cell‐mediated autoimmune disease, is the most common inflammatory demyelinating disease of the central nervous system (CNS). We examined whether daphnetin treatment can protect mice against experimental autoimmune encephalomyelitis (EAE), an animal model for MS.

Methods

To assess the effect of daphnetin in neuroinflammatory diseases, the EAE mice were established and treated with daphnetin at 8 mg/kg for 28 days. The severity of neuroinflammation and demyelination in the spinal cords was examined histopathologically. Infiltration of CD4+ T cells into the CNS was assessed by immunohistochemistry, and the cytokine production was determined by ELISA. Meanwhile, the effect of daphnetin on the activity of dendritic cells (DCs) was evaluated, as assessed by DCs’ capability to express surface markers, secrete cytokines, and activate naïve CD4+ T cells. Furthermore, we explored the molecular mechanisms whereby DAPH regulated DCs’ activity and thereby CD4+ T cell responses.

Results

The administration of daphnetin markedly alleviated the clinical symptoms of EAE and reduced the CNS inflammation and demyelination in experimental mice. Th1 and Th17 cell responses were profoundly repressed in daphnetin‐treated EAE mice. Mechanistically, daphnetin treatment significantly repressed the activation, maturation, and antigen‐presenting capability of DCs. NF‐κB signaling was significantly reduced in daphnetin‐treated DCs, along with a concomitant induction of heme oxygenase‐1, a negative regulator of inflammatory signaling.

Conclusions

Our findings for the first time demonstrate the property of daphnetin in regulating DCs’ function and subsequently Th development. Given the low or absent toxicity associated with daphnetin, our data may suggest a novel safe and effective approach to control autoimmune neuroinflammation.
Visualizing the early infection of Agathis australis by Phytophthora agathidicida, using microscopy and fluorescent in situ hybridization
Authors: Bellgard S. E. , Padamsee M. , Probst C. M. , Lebel T. , Williams S. E.
Published: March 2016

Phytophthora agathidicida (PTA) causes a root rot and collar rot of New Zealand kauri (Agathis australis). This study developed techniques to visualize early infection of kauri by PTA in deliberately inoculated seedlings. Conventional light microscopy was carried out on cleared and stained roots using trypan blue to observe PTA structures. Additionally, scanning electron microscopy (SEM) was used to study the PTA root structures at a higher resolution. A fluorescent in situ hybridization assay (FISH) was developed using a PTA‐specific probe to label PTA structures in planta. Infection progression in roots of 2‐year‐old kauri inoculated with PTA at 5, 10, 16 and 20 days post‐inoculation (d.p.i.) was compared using these three approaches. Light microscopy identified no Phytophthora‐like structures in the control treatments. In PTA‐inoculated plants, lignitubers were produced 5 d.p.i. in cortical cells. Infection was localized after 5 days, but as the infection progressed (up to 20 d.p.i.), the ‘degree’ of root infection increased, as did the number of replicates in which structures were observed. SEM provided higher resolution images; again, no PTA structures were observed in the negative control material examined. The slide‐based FISH‐specificity assay successfully hybridized with PTA hyphae. Fluorescence was observed using 330–380 nm excitation and an emission filter at 420 nm (DAPI), with PTA nuclei fluorescing a bright greenish‐yellow. Cross‐reactivity was not observed when the assay was applied to six other non‐target Phytophthora species. Successful hybridization reactions occurred between the primer and PTA structures in planta. Applying this FISH assay has allowed clear differentiation of the intracellular and intercellular structures of PTA. The technique can be applied to longer term studies or analysis of ex situ inoculation studies aiming to elucidate differential host‐responses to the pathogen. Additionally, the technique could be applied to study the interactions with other fungal endophytes (e.g. mycorrhizal fungi), which could be assessed for biocontrol potential as part of the integrated management of the disease.
Current use of imaging and electromagnetic source localization procedures in epilepsy surgery centers across Europe
Authors: Mouthaan Brian E. , Rados Matea , Barsi Péter , Boon Paul , Carmichael David W. , Carrette Evelien , Craiu Dana , Cross J. Helen , Diehl Beate , Dimova Petia , Fabo Daniel , Francione Stefano , Gaskin Vladislav , Gil‐Nagel Antonio , Grigoreva Elena , Guekht Alla , Hirsch Edouard , Hecimovic Hrvoje , Helmstaedter Christoph , Jung Julien , Kalviainen Reetta , Kelemen Anna , Kimiskidis Vasilios , Kobulashvili Teia , Krsek Pavel , Kuchukhidze Giorgi , Larsson Pål G. , Leitinger Markus , Lossius Morten I. , Luzin Roman , Malmgren Kristina , Mameniskiene Ruta , Marusic Petr , Metin Baris , Özkara Cigdem , Pecina Hrvoje , Quesada Carlos M. , Rugg‐Gunn Fergus , Rydenhag Bertil , Ryvlin Philippe , Scholly Julia , Seeck Margitta , Staack Anke M. , Steinhoff Bernhard J. , Stepanov Valentin , Tarta‐Arsene Oana , Trinka Eugen , Uzan Mustafa , Vogt Viola L. , Vos Sjoerd B. , Vulliémoz Serge , Huiskamp Geertjan , Leijten Frans S. S. , Van Eijsden Pieter , Braun Kees P. J. ,   the E‐PILEPSY consortium
Published: March 2016

Objective

In 2014 the European Union–funded E‐PILEPSY project was launched to improve awareness of, and accessibility to, epilepsy surgery across Europe. We aimed to investigate the current use of neuroimaging, electromagnetic source localization, and imaging postprocessing procedures in participating centers.

Methods

A survey on the clinical use of imaging, electromagnetic source localization, and postprocessing methods in epilepsy surgery candidates was distributed among the 25 centers of the consortium. A descriptive analysis was performed, and results were compared to existing guidelines and recommendations.

Results

Response rate was 96%. Standard epilepsy magnetic resonance imaging (MRI) protocols are acquired at 3 Tesla by 15 centers and at 1.5 Tesla by 9 centers. Three centers perform 3T MRI only if indicated. Twenty‐six different MRI sequences were reported. Six centers follow all guideline‐recommended MRI sequences with the proposed slice orientation and slice thickness or voxel size. Additional sequences are used by 22 centers. MRI postprocessing methods are used in 16 centers. Interictal positron emission tomography (PET) is available in 22 centers; all using 18F‐fluorodeoxyglucose (FDG). Seventeen centers perform PET postprocessing. Single‐photon emission computed tomography (SPECT) is used by 19 centers, of which 15 perform postprocessing. Four centers perform neither PET nor SPECT in children. Seven centers apply magnetoencephalography (MEG) source localization, and nine apply electroencephalography (EEG) source localization. Fourteen combinations of inverse methods and volume conduction models are used.

Significance

We report a large variation in the presurgical diagnostic workup among epilepsy surgery centers across Europe. This diversity underscores the need for high‐quality systematic reviews, evidence‐based recommendations, and harmonization of available diagnostic presurgical methods.
Anticonvulsant drug–induced cell death in the developing white matter of the rodent brain
Authors: Kaushal Suhasini , Tamer Zenab , Opoku Freda , Forcelli Patrick A.
Published: March 2016

Objective

During critical periods of brain development, both seizures and anticonvulsant medications can affect neurodevelopmental outcomes. In rodent models, many anticonvulsants trigger neuronal apoptosis. However, white matter apoptosis (WMA) has not been examined after anticonvulsant drug treatment. Herein, we sought to determine if anticonvulsant drugs induced apoptosis in the developing white matter (WM) in a rodent model.

Methods

Postnatal day (P)7 rats were treated with phenobarbital (PB‐75), MK‐801 (dizocilpine, 0.5), lamotrigine (LTG‐20), carbamazepine (CBZ‐100), phenytoin (PHT‐50), levetiracetam (LEV‐250), or saline; all doses are mg/kg. Brain tissue collected 24 h after treatment was stained using the terminal deoxynucleotidyl transferase dUTP nick end labeling method. The number of degenerating cells within WM, that is, anterior commissure (AC), corpus callosum, cingulum, and hippocampus‐associated WM tracts, was quantified.

Results

Saline‐treated rats showed low baseline level of apoptosis in developing WM on P8 in all the areas examined. PB, PHT, and MK‐801 significantly increased apoptosis in all four brain areas examined. Exposure to CBZ, LTG, or LEV failed to increase apoptosis in all regions.

Significance

Commonly used anticonvulsants (PB, PHT) cause apoptosis in the developing WM in a rat model; the N‐methyl‐d‐aspartate (NMDA) receptor antagonist MK‐801 has a similar effect. These results are consistent with reports of anesthesia‐induced WMA during brain development. Consistent with the lack of neuronal apoptosis caused by LTG, LEV, and CBZ, these drugs did not cause WMA. Many infants treated with anticonvulsant drugs have underlying neurologic injury, including WM damage (e.g., following intraventricular hemorrhage [IVH] or hypoxic‐ischemic encephalopathy [HIE]). The degree to which anticonvulsant drug treatment will alter outcomes in the presence of underlying injury remains to be examined, but avoiding drugs (when possible) that induce WMA may be beneficial.
Using soil from pellets of White StorksCiconia ciconiato assess the number of earthworms (Lumbricidae) consumed as primary and secondary prey
Authors: Orłowski Grzegorz , Książkiewicz‐Parulska Zofia , Karg Jerzy , Bocheński Marcin , Jerzak Leszek , Zub Karol
Published: March 2016

Earthworms (Oligochaeta, Lumbricidae) form a significant component of the food web and are the staple diet of many higher‐trophic‐level predators, such as invertebrate‐feeding birds and mammals. Their almost complete digestion in the predator's gut hampers their detection or quantification in faeces or pellets except through labour‐intensive microscopic examination. As a result, the evaluation of earthworms as a component of diet has been neglected in most studies based on pellet analysis. We assess whether the earthworm component of the diet of White StorksCiconia ciconiacan be estimated reliably by measuring soil mass in pellets, and whether the fact that White Storks also consume European MolesTalpa europaea(themselves consumers of earthworms) affects this relationship. We found a significantly higher density of earthworm chaetae, but less soil material, in pellets containing the remains of Moles. This may indicate the secondary origin of some chaetae from the intestines of the ingested Moles. There was a strong relationship and close fit between the number of earthworm chaetae and the mass of soil (material < 0.2 mm) retrieved from all the pellets analysed. Approximating the number of chaetae based on a soil mass of 192 mg per 1000 chaetae yielded results differing by only 4–5% from numbers of chaetae counted directly. This validates the proposed method of indirectly calculating the number of earthworms consumed from the ingested soil mass, which simplifies and shortens the time‐consuming direct counting of chaetae and could contribute to a more detailed description and analysis of diets in wild birds. Such assessments are important in order to improve the detection of changes induced by the progressive simplification and loss of primary food web resources (such as earthworms) within agro‐ecosystems as a consequence of both the rapid intensification of agricultural production and climate change.
Functional infertility in a wild passerine bird
Authors: Schmoll Tim , Kleven Oddmund
Published: March 2016

Information about male infertility in free‐living bird populations and its underlying causes are poorly documented in the literature. Here, we assessed sperm quality and infertility among males in a wild population of Blue Tits Cyanistes caeruleus, a socially monogamous passerine with frequent extra‐pair mating. One of 30 males (3.3%) studied across two breeding seasons had morphologically abnormal and nearly immotile spermatozoa in combination with zero annual fertilization success. Demonstration of male functional infertility suggests the possibility that socially monogamous females of the study population could obtain a direct fitness benefit by mating polyandrously to increase fertilization success, which could contribute to selection on extra‐pair mating behaviour.
The phylogenetic position of the world's smallest passerine, the Pygmy Bushtit Psaltria exilis
Authors: Johansson Ulf S. , Ericson Per G. P. , Fjeldså Jon , Irestedt Martin
Published: March 2016

The Pygmy Bushtit is confined to the montane forests of Java. It is the world's smallest passerine and morphologically resembles a small, drab long‐tailed tit or bushtit (Aegithalidae). In its behaviour the Pygmy Bushtit show similarities with the members of the Aegithalidae, but owing to its small size and isolated geographical distribution relative to the other members of the Aegithalidae, it has always been placed in a monotypic genus within the family. The affinities of the Pygmy Bushtit have never been tested in a phylogenetic context and the species has to date not been included in any molecular studies. In this study we use sequence data from four different genetic markers to place it in the passerine phylogenetic tree. Our results confirm the inclusion of the Pygmy Bushtit in the Aegithalidae, but rather than being an isolated lineage, our results strongly suggest that it is nested in the Aegithalos clade, and most closely related to the Black‐throated Bushtit Aegithalos concinnus. The range of the Black‐throated Bushtit extends south into subtropical Indochina, with an isolated subspecies occurring in southern Vietnam. The Black‐throated Bushtit contains several morphologically and genetically distinct lineages, which could represent distinct species, but the phylogenetic relationships within this complex are poorly resolved and partly in conflict with current taxonomic treatment based on morphology.
Effects of a novel light‐curable material on odontoblastic differentiation of human dental pulp cells
Authors: Lee B.‐N. , Lee B.‐G. , Chang H.‐S. , Hwang Y.‐C. , Hwang I.‐N. , Oh W.‐M.
Published: March 2016

Aim

To assess the biological effects, including odontoblastic differentiation of a novel light‐curable material (TheraCal), on human dental pulp cells (hDPCs).

Methodology

The hDPCs were isolated from freshly extracted, caries‐free third molars. Ten discs of TheraCal and MTA (8 mm in diameter and 3 mm in height) were incubated in α‐minimum essential medium (α‐MEM) and the supernatant collected. Viability of hDPCs in response to TheraCal and MTA was measured using the WST‐1 assay. RT‐PCR and real‐time PCR were used to detect the gene expression of dentine sialophosphoprotein (DSPP) and dentine matrix protein‐1 (DMP‐1). ALP staining and Alizarin red S staining were used to evaluate the expression of alkaline phosphatase (ALP) and mineralization behaviour. One‐way analysis of variance and Tukey's post hoc test were used to determine the statistically significant differences as a result of the variation in test materials (P < 0.05).

Results

The effects of TheraCal and MTA on cell viability were similar except at the highest concentration. The mRNA level of DSPP increased significantly in the MTA group relative to the control at day 1 and 3 (P < 0.05). Also, the mRNA level of DSPP increased significantly in the TheraCal group relative to the control at day 3 (P < 0.05). The increased mRNA level of DMP‐1 was 2.5‐fold and 2.3‐fold each in the MTA and TheraCal groups relative to the control (P < 0.05). Cells exposed to MTA exhibited a 1.4‐fold increase of ALP staining relative to control (P < 0.05). In the mineralization assay, increased calcium nodule formation was twofold and 1.3‐fold each in the MTA and TheraCal groups compared to the control (P < 0.05).

Conclusions

TheraCal and MTA had the ability to induce odontoblastic differentiation and mineralization of hDPCs.
Effect of laser‐activated irrigation on biofilms in artificial root canals
Authors: De Meyer S. , Meire M. A. , Coenye T. , De Moor R. J. G.
Published: March 2016

Aim

To evaluate the antimicrobial effect of laser‐activated irrigation (LAI) on biofilms formed in simulated root canals.

Methodology

A dual‐species biofilm of Enterococcus faecalis and Streptococcus mutans was grown in a resin root canal model. Biofilms were formed over 48 h and subsequently subjected to the following treatments, all executed for 20 s: syringe irrigation (SI) with a 27G needle, ultrasonically activated irrigation (UAI) with a size 20 Irrisafe file, and LAI with a 2940 nm Er:YAG laser (20 Hz, 50 μs, 20 or 40 mJ, conical fibre tip at two positions). Tests were performed with both sterile saline as well as NaOCl (2.5%) as the irrigant. Surviving bacteria were harvested and the number of CFU was determined by plate counting and compared across groups (anova, P ≤ 0.05).

Results

Using saline as the irrigant, significant reductions in viable counts compared to untreated controls were observed for ultrasonically activated irrigation (0.52 log10 reduction) and for all laser‐activated irrigation groups (>1 log10 reduction), but not for syringe irrigation (<0.25 log10 reduction). The reductions in the laser‐activated irrigation groups were significantly greater than those of ultrasonically activated irrigation. With NaOCl as the irrigant, significant reductions (>2.2 log10 units) in the number of attached bacteria were observed for all treatment groups with no significant differences between laser‐activated and ultrasonically activated irrigation.

Conclusions

Within the limitations of this in vitro set‐up, laser‐activated irrigation removed more biofilm than ultrasonically activated irrigation when using saline as the irrigant, indicating greater physical biofilm removal. The use of NaOCl resulted in greater biofilm reduction with no significant differences between treatment groups.