bluuebunny/crossref_metadata_2025 huggingface dataset:
Long-Term Abandonment of Forest Management Has a Strong Impact on Tree Morphology and Wood Volume Allocation Pattern of European Beech (Fagus sylvatica L.)
Authors: Georgi Louis , Kunz Matthias , Fichtner Andreas , Härdtle Werner , Reich Karl Friedrich , Sturm Knut , Welle Torsten , Oheimb Goddert von
Published: November 2018

The three-dimensional (3D) morphology of individual trees is critical for light interception, growth, stability and interactions with the local environment. Forest management intensity is a key driver of tree morphology, but how the long-term abandonment of silvicultural measures impacts trunk and crown morphological traits is not fully understood. Here, we take advantage of a long management intensity gradient combined with a high-resolution terrestrial laser scanning (TLS) approach to explore how management history affects the 3D structure of mature beech (Fagus sylvatica L.) trees. The management gradient ranged from long-term (>50 years) and short-term (>20 years) unmanaged to extensively and intensively managed beech stands. We determined 28 morphological traits and quantified the vertical distribution of wood volume along the trunk. We evaluated the differences in tree morphological traits between study stands using Tukey’s HSD test. Our results show that 93% of the investigated morphological traits differed significantly between the study stands. Significant differences, however, emerged most strongly in the stand where forest management had ceased >50 years ago. Furthermore, we found that the vertical distribution of trunk wood volume was highly responsive between stands with different management intensity, leading to a 67% higher taper top height and 30% lower taper of beech trees growing in long-term unmanaged stands compared to those in short-term unmanaged or managed stands. These results have important implications for management intensity decisions. It is suggested that the economic value of individual beech trees from long-term unmanaged forests can be expected to be very high. This might also translate to beech forests that are extensively managed, but we found that a few decades of implementation of such a silvicultural system is not sufficient to cause significant differences when compared to intensively managed stands. Furthermore, TLS-based high-resolution analyses of trunk and crown traits play a crucial role in the ability to better understand or predict tree growth responses to the current drivers of global change.
Characterisation of Monovarietal Olive Oils Obtained from Croatian cvs. Drobnica and Buza during the Ripening Period
Authors: Giacometti Jasminka , Milin Čedomila , Giacometti Fabio , Ciganj Zlatko
Published: November 2018

The aim of this study was the monitoring of the chemical composition of olive oil at different ripening stages to determine the appropriate harvesting time during any given crop season in the northern Adriatic region. For this purpose, from September to November, two Croatian olive cultivars (Drobnica and Buza) were taken from two different olive orchards and for the respective olive oils, prepared on a laboratory scale, the major saponifiable, unsaponifiable and phenolic compounds were determined. Based on the chemical analyses performed, the optimal harvesting time has been set in October for both cultivars. Buza had a higher oleic acid, but lower total sterols, squalene and total alkanols. Compared to the local cultivars, the studied cultivars had a high total phenolic content and antioxidant activity. The antioxidant activity and concentrations of total phenols correlated with α-tocopherol in oil samples taken during the ripening progress. Finally, trace minerals detected in Buza and Drobnica oil differed, which can be an indicator of oxidative stability and authenticity of oils.
Special Issue: Coevolution of Hosts and Their Microbiome
Authors: Limborg Morten T. , Heeb Philipp
Published: November 2018

The evolution of life-history traits in plants and animals has taken place in the midst of complex microbial communities. [...]
Cryptic Diversity Hidden within the Leafminer Genus Liriomyza (Diptera: Agromyzidae)
Authors: Carapelli Antonio , Soltani Abir , Leo Chiara , Vitale Matteo , Amri Moez , Mediouni-Ben Jemâa Jouda
Published: November 2018

Leafminer insects of the genus Liriomyza are small flies whose larvae feed on the internal tissue of some of the most important crop plants for the human diet. Several of these pest species are highly uniform from the morphological point of view, meaning molecular data represents the only reliable taxonomic tool useful to define cryptic boundaries. In this study, both mitochondrial and nuclear molecular markers have been applied to investigate the population genetics of some Tunisian populations of the polyphagous species Liriomyza cicerina, one of the most important pest of chickpea cultivars in the whole Mediterranean region. Molecular data have been collected on larvae isolated from chickpea, faba bean, and lentil leaves, and used for population genetics, phylogenetics, and species delimitation analyses. Results point toward high differentiation levels between specimens collected on the three different legume crops, which, according to the species delimitation methods, are also sufficient to define incipient species differentiation and cryptic species occurrence, apparently tied up with host choice. Genetic data have also been applied for a phylogenetic comparison among Liriomyza species, further confirming their decisive role in the systematic studies of the genus.
How to Define Priorities in Coastal Vulnerability Assessment
Authors: De Serio Francesca , Armenio Elvira , Mossa Michele , Petrillo Antonio Felice
Published: November 2018

Awareness of coastal landscapes vulnerability to both natural and man-made hazards induce to monitor their evolution, adaptation, resilience and to develop appropriate defence strategies. The necessity to transform the monitoring results into useful information is the motivation of the present paper. Usually, to this scope, a coastal vulnerability index is deduced, by assigning ranking values to the different parameters governing the coastal processes. The principal limitation of this procedure is the individual discretion used in ranking. Moreover, physical parameters are generally considered, omitting socio-economic factors. The aim of the present study is to complement a geographical information system (GIS) with an analytical hierarchical process (AHP), thus allowing an objective prioritization of the key parameters. Furthermore, in the present case, socio-economic parameters have been added to physical ones. Employing them jointly, an integrated coastal vulnerability index (ICVI) has been estimated and its effectiveness has been investigated. To show how it works, the proposed method has been applied to a portion of the Adriatic coastline, along the Apulian region in southern Italy. It has permitted to identify and prioritize the most vulnerable areas, revealing its efficacy as a potential tool to support coastal planning and management.
Hellenic Karst Aquifers Vulnerability Approach Using Factor Analysis: The Example of the Louros Karst Aquifers
Authors: Katsanou Konstantina
Published: November 2018

The karst aquifers of the Hellenic territory display high vulnerability that is related to the existence of the epikarst zone. If present, the epikarst zone regulates the vertical movement of the groundwater, which results in the chemical pollutants staying longer within it, thus facilitating the inactivation of the microbial loads. The Hellenic karst is well developed; it displays high hydraulic conductivity, relatively large storage, and the characteristics of an important water reservoir. Although its porosity was calculated to be between 0.005–8%, the statistical processing of the springs’ discharge time series points to an increased storage. The increased storage was attributed to the presence of the epikarst zone, which regulates the water movement to the underlying formations, and finally to its discharge from the karst system through springs. In these areas, the influence of nitrogen compounds on the water quality is evident. The presence of cyanobacteria and toxic substances at concentrations that are too high for fresh, flowing waters whose temperature does not exceed 17 °C advocates the role of nutrients, even at concentrations that do not exceed the maximum permissible limits of drinking water. In mountainous areas, where agriculture is limited, the presence of these compounds is attributed to heavily polluting land uses. The impact of such uses became apparent from the application of factor analysis, which not only highlighted their contribution to the overall groundwater quality, but also determined their geographical distribution and origin. From the above, it becomes evident that there is a need for protection of the karst aquifers, and investigation of their vulnerability mechanisms. The Hellenic karst, which is expected to cover the drinking water needs in the near future, proves to be very vulnerable to any kind of pollution.
Estimating Groundwater Abstractions at the Aquifer Scale Using GRACE Observations
Authors: Gemitzi Alexandra , Lakshmi Venkat
Published: November 2018

Groundwater monitoring requires costly in situ networks, which are difficult to maintain over long time periods, especially in countries facing economic recession such as Greece. Our work aims at providing a methodology to estimate groundwater abstractions at the aquifer scale using publicly available remotely sensed data from the NASA’s Gravity Recovery and Climate Experiment (GRACE) together with publicly available meteorological observations that serve as input variables to an Artificial Neural Network (ANN) method. The methodology was demonstrated in an alluvial aquifer in NE Greece for a 10-year period (2005–2014), where irrigation agriculture poses a serious threat to both groundwater resources and their dependent ecosystems. To generalize the developed model, an ensemble of 100 ANNs was created by the initial weight randomization approach and output was computed by averaging the output of each individual model. Scaled Root Mean Square Error and Nash–Sutcliffe coefficient were used to test the model efficiency. Both of these performance metrics indicated that monthly groundwater abstractions can be estimated efficiently and that the developed methodology offers an inexpensive substitute for in situ groundwater monitoring when in situ networks are not available or cannot operate properly.
The Impact of Biochar Incorporation on Inorganic Nitrogen Fertilizer Plant Uptake; An Opportunity for Carbon Sequestration in Temperate Agriculture
Authors: Hood-Nowotny Rebecca , Watzinger Andrea , Wawra Anna , Soja Gerhard
Published: November 2018

Field studies of biochar addition to soil and nutrient cycling using 15N fertilizers in temperate agriculture are scant. These data are required in order to make evidence based assessments. This study was conducted to test the hypothesis that biochar application can increase crop yields through improving the nitrogen uptake and utilization of added inorganic fertilizer, whilst sequestering significant quantities of carbon. Results showed that although biochar addition led to significant spring barley grain yield increases in the first year of biochar application, an unusually dry year; this was possibly not solely the result of improved nitrogen uptake, as total crop N was similar in both treatments. Results suggested it was improved water utilization, indicated by the crop carbon isotope values and soil moisture characteristics. In the second year, there were no significant effects of the previous year’s biochar addition on the sunflower yield, N status, fertilizer recovery or any signs of improved water utilization. These data add to a growing body of evidence, suggesting that biochar addition has only slightly positive or neutral effects on crop growth and fertilizer retention but has the potential to sequester vast amounts of carbon in the soil with minimal yield losses in temperate agriculture.
Statistical Analysis of Displacement and Length Relation for Normal Faults in the Barents Sea
Authors: Kolyukhin Dmitriy , Torabi Anita , Libak Audun , Alaei Behzad , Khachkova Tatiana
Published: November 2018

This paper is devoted to the statistical analysis of dependence between fault length (L) and displacement (D). The main purpose of this work is to study the scaling relations between fault length and displacement using a database that includes datasets of 21 faults with geometric data extracted from 3D seismic coherence cubes of the Norwegian Barents Sea. Multiple linear regression and Bayesian and Akaike information criterions are applied to obtain optimal regression parameters. Our dataset is unique since it includes segment lengths of individual faults, unlike the previously published datasets. Hence, we studied both the dependence of fault segment length and accumulated fault length on displacement. The latter relation (accumulated fault length versus displacement) shows a general agreement (positive correlation and power-law relation) with the previously published results that are mainly obtained from outcrop studies, although the slopes vary for different lithologies. The differences could be attributed to the unique characteristics of our dataset that includes data of all segment lengths of individual faults.
An Analysis of Geriatric Medicine in Malaysia-Riding the Wave of Political Change
Authors: Tan Maw Pin , Kamaruzzaman Shahrul B. , Poi Philip Jun Hua
Published: November 2018

Malaysia became the centre of international attention when it democratically removed a semi-authoritarian government of 62 years during its 14th general election this year. This electoral success has provided geriatric medicine in Malaysia with a high-impact ageing icon by installing the oldest prime minister in the world. A wave of optimism for the expansion of geriatric services in Malaysia, which met with numerous challenges in the last two decades, has emerged as a result of this political change. The number of geriatrics specialists and services had begun to see slow expansions under the previous government. However, existing geriatricians will need to reassess the landscape of delivery and access to care in our rapidly growing ageing population and develop new strategies to truly expand their services. In addition to unrelenting efforts in the recruitment and training of future geriatricians, the steady expansion of the geriatric workforce should take into account the inclusion of geriatric medicine in the undergraduate training curricula of all healthcare professionals. Expansion of geriatric services will also be a cost-effective strategy to reduce the growing national healthcare budget incurred by the growing needs of an ageing population.
Ostalgia in Czech Films about Normalisation Created Post-1989
Authors: Ptáček Luboš
Published: November 2018

This piece will introduce Czech ostalgic films set in the normalisation period (1969–1989) and will interpret the basic divide between nostalgic representation of the period and the openly anti-communist stances of the films’ creators. The methodological frame of this research comes from Robert Rosenstone’s approach of representation of history in film. To interpret ostalgia in Czech film, I use ideas from Daphne Berdhal and Svetlana Boym. I described the nostalgic elements and their functions in the structure of the films, taking into account their story, characters, settings, film style, narration, genre, and audience response (identification, causality of emotional experience). Czech ostalgic films about the normalisation period are interpretively ambivalent. The interpretational tension appears out of a fundamental divide between a clear refusal of communism and an idyllic view of the socialist past. They cannot be simply classified into restorative or reflective nostalgia. The younger generation of spectators perceives ostalgic films in the mode of reflective nostalgia; on the other hand, the older generation perceive the films in terms of restorative nostalgia. A different way of perceiving ostalgia reveals a misunderstanding between generations of the current Czech society. Due to singular anti-communist viewpoints and emphasised liberal values, the films cannot be interpreted in a desire for an idealised home in a communist past, but as a desire for a present home and its security, which cannot be clearly conceptualised. The concept of reflective nostalgia can be linked with the theory of Berdhal. The films cannot be perceived as a desire for an idealised home in a communist past due to specific anti-communist viewpoints and highlighted liberal values, but as a need for a home and security that cannot be directly conceptualised. This appearance of reflective nostalgia can be connected with the theory stated by Berdhal.
Health-Related Lifestyle Behavior and Religiosity among First-Generation Immigrants of Polish Origin in Germany
Authors: Morawa Eva , Erim Yesim
Published: November 2018

Background: Health-related lifestyle behaviors such as smoking, alcohol consumption, physical inactivity and obesity are major cardiovascular risk factors. Previous studies have mostly demonstrated a favorable association between religiosity and these cardiovascular risk factors; however, no studies have investigated this relationship in Polish immigrants. The aim of this cross-sectional study was to examine the association between health-related lifestyle behaviors and religiosity in Polish immigrants in Germany. Methods: The smoking patterns, frequency of alcohol consumption, physical activity, and presence of overweight/obesity were assessed in 257 first-generation immigrants of Polish origin living in Germany. Religiosity was measured with the Centrality of Religiosity Scale (CRS, Huber, 2003) consisting of 15 items that categorized the respondents into intrinsically, extrinsically, and not/marginally religious. Results: After adjusting for various sociodemographic, migration, and health-related characteristics, intrinsic religiosity was significantly associated with a lower risk of being a smoker (odds ratios (OR) = 0.34, confidence intervals (CI) = 0.15–0.76) and was also associated with a lower risk of alcohol consumption (OR = 0.33, CI = 0.15–0.71), but a higher risk of being overweight/obese (OR = 2.53, CI = 1.15–5.56) in comparison with extrinsic/marginal religiosity. No significant relationship was found between religiosity and physical activity. Conclusions: In Polish immigrants, intrinsic religiosity acts as a protective factor against some cardiovascular risk factors (smoking and alcohol consumption).
The Impact of Union of European Football Associations (UEFA) Financial Fair Play Regulation on Audit Fees: Evidence from Spanish Football
Authors: Mareque Mercedes , Barajas Angel , Lopez-Corrales Francisco
Published: November 2018

This paper analyzes whether the Financial Fair Play (FFP) regulations set by Union of European Football Associations (UEFA) have influenced the auditing fees charged to football clubs. In addition, it explores the determinants of audit fees. We used a two-sample t-test with equal variances to determine whether differences are present. After this, we carried out a panel data regression with the clubs fix effect to estimate the determinants of audit fees in football clubs. Our findings revealed an increase of audit fees after the implementation of FFP regulations. On top of that, audit fees were explained by the presence of foreign investors if the audit firm was one of the Big 4 and if the auditor was a woman. The regulation change has had an impact on the audit fees charged by auditors for their services. However, this increase may be compensated over future years given the improving financial situation of clubs; therefore, the auditors’ risk diminishes and subsequent audit fees may be reduced. UEFA should monitor audit fees as well as the quality of the audit reports, which have become crucial to obtaining the license to participate in UEFA competitions.
Complying with Privacy Legislation: From Legal Text to Implementation of Privacy-Aware Location-Based Services
Authors: Ataei Mehrnaz , Degbelo Auriol , Kray Christian , Santos Vitor
Published: November 2018

An individual’s location data is very sensitive geoinformation. While its disclosure is necessary, e.g., to provide location-based services (LBS), it also facilitates deep insights into the lives of LBS users as well as various attacks on these users. Location privacy threats can be mitigated through privacy regulations such as the General Data Protection Regulation (GDPR), which was introduced recently and harmonises data privacy laws across Europe. While the GDPR is meant to protect users’ privacy, the main problem is that it does not provide explicit guidelines for designers and developers about how to build systems that comply with it. In order to bridge this gap, we systematically analysed the legal text, carried out expert interviews, and ran a nine-week-long take-home study with four developers. We particularly focused on user-facing issues, as these have received little attention compared to technical issues. Our main contributions are a list of aspects from the legal text of the GDPR that can be tackled at the user interface level and a set of guidelines on how to realise this. Our results can help service providers, designers and developers of applications dealing with location information from human users to comply with the GDPR.
DNA Methylation Analysis of Dormancy Release in Almond (Prunus dulcis) Flower Buds Using Epi-Genotyping by Sequencing
Authors: Prudencio Ángela S. , Werner Olaf , Martínez-García Pedro J. , Dicenta Federico , Ros Rosa M. , Martínez-Gómez Pedro
Published: November 2018

DNA methylation and histone post-translational modifications have been described as epigenetic regulation mechanisms involved in developmental transitions in plants, including seasonal changes in fruit trees. In species like almond (Prunus dulcis (Mill.) D.A: Webb), prolonged exposure to cold temperatures is required for dormancy release and flowering. Aiming to identify genomic regions with differential methylation states in response to chill accumulation, we carried out Illumina reduced-representation genome sequencing on bisulfite-treated DNA from floral buds. To do this, we analyzed almond genotypes with different chilling requirements and flowering times both before and after dormancy release for two consecutive years. The study was performed using epi-Genotyping by Sequencing (epi-GBS). A total of 7317 fragments were sequenced and the samples compared. Out of these fragments, 677 were identified as differentially methylated between the almond genotypes. Mapping these fragments using the Prunus persica (L.) Batsch v.2 genome as reference provided information about coding regions linked to early and late flowering methylation markers. Additionally, the methylation state of ten gene-coding sequences was found to be linked to the dormancy release process.
Inhibition of Microglia-Derived Oxidative Stress by Ciliary Neurotrophic Factor Protects Dopamine Neurons In Vivo from MPP+ Neurotoxicity
Authors: Baek Jeong Yeob , Jeong Jae Yeong , Kim Kyoung In , Won So-Yoon , Chung Young Cheul , Nam Jin Han , Cho Eun Ju , Ahn Tae-Beom , Bok Eugene , Shin Won-Ho , Jin Byung Kwan
Published: November 2018

We demonstrated that capsaicin (CAP), an agonist of transient receptor potential vanilloid subtype 1 (TRPV1), inhibits microglia activation and microglia-derived oxidative stress in the substantia nigra (SN) of MPP+-lesioned rat. However, the detailed mechanisms how microglia-derived oxidative stress is regulated by CAP remain to be determined. Here we report that ciliary neurotrophic factor (CNTF) endogenously produced by CAP-activated astrocytes through TRPV1, but not microglia, inhibits microglial activation and microglia-derived oxidative stress, as assessed by OX-6 and OX-42 immunostaining and hydroethidine staining, respectively, resulting in neuroprotection. The significant increase in levels of CNTF receptor alpha (CNTFRα) expression was evident on microglia in the MPP+-lesioned rat SN and the observed beneficial effects of CNTF was abolished by treatment with CNTF receptor neutralizing antibody. It is therefore likely that CNTF can exert its effect via CNTFRα on microglia, which rescues dopamine neurons in the SN of MPP+-lesioned rats and ameliorates amphetamine-induced rotations. Immunohistochemical analysis revealed also a significantly increased expression of CNTFRα on microglia in the SN from human Parkinson’s disease patients compared with age-matched controls, indicating that these findings may have relevance to the disease. These data suggest that CNTF originated from TRPV1 activated astrocytes may be beneficial to treat neurodegenerative disease associated with neuro-inflammation such as Parkinson’s disease.
Characterization of Ecklonia cava Alginate Films Containing Cinnamon Essential Oils
Authors: Baek Su-Kyoung , Kim Sujin , Song Kyung Bin
Published: November 2018

In this study, Ecklonia cava alginate (ECA) was used as a base material for biodegradable films. Calcium chloride (CaCl2) was used as a cross-linking agent, and various concentrations (0%, 0.4%, 0.7%, and 1.0%) of cinnamon leaf oil (CLO) or cinnamon bark oil (CBO) were incorporated to prepare active films. The ECA film containing 3% CaCl2 had a tensile strength (TS) of 17.82 MPa and an elongation at break (E) of 10.36%, which were higher than those of the film without CaCl2. As the content of essential oils (EOs) increased, TS decreased and E increased. Addition of CLO or CBO also provided antioxidant and antimicrobial activities to the ECA films. The antioxidant activity of the ECA film with CBO was higher than that of the film containing CLO. In particular, the scavenging activities of the 2,2-diphenyl-1-picrylhydrazyl (DPPH) and 2,2′-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) radicals in the ECA film containing 1% CBO were 50.45% and 99.37%, respectively. In contrast, the antimicrobial activities against Escherichia coli O157:H7, Salmonella Typhimurium, Staphylococcus aureus, and Listeria monocytogenes were superior in the ECA films with CLO. These results suggest that ECA films containing CLO or CBO can be applied as new active packaging materials.
Role of Overexpressed Transcription Factor FOXO1 in Fatal Cardiovascular Septal Defects in Patau Syndrome: Molecular and Therapeutic Strategies
Authors: Abuzenadah Adel , Alsaedi Saad , Karim Sajjad , Al-Qahtani Mohammed
Published: November 2018

Patau Syndrome (PS), characterized as a lethal disease, allows less than 15% survival over the first year of life. Most deaths owe to brain and heart disorders, more so due to septal defects because of altered gene regulations. We ascertained the cytogenetic basis of PS first, followed by molecular analysis and docking studies. Thirty-seven PS cases were referred from the Department of Pediatrics, King Abdulaziz University Hospital to the Center of Excellence in Genomic Medicine Research, Jeddah during 2008 to 2018. Cytogenetic analyses were performed by standard G-band method and trisomy13 were found in all the PS cases. Studies have suggested that genes of chromosome 13 and other chromosomes are associated with PS. We, therefore, did molecular pathway analysis, gene interaction, and ontology studies to identify their associations. Genomic analysis revealed important chr13 genes such as FOXO1, Col4A1, HMGBB1, FLT1, EFNB2, EDNRB, GAS6, TNFSF1, STARD13, TRPC4, TUBA3C, and TUBA3D, and their regulatory partners on other chromosomes associated with cardiovascular disorders, atrial and ventricular septal defects. There is strong indication of involving FOXO1 (Forkhead Box O1) gene—a strong transcription factor present on chr13, interacting with many septal defects link genes. The study was extended using molecular docking to find a potential drug lead for overexpressed FOXO1 inhibition. The phenothiazine and trifluoperazine showed efficiency to inhibit overexpressed FOXO1 protein, and could be potential drugs for PS/trisomy13 after validation.
Blood‒Brain Barrier Pathology and CNS Outcomes in Streptococcus pneumoniae Meningitis
Authors: Yau Belinda , Hunt Nicholas H. , Mitchell Andrew J. , Too Lay Khoon
Published: November 2018

Streptococcus pneumoniae is a major meningitis-causing pathogen globally, bringing about significant morbidity and mortality, as well as long-term neurological sequelae in almost half of the survivors. Subsequent to nasopharyngeal colonisation and systemic invasion, translocation across the blood‒brain barrier (BBB) by S. pneumoniae is a crucial early step in the pathogenesis of meningitis. The BBB, which normally protects the central nervous system (CNS) from deleterious molecules within the circulation, becomes dysfunctional in S. pneumoniae invasion due to the effects of pneumococcal toxins and a heightened host inflammatory environment of cytokines, chemokines and reactive oxygen species intracranially. The bacteria‒host interplay within the CNS likely determines not only the degree of BBB pathological changes, but also host survival and the extent of neurological damage. This review explores the relationship between S. pneumoniae bacteria and the host inflammatory response, with an emphasis on the BBB and its roles in CNS protection, as well as both the acute and long-term pathogenesis of meningitis.
Editorial for the Special Issue “Dietary Fibre: New Insights on Biochemistry and Health Benefits”
Authors: Van der Kamp Jan Willem , Harris Philip J
Published: November 2018

When the term dietary fibre was first coined, over sixty years ago, it only referred to plant cell walls in the diet. [...]
QTL Mapping Reveals the Relationship between Pasting Properties and Malt Extract in Barley
Authors: Wang Junmei , Yang Jianming , Hua Wei , Wu Xiaojian , Zhu Jinghuan , Shang Yi , Zhou Meixue
Published: November 2018

Pasting properties are important characteristics of barley starch from a processing standpoint. Many studies reported the close relationship between pasting properties and malting quality, especially malt extract. However, most conclusions were derived from the correlation between pasting properties and malting quality using a set of cultivars or breeding lines. In this study, a doubled haploid population of 150 lines from a cross between a Japanese malting barley and a Chinese feed barley was grown in four different environments (two sites × two years). Based on average values from all different environments, 17 significant quantitative trait loci (QTL) were identified for pasting properties. The genetic variance explained by these QTL varied from 7.0 to 23.2%. Most QTL controlling pasting properties were located on 1H, 2H, 5H, and 7H. Results confirmed the linkage between pasting properties and malt extract, with most of the QTL for pasting properties becoming nonsignificant when using malt extract as a covariate. Breakdown showed the closest correlation with malt extract. Molecular markers closely linked to the QTL can be used to select desired pasting properties to improve malting quality.
IL-24 Promotes Apoptosis through cAMP-Dependent PKA Pathways in Human Breast Cancer Cells
Authors: Persaud Leah , Mighty Jason , Zhong Xuelin , Francis Ashleigh , Mendez Marifer , Muharam Hilal , Redenti Stephen M. , Das Dibash , Aktas Bertal Huseyin , Sauane Moira
Published: November 2018

Interleukin 24 (IL-24) is a tumor-suppressing protein, which inhibits angiogenesis and induces cancer cell-specific apoptosis. We have shown that IL-24 regulates apoptosis through phosphorylated eukaryotic initiation factor 2 alpha (eIF2α) during endoplasmic reticulum (ER) stress in cancer. Although multiple stresses converge on eIF2α phosphorylation, the cellular outcome is not always the same. In particular, ER stress-induced apoptosis is primarily regulated through the extent of eIF2α phosphorylation and activating transcription factor 4 (ATF4) action. Our studies show for the first time that cyclic adenosine monophosphate (cAMP)-dependent protein kinase A (PKA) activation is required for IL-24-induced cell death in a variety of breast cancer cell lines and this event increases ATF4 activity. We demonstrate an undocumented role for PKA in regulating IL-24-induced cell death, whereby PKA stimulates phosphorylation of p38 mitogen-activated protein kinase and upregulates extrinsic apoptotic factors of the Fas/FasL signaling pathway and death receptor 4 expression. We also demonstrate that phosphorylation and nuclear import of tumor suppressor TP53 occurs downstream of IL-24-mediated PKA activation. These discoveries provide the first mechanistic insights into the function of PKA as a key regulator of the extrinsic pathway, ER stress, and TP53 activation triggered by IL-24.
Transcriptome Analysis Provides Insights into the Markers of Resting and LPS-Activated Macrophages in Grass Carp (Ctenopharyngodon idella)
Authors: Hu Yazhen , Wei Xiaolei , Liao Zhiwei , Gao Yu , Liu Xiaoling , Su Jianguo , Yuan Gailing
Published: November 2018

Macrophages are very versatile immune cells, with the characteristics of a proinflammatory phenotype in response to pathogen-associated molecular patterns. However, the specific activation marker genes of macrophages have not been systematically investigated in teleosts. In this work, leukocytes (WBC) were isolated using the Percoll gradient method. Macrophages were enriched by the adherent culture of WBC, then stimulated with lipopolysaccharide (LPS). Macrophages were identified by morphological features, functional activity and authorized cytokine expression. Subsequently, we collected samples, constructed and sequenced transcriptomic libraries including WBC, resting macrophage (Mø) and activated macrophage (M(LPS)) groups. We gained a total of 20.36 Gb of clean data including 149.24 million reads with an average length of 146 bp. Transcriptome analysis showed 708 differential genes between WBC and Mø, 83 differentially expressed genes between Mø and M(LPS). Combined with RT-qPCR, we proposed that four novel cell surface marker genes (CD22-like, CD63, CD48 and CD276) and two chemokines (CXCL-like and CCL39.3) would be emerging potential marker genes of macrophage in grass carp. Furthermore, CD69, CD180, CD27, XCL32a.2 and CXCL8a genes can be used as marker genes to confirm whether macrophages are activated. Transcriptome profiling reveals novel molecules associated with macrophages in C. Idella, which may represent a potential target for macrophages activation.
The Protective Role of Dormant Origins in Response to Replicative Stress
Authors: Courtot Lilas , Hoffmann Jean-Sébastien , Bergoglio Valérie
Published: November 2018

Genome stability requires tight regulation of DNA replication to ensure that the entire genome of the cell is duplicated once and only once per cell cycle. In mammalian cells, origin activation is controlled in space and time by a cell-specific and robust program called replication timing. About 100,000 potential replication origins form on the chromatin in the gap 1 (G1) phase but only 20–30% of them are active during the DNA replication of a given cell in the synthesis (S) phase. When the progress of replication forks is slowed by exogenous or endogenous impediments, the cell must activate some of the inactive or “dormant” origins to complete replication on time. Thus, the many origins that may be activated are probably key to protect the genome against replication stress. This review aims to discuss the role of these dormant origins as safeguards of the human genome during replicative stress.
Pretreatment with NaCl Promotes the Seed Germination of White Clover by Affecting Endogenous Phytohormones, Metabolic Regulation, and Dehydrin-Encoded Genes Expression under Water Stress
Authors: Cao Yiqin , Liang Linlin , Cheng Bizhen , Dong Yue , Wei Jiaqi , Tian Xiaolan , Peng Yan , Li Zhou
Published: November 2018

This study was designed to examine the effects of NaCl pretreatment on the seed germination of white clover (Trifolium repens cv. Ladino) under water stress induced by 19% polyethylene glycol (PEG) 6000. Lower concentrations of NaCl (0.5, 1, and 2.5 mM) pretreatment significantly alleviated stress-induced decreases in germination percentage, germination vigor, germination index, and radicle length of seedlings after seven days of germination under water stress. The soaking with 1 mM of NaCl exhibited most the pronounced effects on improving seed germination and alleviating stress damage. NaCl-induced seeds germination and growth could be associated with the increases in endogenous gibberellic acid (GA) and indole-3-acetic acid (IAA) levels through activating amylases leading to improved amylolysis under water stress. Seedlings pretreated with NaCl had a significantly lower osmotic potential than untreated seedlings during seed germination, which could be related to significantly higher soluble sugars and free proline content in NaCl-treated seedlings under water stress. For antioxidant metabolism, NaCl pretreatment mainly improved superoxide dismutase, peroxidase, ascorbate peroxidase, and glutathione reductase activities, transcript levels of FeSOD, APX, and DHAR, and the content of ascorbic acid, reduced glutathione, and oxidized glutathione during seed germination under water stress. The results indicated that seeds soaking with NaCl could remarkably enhance antioxidant metabolism, thereby decreasing the accumulation of reactive oxygen species and membrane lipid peroxidation during germination under water stress. In addition, NaCl-upregulated dehydrin-encoded genes SK2 expression could be another important mechanism of drought tolerance during seeds germination of white clover in response to water stress.
The Melting Diagram of Protein Solutions and Its Thermodynamic Interpretation
Authors: Tompa Kálmán , Bokor Mónika , Tompa Péter
Published: November 2018

Here we present a novel method for the characterization of the hydration of protein solutions based on measuring and evaluating two-component wide-line 1H NMR signals. We also provide a description of key elements of the procedure conceived for the thermodynamic interpretation of such results. These interdependent experimental and theoretical treatments provide direct experimental insight into the potential energy surface of proteins. The utility of our approach is demonstrated through the examples of two proteins of distinct structural classes: the globular, structured ubiquitin; and the intrinsically disordered ERD10 (early response to dehydration 10). We provide a detailed analysis and interpretation of data recorded earlier by cooling and slowly warming the protein solutions through thermal equilibrium states. We introduce and use order parameters that can be thus derived to characterize the distribution of potential energy barriers inhibiting the movement of water molecules bound to the surface of the protein. Our results enable a quantitative description of the ratio of ordered and disordered parts of proteins, and of the energy relations of protein–water bonds in aqueous solutions of the proteins.
Revisiting Bacterial Ubiquitin Ligase Effectors: Weapons for Host Exploitation
Authors: Pisano Antonio , Albano Francesco , Vecchio Eleonora , Renna Maurizio , Scala Giuseppe , Quinto Ileana , Fiume Giuseppe
Published: November 2018

Protein ubiquitylation plays a central role in eukaryotic cell physiology. It is involved in several regulatory processes, ranging from protein folding or degradation, subcellular localization of proteins, vesicular trafficking and endocytosis to DNA repair, cell cycle, innate immunity, autophagy, and apoptosis. As such, it is reasonable that pathogens have developed a way to exploit such a crucial system to enhance their virulence against the host. Hence, bacteria have evolved a wide range of effectors capable of mimicking the main players of the eukaryotic ubiquitin system, in particular ubiquitin ligases, by interfering with host physiology. Here, we give an overview of this topic and, in particular, we detail and discuss the mechanisms developed by pathogenic bacteria to hijack the host ubiquitination system for their own benefit.
Revisiting the Role of Ethylene and N-End Rule Pathway on Chilling-Induced Dormancy Release in Arabidopsis Seeds
Authors: Wang Xu , Yesbergenova-Cuny Zhazira , Biniek Catherine , Bailly Christophe , El-Maarouf-Bouteau Hayat , Corbineau Françoise
Published: November 2018

Dormant Arabidopsis (Arabidopsis thaliana) seeds do not germinate easily at temperatures higher than 10–15 °C. Using mutants affected in ethylene signaling (etr1, ein2 and ein4) and in the N-end-rule pathway of the proteolysis (prt6 and ate1-ate2) we have investigated the effects of cold and ethylene on dormancy alleviation. Ethylene (10–100 ppm) and 2–4 days chilling (4 °C) strongly stimulate the germination of wild type (Col-0) seeds at 25 °C. Two to four days of chilling promote the germination at 25 °C of all the mutants suggesting that release of dormancy by cold did not require ethylene and did not require the N-end-rule pathway. One mutant (etr1) that did not respond to ethylene did not respond to GA3 either. Mutants affected in the N-end rule (prt6 and ate1-ate2) did not respond to ethylene indicating that also this pathway is required for dormancy alleviation by ethylene; they germinated after chilling and in the presence of GA3. Cold can activate the ethylene signaling pathway since it induced an accumulation of ETR1, EINI4, and EIN2 transcripts, the expression of which was not affected by ethylene and GA3. Both cold followed by 10 h at 25 °C and ethylene downregulated the expression of PRT6, ATE1, ATE2, and of ABI5 involved in ABA signaling as compared to dormant seeds incubated at 25 °C. In opposite, the expression of RGA, GAI, and RGL2 encoding three DELLAs was induced at 4 °C but downregulated in the presence of ethylene.
Label-Free Quantitative Proteomics in a Methylmalonyl-CoA Mutase-Silenced Neuroblastoma Cell Line
Authors: Costanzo Michele , Cevenini Armando , Marchese Emanuela , Imperlini Esther , Raia Maddalena , Del Vecchio Luigi , Caterino Marianna , Ruoppolo Margherita
Published: November 2018

Methylmalonic acidemias (MMAs) are inborn errors of metabolism due to the deficient activity of methylmalonyl-CoA mutase (MUT). MUT catalyzes the formation of succinyl-CoA from methylmalonyl-CoA, produced from propionyl-CoA catabolism and derived from odd chain fatty acids β-oxidation, cholesterol, and branched-chain amino acids degradation. Increased methylmalonyl-CoA levels allow for the presymptomatic diagnosis of the disease, even though no approved therapies exist. MMA patients show hyperammonemia, ketoacidosis, lethargy, respiratory distress, cognitive impairment, and hepatomegaly. The long-term consequences concern neurologic damage and terminal kidney failure, with little chance of survival. The cellular pathways affected by MUT deficiency were investigated using a quantitative proteomics approach on a cellular model of MUT knockdown. Currently, a consistent reduction of the MUT protein expression was obtained in the neuroblastoma cell line (SH-SY5Y) by using small-interfering RNA (siRNA) directed against an MUT transcript (MUT siRNA). The MUT absence did not affect the cell viability and apoptotic process in SH-SY5Y. In the present study, we evaluate and quantify the alterations in the protein expression profile as a consequence of MUT-silencing by a mass spectrometry-based label-free quantitative analysis, using two different quantitative strategies. Both quantitative methods allowed us to observe that the expression of the proteins involved in mitochondrial oxido-reductive homeostasis balance was affected by MUT deficiency. The alterated functional mitochondrial activity was observed in siRNA_MUT cells cultured with a propionate-supplemented medium. Finally, alterations in the levels of proteins involved in the metabolic pathways, like carbohydrate metabolism and lipid metabolism, were found.
Large-Scale Simulation of the Phenotypical Variability Induced by Loss-of-Function Long QT Mutations in Human Induced Pluripotent Stem Cell Cardiomyocytes
Authors: Paci Michelangelo , Casini Simona , Bellin Milena , Hyttinen Jari , Severi Stefano
Published: November 2018

Loss-of-function long QT (LQT) mutations inducing LQT1 and LQT2 syndromes have been successfully translated to human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) used as disease-specific models. However, their in vitro investigation mainly relies on experiments using small numbers of cells. This is especially critical when working with cells as heterogeneous as hiPSC-CMs. We aim (i) to investigate in silico the ionic mechanisms underlying LQT1 and LQT2 hiPSC-CM phenotypic variability, and (ii) to enable massive in silico drug tests on mutant hiPSC-CMs. We combined (i) data of control and mutant slow and rapid delayed rectifying K+ currents, IKr and IKs respectively, (ii) a recent in silico hiPSC-CM model, and (iii) the population of models paradigm to generate control and mutant populations for LQT1 and LQT2 cardiomyocytes. Our four populations contain from 1008 to 3584 models. In line with the experimental in vitro data, mutant in silico hiPSC-CMs showed prolonged action potential (AP) duration (LQT1: +14%, LQT2: +39%) and large electrophysiological variability. Finally, the mutant populations were split into normal-like hiPSC-CMs (with action potential duration similar to control) and at risk hiPSC-CMs (with clearly prolonged action potential duration). At risk mutant hiPSC-CMs carried higher expression of L-type Ca2+, lower expression of IKr and increased sensitivity to quinidine as compared to mutant normal-like hiPSC-CMs, resulting in AP abnormalities. In conclusion, we were able to reproduce the two most common LQT syndromes with large-scale simulations, which enable investigating biophysical mechanisms difficult to assess in vitro, e.g., how variations of ion current expressions in a physiological range can impact on AP properties of mutant hiPSC-CMs.
Potential Causes of Titanium Particle and Ion Release in Implant Dentistry: A Systematic Review
Authors: Delgado-Ruiz Rafael , Romanos Georgios
Published: November 2018

Implant surface characteristics, as well as physical and mechanical properties, are responsible for the positive interaction between the dental implant, the bone and the surrounding soft tissues. Unfortunately, the dental implant surface does not remain unaltered and changes over time during the life of the implant. If changes occur at the implant surface, mucositis and peri-implantitis processes could be initiated; implant osseointegration might be disrupted and bone resorption phenomena (osteolysis) may lead to implant loss. This systematic review compiled the information related to the potential sources of titanium particle and ions in implant dentistry. Research questions were structured in the Population, Intervention, Comparison, Outcome (PICO) framework. PICO questionnaires were developed and an exhaustive search was performed for all the relevant studies published between 1980 and 2018 involving titanium particles and ions related to implant dentistry procedures. Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed for the selection and inclusion of the manuscripts in this review. Titanium particle and ions are released during the implant bed preparation, during the implant insertion and during the implant decontamination. In addition, the implant surfaces and restorations are exposed to the saliva, bacteria and chemicals that can potentially dissolve the titanium oxide layer and, therefore, corrosion cycles can be initiated. Mechanical factors, the micro-gap and fluorides can also influence the proportion of metal particles and ions released from implants and restorations.