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Tatiana Mamontova,
Elena Lukasheva,
Gregory Mavropolo-Stolyarenko,
Carsten Proksch,
Tatiana Bilova,
Ahyoung Kim,
Vladimir Babakov,
Tatiana Grishina,
Wolfgang Hoehenwarter,
Sergei Medvedev,
Galina Smolikova,
Andrej Frolov
Biology, Plant Sciences; chlorophylls; LC-MS-based proteomics; pea (Pisum sativum L.); proteome functional annotation; proteome map; seeds; seed proteomics
Online: 13 December 2018 (14:09:06 CET)
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Due to low culturing costs and high seed protein contents, legumes represent the main global source of food protein. Pea (Pisum sativum L.) is one of the major economically important legume crops, impacting both animal feed and human nutrition. Therefore, the quality of pea seeds needs to be ensured in the context of sustainable crop production and nutritional efficiency. Obviously, changes in seed protein patterns might directly affect both of these aspects. Thus, here we address the pea seed proteome in more detail and provide, to the best of our knowledge, the most comprehensive annotation of the functions and intracellular localization of pea seed proteins. Accordingly, 1938 and 1989 non-redundant proteins were identified in yellow and green pea seeds, in total. Only 35 and 44 proteins, respectively, could be additionally identified after protamine sulfate precipitation (PSP) potentially indicating the high efficiency of our experimental workflow. In total 981 protein groups could be assigned to 34 functional classes, which were to a large extent differentially represented in yellow and green seeds. Closer analysis of these differences by processing of the data in KEGG and String databases revealed their possible relation to a higher metabolic status and reduced longevity of green seeds.
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Guangyi Fan,
Jianwei Chen,
Tao Jin,
Chengcheng Shi,
Xiao Du,
He Zhang,
Yaolei Zhang,
Hanbo Li,
Ting Luo,
Pengxu Yan,
Guang Liu,
Xiangqun Chi,
Xiaoxuan Tan,
Liangwei Li,
Guilin Liu,
Xiaochuan Liu,
Shijie Hao,
Kai Han,
Xiaoyun Huang,
Shuai Sun,
Jing Zhou,
Mengjun Yu,
Lingfeng Meng,
Yue Chang,
Rui Zhang,
Kaiqiang Liu,
Mengqi Zhang,
Yong Zhao,
Chang Li,
Jiao Guo,
Xinyu Guo,
Jiahao Wang,
Meiqi Lv,
Haoyang Gao,
Yujie Liu,
Yue Song,
Shengjun Wang,
Yang Deng,
Binjie Ouyang,
Jinzhong Lin,
Yingjia Yu,
lynn Fink,
Xianwei Yang,
Xun Xu,
Xin Liu
Biology, Ecology; Marine microorganisms, marine fungi, algae, marine plants, marine invertebrates, marine vertebrates, genome, metagenome
Online: 12 December 2018 (15:44:09 CET)
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With the continuing development of sequencing technology, genomics has been applied in a variety of biological research areas. In particular, the application of genomics to marine species, which boast a high diversity, promises great scientific and industrial potential. Significant progress has been made in marine genomics especially over the past few years. Consequently, BGI, leveraging its prominent contributions in genomics research, established BGI-Qingdao, an institute specifically aimed at exploring marine genomics. In order to accelerate marine genomics research and related applications, BGI-Qingdao initiated the International Conference on Genomics of the Ocean (ICG-Ocean) to develop international collaborations and establish a focused and coherent global research plan. Last year, the first ICG-Ocean conference was held in Qingdao, China, during which 47 scientists in marine genomics from all over the world reported on their research progress to an audience of about 300 attendees. This year, we would like to build on that success, drafting a report on marine genomics to draw global attention to marine genomics. We summarized the recent progress, proposed future directions, and we would like to enable additional profound insights on marine genomics. Similar to the annual report on plant and fungal research by Kew Gardens, and the White Paper of ethical issues on experimental animals, we hope our first report on marine genomics can provide some useful insights for researchers, funding agencies as well as industry, and that future versions will expand upon the foundation established here in both breadth and depth of knowledge.This report summarizes the recent progress in marine genomics in six parts including: marine microorganisms, marine fungi, marine algae and plants, marine invertebrates, marine vertebrates and genomics-based applications.
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Biology, Ecology; Keywords: ammonia oxidation; ammonia-oxidizing archaea; ammonia-oxidizing bacteria; gene function stream; nitrification.
Online: 12 December 2018 (15:34:15 CET)
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Ammonia-oxidizing microorganism communities are abundant and functionally efficacious in nitrification. However, ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) groups complicate this process in subtropical streams. This study investigates the abundance of ammonia-oxidizing communities south of the Dabie Mountains, China, using quantitative polymerase chain reaction (qPCR). Clone libraries were utilized to analyze the abundance and microbial structures of AOA and AOB in sediments. Such analysis may provide strong evidence reflecting the links within the environment. The results show that AOB had a lower abundance of copies of the ammonia-oxidizing gene (amoA) than AOA. Interestingly, the AOA and AOB community compositions were correlated with ecological characteristics. The dissolved oxygen (DO) and oxidation-reduction potential (ORP) had significant positive correlations, whereas the phosphorus within the structure had a negative correlation with the abundance of both groups. Our study shows that it might adopt some species related to Nitrosotalea clusters that can resist comparably higher pH (toward pH 6.5). Together, these results imply that the physiological adaptation of microbial guilds to environmental pressures in ammonia-oxidizing archaea might allow them to have a more substantial function of ammonia-oxidizing communities in natural habitats.
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Biology, Ecology; Peripatidae, conservation status, survival, urban populations, threatened species
Online: 12 December 2018 (14:07:09 CET)
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ABSTRACT: Charismatic species, like the panda, play an important role in conservation, and velvet worms arguably are charismatic worms. Thanks to their extraordinary hunting mechanism, they have inspired from a female metal band in Japan, to origami worms in Russia and video game monsters in the USA. Objective: To assess their conservation status in Costa Rica. Methods: we located all collection records of the 29 known species from the Onychophora Database in the map of the Costa Rican Conservation Network. Results: We found that seven species are protected inside forest reserves, five in Protected Zones, four in Wildlife Refuges, two in National Parks and one, Principapillatus hitoyensis, in a strictly pristine Biological Reserve. The largest species in the world, Peripatus solorzanoi, occurs both inside a Forest Reserve and in protected private land. Protection inside Costa Rican nature areas is enforced year round by personnel that includes armed guards, and is supported by educational programs in surrounding communities. Twelve species have not been found in protected areas, but in Costa Rica, all biological species, named and unnamed, are protected by law and cannot be legally collected, or exported, without technically issued permits. Conclusion: Like in the only other country with similar information (New Zealand), the conservation of onychophorans seems to be of least concern for at least two thirds of the known species. Epiperipatus isthmicola, recently rediscovered after a century of absence in collections, can be considered Threatened because nearly all of its natural habitat has now been covered by a city.
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Biology, Plant Sciences; phytohormone; transcriptional regulation; apical hook; root elongation; lateral root development; root hair formation; mathematical modeling
Online: 11 December 2018 (13:50:45 CET)
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Auxin and ethylene pathways cooperatively regulate a variety of developmental processes in plants. Growth responses to ethylene are largely dependent on auxin, the key regulator of plant morphogenesis. Auxin, in turn, is capable of inducing ethylene biosynthesis and signaling making the interaction of these hormones reciprocal. Recent studies discovered a bunch of molecular events underlying auxin-ethylene crosstalk. In this review, we summarize the results of fine-scale and large-scale experiments on interaction of auxin and ethylene pathways in Arabidopsis. We integrate the knowledge on the molecular crosstalk events, their tissue specificity and associated phenotypic responses to decipher the crosstalk mechanisms at a systems level. We also discuss the prospects of applying systems biology approaches to study the mechanisms of crosstalk between plant hormones.
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Biology, Animal Sciences & Zoology; Methionine, milk protein synthesis, proteome, HMBi
Online: 11 December 2018 (09:45:41 CET)
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This study was conducted to investigate the effect of supplementing different types of methionine (L and D-type) and its precursor (HMBi) on milk protein synthesis using immortalized bovine mammary epithelial cell line (MAC-T Cell); D-methionine (D-Met), L-methionine (L-met) and 2-hydroxy-4-methylthiobutanoic acid I (HMBi), an isopropyl ester of the hydroxy analogue precursor of methionine. The underlying mechanism of milk protein synthesis by adding D- and L-type amino acid as well as HMBi was elucidated through omics analysis to verify the metabolism pathway. Results showed that HMBi group showed the highest beta casein mRNA expression levels compared to D- and L-Met groups and highest medium protein although not different with the L-Met treatment. The observed upregulated (>2 protein expression vs. control) and downregulated (<0.5 protein expression vs. control) proteins in L-Met, D-Met and HMBi treated groups were: 39, 77; 46, 68; and 40, 78, respectively. Interestingly, based on protein pathway analysis, L-Met treated group stimulated the ATP synthesis, PI3 kinase and pyruvate metabolism. On the other hand, the D-Met group stimulated fructose-galactose metabolism, glycolysis pathway, PI3 kinase and pyruvate metabolism. And lastly HMBi-treated group stimulated pentose phosphate pathway and glycolysis pathway. Metabolite analysis revealed that L-Met treated group resulted in the increase in 11 metabolites. On the other hand, D-Met treated group showed increase in 7 metabolites and decreased of uridine monophosphate (UMP). HMBi supplementation caused increases of 3 metabolites and decreased of UMP and N-acetyl-L-glutamate Addition of different isoforms of Met stimulated the production of intermediate metabolites for energy production. Addition of L-Met stimulated the production of energy metabolites such as pyruvate, malate, and fumarate, well-known as intermediates of Krebs cycle. On the other hand, HMBi supplementation resulted in increases of energy metabolite glucose 1-phosphate and 6-phosphogluconate. Results showed that HMBi-treated group exhibited highest expression of β-casein mRNA expression by stimulating proteins and metabolites as well as protein and metabolic pathways involved in protein and energy synthesis. As a result, HMBi-treated group resulted in highest protein concentration but not significantly different with L-Met. Both the D- and L-isoforms has considerably the same medium protein concentration and β-casein mRNA expression higher than the control. So, D- and L-Met isoforms can be used alternatively without any significant change in protein synthesis efficiency in bovine mammary epithelial cells.
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Biology, Other; radioresistance; DNA-damage recognition; CRISPRa; multiplex overexpression
Online: 11 December 2018 (09:27:42 CET)
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Current understanding of mechanisms of cellular resistance to genotoxic stress is incomplete but is critical for a variety of medical applications. Recent developments in the CRISPR/Cas technologies open new opportunities for targeted interrogation of resistance genes and pathways. In the present work, we used nuclease dead Cas9 constructs to achieve targeted overexpression of endogenous genes encoding two essential subunits of DNA damage sensor complex, XPC and HR23B, in HEK293T cells. Both individual and simultaneous overexpression of the two genes was achieved and the effects on cellular resistance to ionizing radiation and paraquat was examined. Using the fluorometric microculture cytotoxicity assay, we showed that simultaneous, but not separate overexpression of the two genes lead to a 30% increase in survivability. Irradiated cells that overexpressed both XPC and HR23B genes showed higher clonogenic capacity and proliferation rate compared to the irradiated transfection control as revealed by the clonogenic survival assay. Modulation of the gene expression did not affect cell resistance to paraquat. In summary, our results demonstrate a high potential of CRISPR/dCas9-enabled multiplex overexpression of stress-response genes in functionally justified combinations, exemplified here by the XPC-HR23B complex, for achieving an enhanced cellular radioresistance.
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Biology, Other; Photosynthesis, Photosystem, Water oxidation, Oxygenic, Anoxygenic, Reaction centre
Online: 6 December 2018 (14:06:10 CET)
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Sam Granick opened his seminal 1957 paper titled Speculations on the Origins and Evolution of Photosynthesis with the assertion that there is a constant urge in human beings to seek beginnings (I concur). This urge has led to an incessant stream of speculative ideas and debates on the evolution of photosynthesis that started in the first half of the twentieth century and shows no signs of abating. Some of these speculative ideas have become common place, are taken as fact, but find little support. Here I review and scrutinise three widely accepted ideas that underpin the current study of the evolution of photosynthesis: firstly, that the photochemical reaction centres used in anoxygenic photosynthesis are more primitive than those in oxygenic photosynthesis; secondly, that the probability of acquiring photosynthesis via horizontal gene transfer is greater than the loss of photosynthesis; and thirdly, and most importantly, that the origin of anoxygenic photosynthesis predates the origin of oxygenic photosynthesis. I shall attempt to demonstrate that these three ideas are often grounded on incorrect assumptions built on more assumptions with no experimental nor observational support. I hope that this brief review will not only serve as cautionary tale, but also that it will open new avenues of research aimed at disentangling the complex evolution of photosynthesis and its impact on the early history of life and the planet.
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Biology, Ecology; mixture toxicity; concentration addition; pesticide; pharmaceuticals; Aliivibrio fischeri
Online: 6 December 2018 (11:08:43 CET)
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This work introduced the potential synergistic toxicity of binary mixtures of pesticides and pharmaceuticals, which have been substantially detected in major river basins in South Korea. Different dose-response curve functions were employed in each experimental toxicity dataset for Aliivibrio fischeri. We tested the toxicity of 30 binary mixtures at two effect concentrations: high effect concentration [EC50] and low effect concentration [EC10] ranges. Thus, the toxicological interactions were evaluated at 60 effected concentration data points in total and based on model deviation ratios (MDRs) between predicted and observed toxicity values (e.g., three types of combined effects: synergistic (MDR > 2), additive (0.5 ≤ MDR ≤ 2), and antagonistic (MDR < 0.5)). From the 60 data points, MDRs could not be applied to 17 points, since their toxicities could not be measured. The result showed 48 %-additive (n = 20), 40 %-antagonistic (n = 17), and 12 %-synergistic (n = 6) toxicity effects from 43 binaries (excluding the 17 combinations without MDRs). In this study, EC10 ratio mixtures at a low overall effect range showed a general tendency to have more synergistic effects than the EC50 ratio mixtures at a high effect range. We also found an inversion phenomenon, which detected three binaries of the combination of synergism at low concentrations and additive antagonism at high concentrations.
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Biology, Ecology; post-mining regeneration; succession; tropical dry forest; post-mining recovery
Online: 6 December 2018 (11:04:06 CET)
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Open pit mining is a common activity in the Yucatan peninsula for the extraction of limestone. This mining is known under the generic name of quarries, and regionally as sascaberas (sascab=white soil in Mayan language). These areas are characterized by the total removal of the natural vegetation cover and soil in order to have access to the calcareous material. The present study shows the composition and structure of the vegetation in five quarries after approximately ten years of abandonment, and the conserved vegetation near to each one of the quarries in southeastern Quintana Roo. Using a canonical correspondence analysis (CCA), the distribution of the species was determined in relation to the edaphic variables: soil depth, percentage of organic matter (OM), cationic exchange capacity (CEC), pH and texture. 26 families, 46 genera and 50 species were recorded in the quarries and 25 families, 45 genera and 47 species were recorded in the conserved areas. The dominant species in the quarries belong to the families Poaceae, Fabaceae, Rubiaceae and Anacardiaceae. The quarries with higher values of OM (1.63%), CEC (24.05 Cmol/kg), depth (11 cm) and sand percentage (31.33%) include the following species like Lysiloma latisiliquum, Metopium brownei and Bursera simaruba which are commonly found in secondary forests. On the other hand, quarries with lower values of OM (0.39%), CEC (16.58 Cmol/kg) and depth (5.02), and higher percentage of silt (42.44%) were dominated by herbaceous species belonging to the Poaceae family and by Borreria verticillata, which are typical in disturbed areas of southeastern Mexico. In all cases, the pH was slightly alkaline due to the content of calcium carbonate (CaCO3), characteristic of the soils of the region. The edaphic variables are significantly correlated with the development and distribution of vegetation, and with the structure of the communities.
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Biology, Forestry; black timber bark beetle; biological invasion; Xyleborini; ambrosia beetle; spread; occurrence; ethanol; forest management
Online: 4 December 2018 (09:57:21 CET)
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The black timber bark beetle Xylosandrus germanus (Blandford) is an invasive ambrosia beetle originating from Southeastern Asia that has become successfully established within Europe and North America. Herein, we provide a review of the spread and distribution of this pest of trees and timber across Europe before and after 2000, along with a review of its habitat preferences. Since the spread of X. germanus across Europe has accelerated rapidly post-2000, emphasis is placed on this period. X. germanus was first recorded in Germany in 1951 and since then in 21 European countries along with Russia. Ethanol-baited traps were deployed in oak, beech, and spruce forest ecosystems in the Western Carpathians, Central Europe, Slovakia, to characterize the distribution and habitat preference of this non-native ambrosia beetle. Captures of X. germanus within Slovakia have been rising rapidly since its first record in 2010, and now this species dominates captures of native ambrosia beetles. X. germanus has spread throughout the whole Slovakia from the south-southwest to the north-northeast over the period of 5–10 years and has also spread vertically into higher altitudes within this country. While living but weakened trees in Europe and North America are attacked by X. germanus, the greatest negative impact within Slovakia is attacks on recently felled logs of oak, beech and spruce trees providing high quality timber/lumber. We suggest that the recent rapid spread of X. germanus in Central Europe is being facilitated by environmental changes, specifically global warming, and the increasing frequency of timber trade. Recommendations for management of X. germanus in forest ecosystems are proposed and discussed, including early detection, monitoring, sanitary measures, etc.
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Biology, Agricultural Sciences & Agronomy; ROS; histochemical; superoxide; hydrogen peroxide
Online: 3 December 2018 (16:17:03 CET)
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The present protocol described staining protocol for Reactive Oxygen Species (ROS) in aromatic crop grown under nutrient stress through DAB and NBT histochemical method. Spearmint (Mentha spicata) were grown under manganese and salt toxicity stresses and after 10 and 20 days of the stress treatments, plants showed stunted growth. The morphological characteristics of leaves under stresses were observed. Manganese toxicity and salt stress induced the production of ROS. Accumulation of hydrogen peroxide was characterised as brown spots from the DAB polymerisation which were emerged and clearly observed in leaves from plant grown under 2.5 and 5 mM concentrations of manganese as well as 300 mM concentration of salt. Furthermore, accumulation of superoxide anion was characterised as blue pigments based upon the ability of cells to reduce NBT. Spearmint leaves showed the distribution of the blue pigment which was obviously observed under the 5 mM of manganese and 300 mM of salt. DAB and NBT staining method can be the rapid method to characterise ROS accumulation in plant cell under the abiotic stresses.
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Biology, Plant Sciences; stomatal movement; calcium sensing receptor; phosphorylation; abiotic stress; calcium signaling
Online: 3 December 2018 (14:02:28 CET)
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The calcium-sensing receptor (CAS), as a chloroplast thylakoid membrane protein, involved in the process of [Ca2+] ext-induced [Ca2+]cyt increase (CICI) in the plant. However, the underlying mechanism regulating this process is lacking. Furthermore, recent evidence suggests that CAS may perform additional roles in the plant. Here, we provide an update covering the multiple roles of CAS in stomatal movement regulation and calcium signaling in the plant. We also analysis the possible phosphorylation mechanism of CAS by light and discuss the role of CAS in abiotic stress (drought, salt stress) and biotic stresses (plant immune signaling). Finally, we provide a perspective for future experiments which are required to fill gaps in our understanding of the biological function of CAS in the plant.
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Biology, Other; Lactobacillus plantarum; phage; new genus; annotation; comparative genomics; phylogenetics; isolation; diversity
Online: 3 December 2018 (13:52:20 CET)
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Lactobacillus plantarum is a bacterium with promising applications to the food industry and agriculture and probiotic properties. So far, bacteriophages of this bacterium have been moderately addressed. We examined the morphology and diversity of five new L. plantarum phages via transmission electron microscopy, whole genome shotgun sequencing and in silico protein predictions. Moreover, we looked into their phylogeny and their potential genomic similarities to other complete phage genome records through extensive nucleotide and protein comparisons. The five phages share a high degree of similarity among them and belong to the family Myoviridae. They have a long genome of 137.973-141.344 bp, a G/C content of 36,3-36,6% that is quite distinct from their host’s, and, surprisingly, seven to 15 tRNAs. Only an average 35/174 of their predicted genes were assigned a function. Overall, the comparative analyses unraveled considerable genetic diversity for our five L. plantarum phages. Hence, the new genus “Semelevirus” was proposed, which comprises exclusively the five phages. This novel lineage of Lactobacillus phages provides further insight into the genetic heterogeneity of phages infecting Lactobacillus sp. Our results on Lactobacillus phages have a potential value for the development of anti-phage strategies as well as for the manipulation of L. plantarum fermentations.
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Biology, Other; colorectal cancer; differentially expressed genes; biomarkers; protein-protein interaction; reporter biomolecules; candidate drugs; systems biology; drug repositioning
Online: 3 December 2018 (09:33:34 CET)
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Background and objectives: Colorectal cancer (CRC) is the 2nd most cause of cancer related death in the world, but early diagnosis ameliorates the survival of CRC. This report directed to identify molecular biomarker signatures in CRC. Materials and Methods: We analyzed two microarray datasets (GSE35279 and GSE21815) to identify common differentially expressed genes (DEGs). We performed functional overrepresentation, pathway enrichment, protein-protein interaction (PPI), reporter biomolecules, survival, and drug repositioning analyses were done on common DEGs. Results: Total 727 up-regulated and 99 down-regulated DEGs were detected. The significantly enriched pathways PI3K-Akt signaling, Wnt signaling, ECM-interaction, cell cycles were identified. The 10 hub proteins (ADNP, CCND1, CD44, CDK4, CEBPB, CENPA, CENPH, CENPN, MYC, and RFC2) were selected as proteomic signatures from PPI network. Analyses revealed 10 reporter transcription factors (ETS1, ESR1, GATA1, GATA2, GATA3, AR, YBX1, FOXP3, E2F4, and PRDM14) and 2 reporter microRNAs (miR-193b-3p and miR-615-3p) as regulatory component. The prognostic power analysis revealed that hub proteins and reporter biomolecules related with worse survival of patients in CRC. Several candidate repositioned drugs including anti-neoplastic and immunomodulating agents were identified using Connectivity map (CMap) and geneXpharma tool. Conclusions: This study presents biomarker signatures at protein and RNA levels with prognostic capability in CRC. We think that the molecular signatures and candidate drugs presented in this study can be potential biomarkers and therapeutic target in CRC.
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Biology, Other; microtubule dynamics; mitosis; spindle; molecular motor protein
Online: 3 December 2018 (09:06:22 CET)
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Proper regulation of microtubules (MTs) is critical for the execution of diverse cellular processes, including mitotic spindle assembly and chromosome segregation. There are a multitude of cellular factors that regulate the dynamicity of MTs and play critical roles in mitosis. Members of the Kinesin-8 family of motor proteins act as MT-destabilizing factors to control MT length in a spatially and temporally regulated manner. In this review, we focus on recent advances in our understanding of the structure and function of the Kinesin-8 motor domain, and the emerging contributions of the C-terminal tail of Kinesin-8 proteins to regulate motor activity and localization.
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Biology, Plant Sciences; genomic selection; genomic prediction; genotyping by sequencing; pasmo resistance; pasmo severity; quantitative trait loci; single nucleotide polymorphism; Septoria linicola; flax
Online: 30 November 2018 (08:39:11 CET)
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Pasmo (Septoria linicola) is a fungal disease causing major losses in seed yield and quality, and stem fibre quality in flax. Pasmo resistance (PR) is quantitative and has low heritability. To improve PR breeding efficiency, the accuracy of genomic prediction (GP) was evaluated using a diverse worldwide core collection of 370 accessions. Four marker sets, including three defined by 500, 134, and 67 previously identified quantitative trait loci (QTL) and one of 52,347 PR-correlated genome-wide single nucleotide polymorphisms, were used to build ridge regression best linear unbiased prediction (RR-BLUP) models using pasmo severity (PS) data collected from field experiments performed during five consecutive years. With five-fold random cross-validation, GP accuracy as high as 0.92 was obtained from the models using the 500 QTL when the average PS was used as the training dataset. GP accuracy increased with training population size, reaching values >0.9 with training population size greater than 185. Linear regression of the observed PS with the number of positive-effect QTL in accessions provided an alternative GP approach with an accuracy of 0.86. The results demonstrate the GP models based on marker information from all identified QTL and the 5-year PS average is highly effective for PR prediction.
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Biology, Physiology; beta-alanine; carnosine; oxidative stress; antioxidant
Online: 28 November 2018 (07:53:09 CET)
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The objective of this study was to perform a systematic review and meta-analysis of the articles that addressed the effect BA or carnosine supplementation on Physical exercise (PE)-induced oxidative stress (OS). Before May 2018 we searched throughout PubMed, CAPES Periodic and SPORTDiscus human model peer review, randomized control studies with chronic BA or carnosine supplementation on PE-induced OS. A total of 128 citations were found. Only four articles met criteria for inclusion. All four studies used healthy young sedentary, recreationally active or athletic participants. After a chronic BA (~30 days) or carnosine (14 days) supplementation, the studies evaluated PE-induced OS both immediately and several hours after exercise (0.5 to 48 h). In response to PE-induced OS, when compared to placebo, BA/carnosine supplementation increased total antioxidant capacity [TAC; Effect Size (ES) = 0.35, 95% Confidence Interval (CI) 0.06 to 0.65, p = 0.02] and glutathione (GSH; ES = 0.75, 95% CI 0.32 to 1.19, p = 0.0007) concentrations while decreased direct OS markers (ES = −1.19, 95% CI −1.48 to −0.80, p < 0.01) and superoxide dismutase (SOD) activity (ES = −0.58, 95% CI −1.10 to −0.06, p = 0.03). BA or carnosine supplementation did not prevent the increase in indirect OS markers (ES: −0.20, 95% CI −0.59 to 0.20, p = 0.33). In humans, following PE-induced OS, initial treatment trials of BA or carnosine supplementation seemed to increase TAC and GSH concentrations, while decreasing SOD activity. Also, albeit mitigating the acute increase in direct OS species (reactive nitrogen and oxygen species), treatment did not decrease measured values of indirect OS markers (peroxidation or molecule oxidation).
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Biology, Physiology; viroid; pathogenicity; RNA silencing; Dicer-like proteins; small interfering RNA; microRNA398; microRNA398a-3p; superoxide dismutase 1; reactive oxygen species; systemic necrosis
Online: 28 November 2018 (06:50:07 CET)
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To examine the role of RNA silencing in defense against viroid, a Dicer-like 2 and 4 (DCL2&4)—double knockdown transgenic tomato line 72E was created. The expression of endogenous DCL2 and DCL4 in line 72E decreased to about a half of the empty cassette line EC. When challenged with potato spindle tuber viroid (PSTVd), 72E allowed significantly higher level of PSTVd accumulation early in infection and showed lethal systemic necrosis. The size distribution of PSTVd-derived small RNA was significantly changed: the numbers of 21 and 22 nucleotides (nt) species in line 72E was approximately 66.7% and 5% of those in line EC, respectively. Conversely, the numbers of 24-nt species increased by 1100%. Furthermore, expression of miR398a-3p and miR398 increased 770–868% in the PSTVd-infected 72E, compared to the PSTVd-infected EC. In parallel, superoxide dismutase (SOD1) in PSTVd-infected 72E showed higher expression levels. In concert with miR398a-3p, SOD1 controls detoxification of reactive oxygen species (ROS) generated in cells. Since high levels of ROS production and its scavenging activity were observed in PSTVd-infected 72E, the lack of full-activity of DCLs was thought to have made the plant incapable to control excessive ROS production and thus resulted in to develop lethal systemic necrosis.
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Biology, Other; HIV-1 assembly, Gag, single molecule microscopy, dynamics
Online: 26 November 2018 (14:12:08 CET)
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HIV-1 assembly is a complex mechanism taking place at the plasma membrane of the host cell. It requires nice spatial and temporal coordination to end up with a full immature virus. Researchers have extensively studied HIV-1 assembly molecular mechanism during the past decades, in order to dissect the respective roles of viral proteins, viral genome and host cell factors. Nevertheless, the time course of the process has been observed in living cells only a decade ago. The very recent revolution of optical microscopy, combining high speed and high spatial resolution now permit to study assemblies and their consequences at the single molecule level within (living) cells. In this review, after a short description of these new approaches, we will show how HIV-1 assembly in cells has been revisited using these advanced super resolution microscopy techniques and how much it could make a bridge in studying assembly from the single molecule to the host cell.
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Biology, Physiology; 3D printing; Bioprinting; Additive Manufacturing, Tissue Engineering, Blood Vessels, Vascular Grafting
Online: 26 November 2018 (11:39:44 CET)
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Abstract: The broad clinical use of synthetic vascular grafts for vascular diseases is limited by their thrombogenicity and low patency rate, especially for vessels with a diameter inferior to 6 mm. Alternatives such as tissue-engineered blood grafts (TEBGs) have gained increasing interest. Among the different manufacturing approaches, 3D bioprinting presents numerous advantages and enables the fabrication of multi-scale, multi-material, and multicellular tissues with heterogeneous and functional intrinsic structures. Extrusion-, inkjet- and light-based 3D printing techniques have been used for the fabrication of TEBG out of hydrogels, cells, and/or solid polymers. This review discusses the state-of-the-art research on the use of 3D printing for TEBG with a focus on the biomaterials and deposition methods.
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Longlong Li,
Yanling Zhu,
Jiajie Sun,
Ting Chen,
Junyi Luo,
Gang Shu,
Songbo Wang,
Xiaotong Zhu,
Qingyan Jiang,
Yongliang Zhang,
Qianyun Xi
Biology, Animal Sciences & Zoology; miR-125b-2; testis; PAP; reproduction; sperm; mitochondria
Online: 23 November 2018 (14:06:22 CET)
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microRNAs can cause male infertility by impacting sperm quality and impaired spermatogenesis. Since the miR-125 family plays an important role in regulating embryo development, but the function of miR-125b-2 in male reproduction remains unknown. In this study, we prepared a model of miR-125b knockout (KO) mice. Among the KO mice, the progeny test showed that litter sizes decreased significantly and the rate of non-parous females increased significantly (p<0.05). At the same time, the testosterone concentration increased significantly (p<0.01), with the remarkable decrease for estradiol (p<0.05). Moreover, sperm count decreased obviously (p<0.05) and the percentage of abnormal sperms increased significantly (p<0.01). Testicular transcriptome sequencing demonstrated that there were 173 up-regulated genes, including Papolb (PAP), and 151 down-regulated genes in KO mice compared with wild type (WT). KEGG and GO analysis showed many of these genes were involved in sperm mitochondrial metabolism and other cellular biological processes. Meanwhile, the sperm mitochondria DNA (mtDNA) copy number was increased significantly (p<0.01) in KO mice, but the integrity of mtDNA and nuclear DNA (nDNA) had no change. In the top 10 up-regulated genes, as a testis specific expressing gene, PAP can affect the process of spermatogenesis. Western blotting and Luciferase Assay validated that PAP was the target of miR-125b-5p. Intriguingly, we also found that both miR-125b and PAP were only highly expressed in germ cells (GC) instead of Leydig cells (LC) and Sertoli cells (SC), and miR-125b-5p could target PAP to regulate TM3 cell secretion of testosterone (p<0.05). Our study firstly demonstrated that miR-125b-2 could regulate testosterone secretion by directly targeting PAP and increase sperm mtDNA copy number to affect semen quality. The study indicated that miR-125b-2 had a positive influence on the reproductive performance of animal and could be a potential therapeutic target for male infertility.
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Biology, Agricultural Sciences & Agronomy; agriculture; kriging; land use; Nepal; soil nutrient variability
Online: 23 November 2018 (03:16:18 CET)
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A study was carried out in the eastern part of Dang district in Nepal to assess the variability of selected soil properties due to different land use and map their spatial distribution. Considering three land use types (agriculture, agroforestry, and grassland), a total of 120 samples were collected from surface soil (0 to 15 cm depth) in May 2015 and analyzed for soil fertility parameters: pH, organic matter (OM), nitrogen (N), phosphorus (P), potassium (K), boron (B), and zinc (Zn). Results revealed that the average value of soil pH significantly (P<0.05) varied from 7.05 in agroforestry to 7.53 in agriculture land use. Soil OM and N contents were medium in range in all land use with slight variation, the highest average OM and N found in grassland (2.87% and 0.14% respectively), followed by agriculture (2.64% and 0.13% respectively), and agroforestry (2.45% and 0.12% respectively). Further, the results showed significant variation for P among agroforestry (18.99 kg ha-1) and grassland (8.49 kg ha-1) while the K content was the highest for grassland (144 mg kg-1) and lowest for agriculture (120 mg kg-1). Micronutrients- B was low (0.28 to 0.35 mg kg-1) and Zn was very low (0.14 mg kg-1) in all land use. There is a need to add appropriate fertilizer N, P, B, and Zn to the soil in order to increase the fertility status under different land use. Spatial variability maps for soil chemical properties can be used by farmers and local planners to make effective soil management strategies.
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Biology, Ecology; Risk analysis, risk assessment, biological invasions, regulations, policy, risk management
Online: 22 November 2018 (14:44:57 CET)
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This report presents a framework for analysing the risk of alien taxa under South Africa's National Environmental Management: Biodiversity Act of 2004, and the Alien and Invasive Species Regulations of 2014. While the report was initially designed to meet a specific South Africa need, the risk analysis processes developed can, we believe, be transferred to any specified geographic region. In outlining a series of questions related to a taxon’s likelihood of invasion and the consequences thereof, i.e. the potential impacts, the report provides a structure for collating data relevant to the process of listing taxa as well as a process for developing recommendations that is both mathematically sound, transparent, and that explicitly takes uncertainty into account. The framework is based on collating information according to international standards in biological invasions (specifically the IUCN Environmental Impact Classification of Alien Taxa Scheme, the CBD's scheme for classifying invasion pathways, and the Unified Framework for Biological Invasions proposed by Blackburn et al. 2011). The risk analysis framework is currently being implemented in South Africa in an effort to underpin national regulatory lists of invasive species.
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Biology, Other; homologous recombination; RAD51 paralogs; BRCA1; BRCA2; RAD51B; RAD51C; RAD51D; XRCC2; XRCC3; Shu complex; cancer
Online: 22 November 2018 (06:49:34 CET)
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Accurate repair of DNA is critical for genome stability and cancer prevention. DNA double-strand breaks are one of the most toxic lesions and can be repaired using homologous recombination (HR). HR is a high-fidelity DNA repair pathway that uses a homologous template for repair. One central HR step is RAD51 nucleoprotein filament formation on the single-stranded DNA ends, a step required for the homology search and strand invasion steps of HR. RAD51 filament formation is tightly controlled by many positive and negative regulators, collectively termed the RAD51 mediators. The RAD51 mediators function to nucleate, elongate, stabilize, and disassemble RAD51 during repair. In model organisms, RAD51 paralogs are RAD51 mediator proteins that structurally resemble RAD51 and promote its HR activity. New functions for the RAD51 paralogs during replication and in RAD51 filament flexibility have recently been uncovered. Mutations in the human RAD51 paralogs (RAD51B, RAD51C, RAD51D, XRCC2, XRCC3, and SWSAP1) are found in a subset of breast and ovarian cancers. Despite their discovery three decades ago, few advances have been made in understanding the function of the human RAD51 paralogs. Here we discuss the current perspective on the RAD51 paralogs in vivo and in vitro function and their relationship with cancer in vertebrate models.
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Biology, Agricultural Sciences & Agronomy; dryland wheat; subsoiling; sowing date; nitrogen accumulation; nitrogen translocation; yield
Online: 21 November 2018 (04:51:17 CET)
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Dryland winter wheat in Loess Plateau is facing yield reduction due to shortage of soil moisture and delayed sowing time. Field experiment was conducted at Loess Plateau in Shanxi Province, China from 2012 to 2014, to study the effect of subsoiling and conventional tillage and different sowing dates on the soil water storage and contribution of N accumulation and remobilization to yield of winter wheat. The results showed that subsoiling significantly improved the soil water storage at 0-300 cm depth, improved the number of tillers and pre-anthesis N translocation in various organs of wheat and post-anthesis N accumulation, eventually increased the yield up to 17-36%. Delaying sowing time had reduced the soil water storage at sowing and winter accumulated temperature by about 180˚C. The contribution of N translocation to grain yield was maximum in glume+spike followed by in leaves and minimum by stem+sheath. In addition a close relationship was found between the N accumulation and translocation and the soil moisture in the 20-300 cm. Subsoiling during the fallow period and the medium sowing date was beneficial for improving the soil water storage and increased the N translocation to grain, thereby increasing the yield of wheat, especially in dry year.
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Biology, Animal Sciences & Zoology; color vision; cone photoreceptors; opponency; retina
Online: 20 November 2018 (11:14:49 CET)
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Vertebrate color vision is evolutionarily ancient. Jawless fish evolved four main spectral types of cone photoreceptor, almost certainly complemented by retinal circuits to process chromatic opponent signals. Subsequent evolution of photoreceptors and visual pigments are now documented for many vertebrate lineages and species, giving insight into evolutionary variation and ecological adaptation of color vision. We look at organization of the photoreceptor mosaic and the functions different types of cone in teleost fish, primates, and birds and reptiles. By comparison less is known about the underlying neural processing. Here we outline the diversity of vertebrate color vision and summarize our understanding of how spectral information picked up by animal photoreceptor arrays is adapted to natural signals. We then turn to the question of how spectral information is processed in the retina. Here, the quite well known and comparatively ‘simple’ system of mammals such as mice and primates reveals some evolutionarily conserved features such as the mammalian BlueON system which compares short and long wavelength receptors signals. We then survey our current understanding of the more complex circuits of fish, amphibians, birds and reptiles. Together, these clades make up more than 90% of vertebrate species, yet we know disturbingly little about their neural circuits for colour vision beyond the photoreceptors. Here, long-standing work on goldfish, freshwater turtles and other species is being complemented by new insights gained from the experimentally amendable retina of zebrafish. From this body of work, one thing is clear: The retinal basis of colour vision in non-mammalian vertebrates is substantially richer compared to mammals: Diverse and complex spectral tunings are established at the level of the cone output via horizontal cell feedforward circuits. From here, zebrafish use cone-selective wiring in bipolar cells to set-up color opponent synaptic layers in the inner retina, which in turn lead a large diversity of color-opponent channels for transmission to the brain. However, while we are starting to build an understanding of the richness of spectral properties in some of these species’ retinal neurons, little is known about inner retinal connectivity and cell-type identify. To gain an understanding of their actual circuits, and thus to build a more generalised understanding of the vertebrate retinal basis of color vision, it will be paramount to expand ongoing efforts in deciphering the retinal circuits of non-mammalian models.
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Biology, Plant Sciences; phospholipase D alpha1; Arabidopsis; proteomics; mitochondrial protein import; quality control; vesicular transport; cytoskeleton
Online: 20 November 2018 (08:08:22 CET)
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Phospholipase Dα1 (PLDα1) belongs to phospholipases, a large phospholipid hydrolyzing protein family. PLDα1 has a substrate preference for phosphatidylcholine leading to enzymatic production of phosphatidic acid, a lipid second messenger with multiple cellular functions. PLDα1 itself is implicated in biotic and abiotic stress responses. We present here a shot-gun differential proteomic analysis on roots of two pldα1 mutants compared to the Col-0 wild type. Our data suggest new roles of PLDα1 in endomembrane transport, mitochondrial protein import and protein quality control and glucosinolate biosynthesis. Thus, we identified proteins involved in endocytosis, endoplasmic reticulum-Golgi transport and attachment sites of endoplasmic reticulum and plasma membrane (V-type proton ATPases, protein transport protein SEC13 homolog A, vesicle-associated protein 1-2, vacuolar protein sorting-associated protein 29, syntaxin-32, all upregulated in the mutants), mitochondrial import and electron transport chain (mitochondrial import inner membrane translocase subunits TIM23-2 and TIM13, mitochondrial NADH dehydrogenases, ATP synthases, cytochrome c oxidase subunit 6b-1, ADP,ATP carrier protein 2, downregulated in the mutants) and glucosinolate biosynthesis (3-isopropylmalate dehydrogenases 1, 2 and 3, methylthioalkylmalate synthase 1, cytochrome P450 83B1, Glutathione S-transferase F9, indole glucosinolate O-methyltransferase 1, adenylyl-sulfate kinase 1, all upregulated in mutants). Our results suggest broader biological roles of PLDα1 as anticipated so far.
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Biology, Other; Japanese encephalitis virus; drug repurposing; systems biology; antiviral agents
Online: 20 November 2018 (04:54:48 CET)
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Japanese encephalitis is a zoonotic disease caused by Japanese encephalitis virus (JEV). It is mainly epidemic in Asia with an estimated 69,000 cases occurring per year. However, no approved agents are available for the treatment of JEV infection, and existing vaccines cannot resist various types of JEV strains. Drug repurposing is a new concept for finding new indication of existing drugs, and recently, it has been used to discover new antiviral agents. Identifying host proteins involved in the progress of JEV infection and using these proteins as targets are the center of drug repurposing for JEV infection. In this study, based on the gene expression data of JEV infection and the phenome-wide association study (PheWAS) data, we identified 286 genes participating in the progress of JEV infection using the systems biology methods. The enrichment analysis of these genes suggested that the genes identified by our methods were predominantly related to viral infection pathways and immune response-related pathways. We found that bortezomib which can target these genes may have potential effect on the treatment of JEV infection. Subsequently, we evaluated the antiviral activity of bortezomib using the JEV-infected mice model. The results showed that bortezomib can lower JEV-induced lethality in mice, alleviate suffering in JEV-infected mice and reduce the damage in brains caused by JEV infection. This work provides a new method for the development of antiviral agents.
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Biology, Other; Mononegavirales; Chaperones; Antivirals; Hsp70; Hsp90; CCT; Respiratory syncytial virus; Measles virus; Mumps Virus; Rabies virus; Ebola virus.
Online: 19 November 2018 (17:22:51 CET)
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The order Mononegavirales harbors numerous viruses of significant relevance for human health, including both established and emerging infections. Currently, vaccines are only available for a small subset of these viruses and antiviral therapies remain limited. Being obligate cellular parasites, viruses must utilize the cellular machinery for their replication and spread. Therefore, targeting cellular pathways used by viruses can provide novel therapeutic approaches. One of the key challenges confronted by both hosts and viruses alike is the successful folding and maturation of proteins. In cells, this task is faced by cellular molecular chaperones, a group of conserved and abundant proteins that oversee protein folding and help maintain protein homeostasis. In this review, we summarize the current knowledge of how the mononegavirales interact with cellular chaperones, highlight key gaps in our knowledge, and discuss the potential of chaperone inhibitors as antivirals.
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Biology, Plant Sciences; brachypodium; neutral red; root; casparian bands; PEG-6000; osmotic stress; real time imaging; PDMS
Online: 19 November 2018 (11:05:36 CET)
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To elucidate dynamic developmental processes in plants, live tissues and organs have to be visualized frequently and for long time periods. The development of roots is studied in depth at a cellular resolution not only to comprehend the basic processes fundamental to maintenance and pattern formation but also study stress tolerance adaptation in plants. Despite technological advancements, maintaining continuous access to samples and simultaneously preserving their morphological structures and physiological conditions without causing damage presents hindrances in the measurement, visualization and analyses of growing organs including plant roots. We propose a preliminary system which integrates the optical real-time visualization through light microscopy with a liquid culture which enables us to image at the tissue and cellular level horizontally growing Brachypodium roots every few minutes and up to 24 hours. We describe a simple setup which can be used to track the growth of the root as it grows including the root tip growth and osmotic stress dynamics. We demonstrate the system’s capability to scale down the PEG-mediated osmotic stress analysis and collected data on gene expression under osmotic stress.
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Biology, Animal Sciences & Zoology; kidney tissue; renal failure; human genetics; eastern part of India
Online: 19 November 2018 (10:01:55 CET)
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Urolithiasis is a painful experience associated with hematuria, damage to kidney tissue and renal failure. It is a multi-factorial disorder while in India, its prevalence is rapidly increasing imposing a large burden for both healthcare and economy globally. In this article, we aimed to evaluate the association between genetic defects in SPP1 gene and urolithiasis from East Indian patients.75 urolithiasis patients were recruited from SSKM Hospital & Institute of Post Graduate Medical Education & Research (IPGME&R), Kolkata, India while 75 healthy controls were recruited from the same community. SNPs based areas of SPP1 gene were analyzed by direct sequencing to identify genetic defects.We identified 3 polymorphisms one synonymous and two 3’UTR variants rs1126616: p.Ala250Ala, rs1126772: 7315 a>g, rs9138: 7471 a>c in SPP1 gene in study individuals. Genotype and allele frequency analysis of these SNPs revealed that, rs9138 SNP was significantly associated with urolithiasis risk in East Indian patients. To our knowledge this is the first study reporting the role of the gene with urolithiasis in the population of West Bengal, India.
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Biology, Physiology; food intake; food diversity; kidney stone disease; social epidemiology
Online: 19 November 2018 (09:20:49 CET)
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Food intake plays a pivotal role of human growth, which necessarily contributes 45% of global economy and wellbeing in general. Consumption of balanced food is elementary for overall good health while a shift of equilibrium can lead to malnutrition, prenatal death, obesity, osteoporosis and bone fractures, coronary heart diseases (CHD), idiopathic hypercalciuria, diabetes and many more. Though CHD, osteoporosis, malnutrition, obesity are being classified thoroughly in the literature, there are fragmented findings in the regime of kidney stone diseases (KSD) and the correlation with food intake therein. KSD associated with hematuria and renal failure poses an increasing threat to the healthcare and global economy while its emergence of Indian populations is being affected with multi-factorial urological disorder resulting from several factors. In this realm, epidemiological, biochemical, macroeconomic situations been portrayed when food intake is also a paramount importance which rarely been forecasted. Hence, in this article we will be reviewing the corollary connotation with diverse food consumption and the efficacy it plays in KSD extrapolating in Indian context.
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Biology, Other; drug repurposing; drug repositioning; computational biology; drug discovery; computational pharmacology; malaria; multitargeting; malaria treatment
Online: 19 November 2018 (07:31:08 CET)
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Drug repurposing is a valuable tool for combating the slowing rates of novel therapeutic discovery. The Computational Analysis of Novel Drug Opportunities (CANDO) platform performs shotgun repurposing of 2030 indications/diseases using 3733 drugs/compounds to predict interactions with 46,784 proteins and relating them via proteomic interaction signatures. An accuracy is calculated by comparing interaction similarities of drugs approved for the same indications. We performed a unique subset analysis by breaking down the full protein library into smaller subsets and then recombining the best performing subsets into larger supersets. Up to 14% improvement in accuracy is seen upon benchmarking the supersets, representing a 100–1000 fold reduction in the number of proteins considered relative to the full library. Further analysis revealed that libraries comprised of proteins with more equitably diverse ligand interactions are important for describing compound behavior. Using one of these libraries to generate putative drug candidates against malaria results in more drugs that could be validated in the biomedical literature than the list suggested by the full protein library. Our work elucidates the role of particular protein subsets and corresponding ligand interactions that play a role in drug repurposing, with implications for drug design and machine learning approaches to improve the CANDO platform.
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Biology, Physiology; fertilization; sperm; capacitation; zinc; proteasome; fertility
Online: 19 November 2018 (07:00:13 CET)
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The importance of zinc for male fertility only emerged recently, propelled in part by consumer interest in nutritional supplements containing ionic trace minerals. Here, we review the properties, biological roles and cellular mechanisms that are relevant to zinc function in the male reproductive system, survey available peer-reviewed data on nutritional zinc supplementation for fertility improvement in livestock animals and infertility therapy in men, and discuss recently discovered signaling pathways involving zinc in sperm maturation and fertilization. Emphasis is on the zinc-interacting sperm proteome and its involvement in the regulation of sperm structure and function, from spermatogenesis and epididymal sperm maturation to sperm interactions with the female reproductive tract, capacitation, fertilization and embryo development. Merits of dietary zinc supplementation and zinc inclusion into semen processing media are considered with livestock artificial insemination (AI) and human assisted reproductive therapy (ART) in mind. Collectively, the currently available data underline the importance of zinc ions for male fertility, which could be harnessed to improve human reproductive health and reproductive efficiency in agriculturally important livestock species. Further research will advance the field of sperm and fertilization biology, provide new research tools, and ultimately optimize semen processing procedures for human infertility therapy and livestock AI.
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Biology, Plant Sciences; red raspberry; cuticle; stomata; micromorphology; anatomy; ultrastructure elements
Online: 16 November 2018 (11:32:10 CET)
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Leaves of Rubus idaeus are a raw material, ingredients of herbal blend and a source of antioxidants. There are no data concerning histochemistry of trichomes and little is known about the leaves structure of this species. The aim of this study was to determine the histochemistry of active compounds and the structure of glandular trichomes, micromorphology, anatomy and ultrastructure of leaves as well as content of elements. To determine the histochemistry of glandular trichomes different chemical compounds were used. The leaves structure was analysed using light, scanning, and transmission electron microscopes. The content of elements was determined with atomic absorption spectrometry and the microanalysis of the epidermis ultrastructure was carried out with transmission electron microscope equipped with a digital X-ray analyser. In glandular trichomes: polyphenols, terpenes, lipids, proteins, and carbohydrates were identified. The main elements in the ultrastructure of the epidermis were: Na, S, Ca, Mg, B, Mo, and Se. In dry matter of leaves K, Mg, Ca, P, and Fe were dominant. Infusions from leaves are safe for health in terms of the Cd and Pb concentrations. Leaves can be a valuable raw material. Non-glandular trichomes prevent clumping of mixed raw materials in herbal mixtures.
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Biology, Agricultural Sciences & Agronomy; U.S.A inbred lines; Combining ability; Machine harvesting characteristics; Yield characteristics; control heterosis
Online: 16 November 2018 (09:01:36 CET)
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In China, there are increasing needs for greater genetic diversity of maize (Zea mays L.) germplasm and for hybrids appropriate for machine harvesting. to test and distinguish American maize inbred lines with exceptional combining ability, Four Chinese maize inbred lines (Chang7-2, Zheng 58,four-144 and four-287) were used to judge combining ability and heterosis of 16 U.S.A inbred lines by a NCII genetic mating method. The result showed: Among the American inbred lines, 6M502A,LH208,NL001,LH212Ht,PHW51,FBLA and LH181 showed excellent GCA for yield characteristics; while RS710,PHP76,FBLA,and PHJ89 showed excellent GCA for machine harvesting characteristics. In hybrid combinations, NL001×Chang7-2,LH212Ht×Chang7-2,FBLA×four-144,LH181×four-287,PHK93×four-287 had better SCA for yield characteristics; while NL001×Chang 7-2,6M502A×Chang7-2,LH212Ht×Chang7-2,LH181×four-287,PHW51×Chang7-2 were better than the check for machine harvesting characteristics. NL001×Chang7-2, 6M502A×Chang7-2,LH212Ht×Chang7-2,LH181×four-287,PHW51×Chang7-2 showed excellent total combined advantages compared to the check and potential for future utilization in Inner Mongolia corn production.
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Biology, Plant Sciences; Arabidopsis thaliana; ER α–glucosidase II; glycoprotein folding quality control; plant immune response; UGGT; elf18; flg22; EFR; FLS2; rsw3; uggt1-1; NB-DNJ
Online: 16 November 2018 (05:02:19 CET)
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Plants offer a simpler and cheaper alternative to mammalian animal models for the study of Endoplasmic Reticulum glycoprotein folding Quality Control (ERQC). In particular, the Arabidopsis thaliana (At) innate immune response to bacterial peptides provides an easy means of assaying ERQC function in vivo. A number of mutants that are useful to study ERQC in planta have been described in the literature, but only for a subset of these mutants the innate immune response to bacterial elicitors has been measured beyond monitoring plant weight and some physio-pathological parameters related to the plant immune response. In order to probe deeper into the role of ERQC in the plant immune response, we monitored expression levels of the PHI-1 and RET-OX genes in the At ER α-Glu II rsw3 and the At UGGT uggt1-1 mutant plants, in response to bacterial peptides elf18 and flg22. The elf18 response was impaired in the rsw3 but not completely abrogated in the uggt1-1 mutant plants, raising the possibility that the latter enzyme is partly dispensable for ERF signalling. In the rsw3 mutant, seedling growth was impaired only by concomitant application of the At ER α-Glu II NB-DNJ inhibitor at concentrations above 500 nM, suggesting residual activity in this mutant. The study highlights the need for extending plant innate immune response studies to assays sampling EFR signalling at the molecular level.
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Biology, Animal Sciences & Zoology; L-methionine, protein synthesis, MAC-T Cell
Online: 15 November 2018 (11:13:55 CET)
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The study was done to determine the effect of supplementing different forms of L-methionine (L-Met) and acetate on protein synthesis in immortalized bovine mammary epithelial cell line (MAC-T Cell): Control, L-Met, conjugated L-Met and acetate (CMA), and non-conjugated L-Met and Acetate (NMA). Protein synthesis mechanism was determined by omics method. NMA group had the highest protein content in the media and β-casein mRNA expression levels (P < 0.05). The number of upregulated and downregulated proteins observed were 77 and 62 in CMA group and 50 and 81 in NMA group from 448 proteins, respectively (P < 0.05). NMA and CMA treatments stimulated pathways related to protein and energy metabolism (P < 0.05). Metabolomic analysis also revealed CMA and NMA treatments resulted in increases of several metabolites (P < 0.05). In conclusion, NMA treatment increased protein concentration and expression level of β-casein mRNA in MAC-T cells compared to CMA.
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Biology, Plant Sciences; gene network; network analysis; transcription regulation network; Cytoscape; gene family evolution; divergence; A. thaliana; abiotic stress
Online: 15 November 2018 (09:02:34 CET)
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Phylostratigraphic analysis is a way to look anew on phylogenetic data in the evolutionary aspect. It allows counting the evolutionary age based on the analysis of genes, their orthologs and finding the last common ancestor. We performed phylostratigraphic analysis of Arabidopsis thaliana genes associated with several types of abiotic stresses (heat, cold, water-related, light, osmotic, salt, and oxidative) determined by the Gene Ontology annotation. Comparison of the distributions of ages of genes associated with stresses of different type has shown the heat stress to involve older genes while the light stress – younger genes. At the same time, all types of stress are characterized by a significantly higher proportion of old genes (common to all eukaryotes) compared to the whole set of A.thaliana genes. This can be explained by the involvement of basic molecular processes in plant cells into the stress response. Reconstruction and graphical analysis of the gene network of the heat stress educed several clusters associated with different response functions. Some of these clusters contain only ancient genes. The results obtained show that the phylostratigraphic analysis reveals the fundamental features of the organization of gene networks and their evolution.
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Biology, Plant Sciences; pasmo resistance, pasmo severity, quantitative trait loci (QTL), quantitative trait nucleotides (QTNs), fiber, linseed, core collection, flax, Linum usitatissimum
Online: 14 November 2018 (10:45:20 CET)
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Pasmo is one of the most widespread diseases threatening flax production. To identify genetic regions associated with pasmo resistance (PR), a genome-wide association study was performed on 370 accessions from the flax core collection. Evaluation of pasmo severity was performed in the field from 2012 to 2016 in Morden, MB, Canada. Genotyping-by-sequencing has identified 258,873 single nucleotide polymorphisms (SNPs) distributed on all 15 flax chromosomes. Marker-trait associations were identified using ten different statistical models. A total of 692 unique quantitative trait nucleotides (QTNs) associated with 500 putative quantitative trait loci (QTL) were detected from six phenotypic PR datasets (five individual years and average across years). Different QTNs were identified with various statistical models and from individual PR datasets, indicative of the complementation between analytical methods and/or genotype × environment interactions of the QTL effects. The single-locus models tended to identify large-effect QTNs while the multi-loci models were able to detect QTNs with smaller effects. Among the putative QTL, 67 had large effects (3-23%), were stable across all datasets and explained 32-64% of the total variation for PR in the various datasets. Forty-five of these QTL spanned 85 resistance gene analogs including a large toll interleukin receptor, nucleotide-binding site, leucine-rich repeat (TNL) type gene cluster on chromosome 8. The number of positive effect QTL (NPQTL) in accessions was significantly correlated with PR (R2=0.55), suggesting additive effects. NPQTL was also significantly associated with morphotype (R2=0.52) and major positive effect QTL were present in the fiber type accessions. The 67 large effect QTL are suited for marker-assisted selection and the 500 QTL for effective genomic prediction in PR molecular breeding.
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Biology, Animal Sciences & Zoology; productive, reproductive, breed, indigenous, traits, chicken
Online: 14 November 2018 (09:12:57 CET)
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A survey study was conducted to analyze the reproductive and productive performances of four indigenous chicken breeds under different rearing system. Six villages located in Eastern Cape, South Africa were used for the study from July 2017 to June 2018. Data on clutch per year (CPY), hatchability (HATCH), egg per clutch (EGC), survivability at 10-12 weeks (SURV), egg per year (EPY), recovery period (RP), average age at production (AA), duration of rearing (DR), mortality, egg laying length (EGL), natural brooding period (NBP) and natural incubating period (NIP) were obtained from Seven thousand, five hundred and thirty eight (7538) indigenous chicken. Potchefstroom Kooekok is observed to be a good egg producing breed with 15.11±0.25eggs per clutch. Venda breed possess good mothering ability (hatchability) and high survivability with 86.03±0.31days and 82.70±0.26 days respectively. Naked Neck is known to be more prone to diseases with least (survivability) 60.08±0.25days. Village was positively correlated with EGC and HATCH, EGY and SURV at p≤0.01 and p≤0.05 respectively. Rearing system was positively correlated with EGC. Rearing system was positively correlated at p≤0.05 on EGC than CPY, HATCH, EGY and SURV. Breed and village interactions were significant at p≤0.05 on RP, AA, DR, EGL, NBP and NIP. Therefore, productive and reproductive traits of indigenous chicken differ across different rearing systems, breeds and villages.
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Biology, Animal Sciences & Zoology; PUFA; oils; body condition score; sheep milk composition; supplementation; canola; flaxseed; safflower; rice bran
Online: 13 November 2018 (10:05:15 CET)
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The Australian dairy sheep industry is small and mostly based on a natural grass grazing system which can limit productivity. The current study tested different plant oil-infused and rumen protected polyunsaturated fats and their interactions with sire breeds to improve lactation traits and body condition score (BCS) of ewes grazing low quality pastures. It was hypothesised that supplementing lactating ewe diets plant-derived polyunsaturated oils will improve milk production and composition without compromising BCS. Sixty ewes (n=10/treatment) in mid-lactation, balanced by sire breed, parity, milk yield, body condition score, and liveweight were supplemented with: 1) control: wheat-based pellets without oil inclusion; wheat-based pellets including 2) canola oil (CO); 3) rice bran oil (RBO); 4) flaxseed oil (FSO), 5); safflower oil (SFO) and 6) rumen protected fat containing eicosapentaenoic acid and docosahexaenoic acid (RPO). Except for the control group, all supplementary diets included the same level of 50 ml/kg DM of oil and all diets were isocaloric and isonitrogenous. Experimental animals were grazed in the same paddock with ad libitum access to pasture, hay and water during the 10-week study. RPO was the most effective diet that enhanced milk, fat and protein yields by approximately 30, 13, and 31% respectively (P<0.0001). Significant increase in milk production was also observed in CO, RBO, and SFO (P<0.0001). Breed significantly influenced animal performance with higher milk yield recorded for crossbred Awassi x East Friesian (AW x EF) (578 g/day) vs purebred Awassi (452 g/day) (P<0.0001). This study provides empirical evidence for the use of rumen-protected and plant-derived oil-infused pellets as supplements under low quality pasture grazing conditions, to improve production performance of purebred Awassi and crossbred AW x EF ewes.
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Biology, Ecology; topographical land surface-area; soil carbon sequestration; climate; earthworms
Online: 13 November 2018 (09:18:25 CET)
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Earth’s land surface area is raised from conventionally flat 15 to 64 Gha to account for hilly undulation and soil relief detail. Three main aspects are: topography, rugosity/tortuosity and micro-relief/porosity of vegetation-free ground. Recalibration is arrived at from four approaches: first, direct empirical estimates from the few compiled satellite or LiDAR data with means of +2.5–26% progressively overlain by +94% at cm2 scale for soil ruggedness then +108% for mm2 micro-relief; second, from digital elevation models with 1.6–2.0 times flat areas; third, by ‘reverse engineering’ global soil bulk densities and carbon reserves requiring x 2–6 land. Finally, a Fermi estimation conveniently sets the World’s new surface area – that exposed to Sun, air and rain – at 100 Gha (with 36 Gha flat ocean). Soil organic carbon (SOC) is thence raised to 8,580 Gt mainly in SOM/humus with its biotic complexity plus roots, VAM-fungi and leaf-litter, that itself = 17,800 Gt. Although four to six times IPCC’s or NASA/NOAA’s calculations of just 1,500–2,300 Gt SOC, this is likely an underestimation. Global biomass and biodiversity are at least doubled (x 2–3.5) and net primary productivity (NPP) similarly increased on land to >270 Gt C yr-1 due to terrain.
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Biology, Agricultural Sciences & Agronomy; degraded land; biodiesel; biomass; energy; Indonesia
Online: 13 November 2018 (05:17:34 CET)
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This study spatially estimates degraded lands in Indonesia that have limited functions for food production, carbon storage, and conservation of biodiversity and native vegetation, and examines their suitability to grow biodiesel species (Calophyllum inophyllum, Pongamia pinnata and Reutealis trisperma) and biomass species (Calliandra calothyrsus and Gliricidia sepium). Results showed that Indonesia has ∼3.5 million ha of degraded lands potentially suitable for these species. With the all-five-species scenario, these lands had the potential to produce 1105 PJ yr−1 of biomass and 3 PJ yr−1 of biodiesel. With the biodiesel-only-species scenario, these lands showed the potential to produce 10 PJ yr−1 of biodiesel. Despite this energy potential, however, the land sizes were too small to support economies of scale for biofuel production. The study findings contribute to identifying lands with limited functions, modeling biofuel-species growth on regional lands and estimating carbon stocks of restored degraded lands in Indonesia.
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Biology, Animal Sciences & Zoology; maize genotypes; starch degradation; soil; in vitro; ruminants
Online: 12 November 2018 (11:42:00 CET)
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Starch is considered a major nutritional factor of maize (Zea mays L.) kernels, and can be influenced by the type of endosperm. The effects of endosperm type (vitreous and non-vitreous) and type of soil (clay and sand) on the starch content of kernels of maize, and on the in vitro degradation of starch were investigated in the rumen fluid after harvesting at 6 different maturity stages during 2008 and five different maturity stages in 2009. Starch degradation, in rumen fluid, was determined after 6 h, 12 h and 20 h of incubation, using the technique of gas production. A positive linear relationship was observed during gas production (ml gas/g organic matter) and starch degradation (g kg-1 starch) at all incubation times, with starch contents of maize kernels to a certain limit of starch accumulation (i.e. at starch contents 451-519 g/kg OM) and negative relationship afterwards. This suggests significant effects of maturity on ruminal starch degradation of maize kernels. At each harvest date, ruminal starch degradation of maize kernels was affected by crop genotype as well as soil type. The in vitro ruminal degradation potential of starch in maize kernels was influenced by the nature of the endosperm, with a higher degradation of non-vitreous kernels than of vitreous kernels. The rumen starch degradation was also influenced by type of soil, with better degradation on clay than sandy soil. For all the incubation times and maturity stages the effects of genotype, soil type and maturity stage were consistent in rumen fluid.
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Biology, Forestry; adaptive forestry; dendroecology; diffuse–porous wood; drought years; vessel traits; wood anatomy
Online: 12 November 2018 (10:31:23 CET)
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The distribution of Mexican Magnolia species´ occur under restricted climatic conditions. As many other tree species from the tropical montane cloud forests (TMCF), Magnolia species appear to be sensitive to drought. Through the use of dendrochronological techniques, this study aims to determine the climate influence on the vessel traits of M. vovidesii and M. schiedeana which are endangered tree species that are endemic to the Sierra Madre Oriental in eastern Mexico. Because most of the tree species in TMCFs are sensitive to climate fluctuations, it is necessary to investigate the differences in the climatic adaptability of the vessel architecture of these trees. This could allow us to further understand the potential peril of climate change on TMCFs. We compared vessel frequency, length and diameter in drought and non–drought years in two Mexican Magnolia species. We used tree–rings width and vessel traits to assess the drought effects on Magnolias’ diffuse–porous wood back to the year 1929. We obtained independent chronologies for M. vovidesii with a span of 75 years (1941–2016), while for M. schiedeana we obtained a span of 319 years (1697–2016). We found that temperature and precipitation are strongly associated with differences in tree–ring width (TRW) between drought and non–drought years. Our results showed anatomical differences in vessel trait response between these two Magnolia species to climatic variation. We suggest that our approach of combining dendroclimatic and anatomical techniques is a powerful tool to analyse anatomic wood plasticity to climatic variation in Magnolia species.
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Biology, Plant Sciences; saponin-containing plants; cleansing plants; bio-surfactant
Online: 12 November 2018 (09:07:26 CET)
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The natural forests of Northern Thailand are the mother source of many utilisable natural products because of their diverse flora and fauna. Among many plant species found within Northern Thai forests, detergent plants are known for its distinctive cleansing properties. Several local species of detergent plants in Thailand are traditionally used by the locals and indigenous people. However, these plants may become extinct because their habitats have been replaced by industrial agriculture, and their uses have been replaced by chemically synthesised detergents. Researchers need to study and communicate the biology, phytochemistry, and the importance of these plants to conserve natural biodiversity of Northern Thailand. Of many utilisable detergent phytochemicals, natural saponins are known as bio-surfactant and foaming agents. Their physiochemical and biological properties feature structural diversity, which leads to many industrial applications. In this review, we explained the term “detergent” from the physiological mechanism perspective and the detergent effects of saponin. We also compiled a list of Thai local plants with cleansing properties focusing on the saponin-containing plants. Future studies should investigate information relative to plant environment, ethnobotanical data and bioactive compound content of these plants. The knowledge acquired from this study will promote the maintenance of the local biodiversity and the conservation of the detergent plant species found in Thailand.
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Biology, Ecology; feeding behavior; Peripatidae; invertebrate behavior; undescribed Costa Rican onychophorans; parental investment
Online: 12 November 2018 (04:51:33 CET)
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We report, for the first time in onychophorans, food hiding, parental feeding investment and an ontogenetic diet shift, from adhesive to prey, after their first two weeks of life.
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Biology, Ecology; physical variables; climate; highland lichens; effect of climate change
Online: 9 November 2018 (11:18:37 CET)
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Lichens are traditionally divided into short “crustose”, intermediate “foliose” and tall “fruticose” types, a practice that hides a growth continuum. Substrate, temperature and water are thought to affect vertical growth, but such factors are difficult to measure, because, for example, the water actually available to lichens does not match rainfall patterns or even ground water levels. To reliably assess the effect of those factors, I recorded temperature, moisture, and substrate in and under individual terricolous lichen colonies in 60 fixed quadrats on April, August, October, and December of 2015 (Cerro de la Muerte, Costa Rica, 9°33′N; 83°45′W). The measurements were taken inside the colonies themselves (rather than on the general environment), covering an annual cycle of the relatively simple páramo habitat, where animals and vegetation have less impact than in lower ecosystems. The hypotheses were that lichens would grow taller on softer, warmer, and moister ground; on the Caribbean versant; and on the rainy season. Results matched the hypotheses, with one exception: lichens on soft ground were not taller than those on rock. Caribbean colonies were, on the average, 7 cm taller than those on the drier Pacific versant. Physiologically available water seems to be the main determinant of lichen vertical growth: more water means taller lichens and greater protection from climatic change for both the lichens and their microcommunities.
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Biology, Physiology; meagre; Argyrosomus regius; protease activity; inhibitions; live foods; in vitro
Online: 9 November 2018 (10:43:38 CET)
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The aim of this study was to gather preliminary data about the potential inhibitory effects and contributions of live foods used from 3 to 32 days after hatching (DAH) in routine feeding protocols on protease activities of meagre, Argyrosomus regius (Asso 1801) larvae, using in vitro techniques. Enriched rotifer, Artemia nauplii and Artemia metanauplii were tested in the present study. The highest values of protease activities of meagre larvae at 7 DAH in 2013 and 2014 years were established. The lowest values at 15 DAH in 2013 and at 20 DAH in 2014 were observed. Protease activities of enriched rotifer, Artemia nauplii, and Artemia metanauplii were 21.76±0.31, 36.00±1.48–29.33±0.93, and 416.44±19.7–403.53±11.85 U/mg protein, respectively (p< 0.05). The highest inhibitions of live foods were observed at 7 DAH. The positive contributions of live food Artemia metanauplii’s on protease activities of meagre larvae were significant (p< 0.05). The inhibitory effects and positive contributions of live foods on survival and growth rates of meagre larvae, should be taken into account in meagre and other marine fish larvae’s future studies. Cysteine protease activities of Artemia sp. should be investigated to provide the higher growth and survival ratio from the feeding protocols used in marine fish larvae.
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Jitrawadee Intirach,
Anuluck Junkum,
Nongkran Lumjuan,
Udom Chaithong,
Pradya Somboon,
Atchariya Jitpakdi,
Doungrat Riyong,
Danita Champakaew,
Roongtawan Muangmoon,
Arpaporn Chansang,
Benjawan Pitasawat
Biology, Entomology; Petroselinum crispum; Aedes aegypti; enzyme activity; esterases, mixed-function oxidases; phosphatases
Online: 8 November 2018 (10:41:59 CET)
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As part of the ongoing screening research for local edible plants in Thailand, Petroselinum crispum fruit oil was considered as a potential bioinsecticide with proven antimosquito activity against both the pyrethroid susceptible and resistant strains of Aedes aegypti. Due to the comparative mosquitocidal efficacy on these mosquitoes, this plant oil is promoted as a natural alternative and attractive candidate for further study in monitoring resistance of mosquito vectors. Therefore, the aim of this study was to evaluate the impact of P. crispum oil on the biochemical characteristics of the target mosquito larvae of Ae. aegypti, by determining quantitative changes of key enzymes responsible for xenobiotic detoxification, including glutathione-S-transferases (GSTs), α- and β-esterases (α-/β-ESTs), acetylcholinesterase (AChE), acid and alkaline phosphatases (ACP and ALP) and mixed-function oxidases (MFO). Three populations of Ae. aegypti, comprising the pyrethroid susceptible Muang Chiang Mai-susceptible (MCM-S) strain and the pyrethroid resistant Pang Mai Dang-resistant (PMD-R) and Upakut-resistant (UPK-R) strains, were used as test organisms. Biochemical study of Ae. aegypti larvae prior to treatment with P. crispum oil revealed that apart from AChE, the baseline activity of most defensive enzymes, such as GSTs, α-/β-ESTs, ACP, ALP and MFO, in resistant UPK-R or PMD-R, was higher than that determined in susceptible MCM-S. However, after 24-h exposure to P. crispum oil, the pyrethroid susceptible and resistant Ae. aegypti showed similarity in biochemical features, with alterations of enzyme activity in the treated larvae, as compared to the controls. A significant increase in the activity levels of GSTs, α-/β-ESTs, ACP and ALP was recorded in all strains of P. crispum oil-treated Ae. aegypti larvae, whereas MFO and AChE activity in these mosquitoes was decreased. The recognizable larvicidal capability on pyrethroid resistant Ae. aegypti, and the inhibitory effect on AChE and MFO, emphasized the potential of P. crispum oil as an attractive alternative application for management of mosquito resistance in current and future control programs.
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Biology, Other; Hierarchical clustering; DNA; Fastq; HcKmer
Online: 7 November 2018 (14:24:53 CET)
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We apply hierarchical clustering (HC) of DNA k-mer counts on multiple Fastq files. The tree structures produced by HC may reflect experimental groups and thereby indicate experimental effects, but clustering of preparation groups indicates the presence of batch effects. Hence, HC of DNA k-mer counts may serve as an unspecific diagnostic device. In order to provide a simple applicable tool we implemented sequential analysis of Fastq reads with low memory usage in an R package (seqTools) available on Bioconductor. The approach is validated by analysis of Fastq file batches containing RNAseq data. Analysis of three Fastq batches downloaded from ArrayExpress indicated experimental effects. Analysis of RNAseq data from two cell types (dermal fibroblasts and Jurkat cells) sequenced in our facility indicate presence of batch effects. The observed batch effects were also present in reads mapped to the human genome and also in reads filtered for high quality (Phred > 30). We propose, that hierarchical clustering of DNA k-mer counts provides an unspecific diagnostic tool and a quality criterion and for RNAseq experiments.
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Biology, Entomology; Bombyx mori; BmNPV; antiviral therapeutic; CRISPR/Cas9; multi-gene editing
Online: 7 November 2018 (10:23:52 CET)
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Clustered regularly interspaced short palindromic repeats/associated protein 9 nuclease (CRISPR/Cas9) technology guided by a single-guide RNA (sgRNA) has recently opened a new avenue for antiviral therapy. A unique capability of the CRISPR/Cas9 system is multiple genome engineering. However, there are few applications in insect viruses by a single Cas9 enzyme targeting two or more sgRNA at different genomic sites for simultaneous production of multiple DNA breaks. To address the need for multi-gene editing and sustained delivery of multiplex CRISPR/Cas9-based genome engineering tools, we developed a one-vector (pSL1180-Cas9-U6-sgRNA) system to express multiple sgRNA and Cas9 protein to excise Bombyx mori nucleopolyhedrovirus (BmNPV) in insect cells. Here, ie-1, gp64, lef-11, and dnapol genes were screened and identified as multiple sgRNA editing sites according to the BmNPV system infection and DNA replication mechanism. Furthermore, we constructed a multiplex editing vector sgMultiple to efficiently regulate multiplex gene editing steps and inhibit BmNPV replication after viral infection. This is the first report that describes the application of multiplex CRISPR/Cas9 system inhibiting insect virus replication. This multiplex system can significant enable the potential of CRISPR/Cas9-based multiplex genome engineering in transgenic silkworms.
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Biology, Forestry; Highway Beautification; Transplant Shock; Transportation; Tree Health; Tree Establishment; Urban Forestry
Online: 6 November 2018 (14:22:48 CET)
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Urban tree planting initiatives can experience high levels of mortality during establishment years. Mortality tied to the stresses of transplanting can be partially negated or exacerbated depending on the species selected, nursery materials used, site conditions present, and management practices employed. Past research has quantified post-planting survival, health, and growth. However, varying climates, species, land use types, and management practices warrant additional region-specific research. The purpose of this study is to assess the success of plantings along Florida highways and identify species, site, and management factors related to tree and palm health and establishment. Results show high annual establishment survival (98.5%) across 21 planting projects ranging from 9 to 58 months after installation, (n = 2711). For transplanted palms, the presence of on-site irrigation significantly improved establishment from 96.2% to 99.4%. No establishment differences were detected with regard to irrigation treatment for small-stature trees, shade trees, and conifers. Additionally, there were significant differences in tree health response among tree groups given species, management, and site factors.
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Biology, Agricultural Sciences & Agronomy; Fusarium graminearum; deoxynivalenol; RGB; water activity
Online: 5 November 2018 (12:09:07 CET)
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Deoxynivalenol (DON) is a well-known mycotoxin, responsible for outbreaks of gastrointestinal disorders in Japan. Fusarium graminearum, a parasite of cereal crops, produces this toxin and this is one of the reasons why it is important to understand its metabolism. It is possible to predict the mold’s color change and the quantity of DON synthesized throughout its lifecycle. Furthermore, aw has been found to affect the amount of DON. This study aimed to analyze the potential of F. graminearum surface color as a predictor of DON concentration at aw = 0.94, 0.97 and 0.99. Thus, 36 specimens were incubated at 25 °C, 12 at each aw. After 4, 8, 12 and 16 days, 3 specimens from each aw were collected for color analysis and DON quantification. For color analysis, photos were taken and red, green and blue (RGB) channels were measured on ImageJ software. DON was quantified through liquid chromatography (HPLC). Color changes were only observed at aw = 0.99 because at lower aw the molds presented high growth of white mycelium. Yet, DON increased in all cases. It was only possible to relate the colors with DON concentration at aw = 0.99, where they presented inverse proportionality.
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Shadi Amini Nia,
Giannina Satta,
Grazianna Intranuovo,
Sonia Sanna,
Mariagrazia Zucca,
Fabio Culurgioni,
Maria Giuseppina Cabras,
Valeria Sogos,
Giovanni Maria Ferri,
Maria Grazia Ennas,
Pierluigi Cocco
Biology, Other; aryl hydrocarbon receptor; DNA damage; single nucleotide polymorphisms; BCL6; lymphoma
Online: 5 November 2018 (10:28:08 CET)
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1) Background: We tested whether AHR activation induces DNA damage, whether polymorphisms in genes related to risk of Non-Hodgkin lymphoma are associated with DNA damage, and whether the two conditions do interact with each other. 2) Methods: Our study population included 36 subjects, randomly selected among the population controls participating in a case-control study on lymphoma in Sardinia, Italy, who donated a blood sample. We investigated 47 single nucleotide polymorphisms (SNPs) previously reported to convey risk of lymphoma; the Dual-Glo® Luciferase Assay System to detect activation of the aryl hydrocarbon receptor (AhR) by the serum of study subjects; and the COMET Assay to detect DNA damage. 3) Results: Activation of the aryl hydrocarbon receptor did not increase DNA damage in our study population. On the other hand, the mutant allele (G) of rs1056932/BCL6 increased the occurrence of DNA damage (p = 0.045); such association was confirmed among AhR negative, but not AhR positive subjects. 4) Conclusions: We observed excess DNA damage associated with a gene polymorphism, namely rs1056932/ BCL6, previously reported in association with risk of lymphoma. No increase in DNA damage was associated with AhR activation per se, nor with the other gene polymorphisms we investigated.
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Biology, Animal Sciences & Zoology; PUFA; oil; prime lamb; feedlot; carcass characteristics; live performance; oils; canola; flaxseed; safflower; rice bran
Online: 5 November 2018 (10:16:48 CET)
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This study investigated live animal performance and carcass characteristics of Australian prime lambs fed oil based polyunsaturated fatty acid (PUFA) enriched pellets in a feedlot system. The tested hypothesis was that supplementation of lambs with a variety of dietary oil based PUFA enriched pellets would enhance growth and carcass characteristics compared with the control lambs on lucerne only. Seventy-two, 6 months old White Suffolk x Corriedale first-cross prime lambs with an average liveweight (LWT) of 35.7 ± 0.9 kg were allocated to six treatment groups in a completely randomised experimental design. The treatments were: (1) control: lucerne hay only; or lucerne hay plus wheat-based pellets infused with 50 ml/kg DM of oils from (2) rice bran (RBO); (3) canola (CO); (4) rumen protected (RPO); (5) flaxseed (FO) and (6) safflower (SO) dietary sources. All lambs had ad libitum access to lucerne hay and clean fresh water. Supplemented lambs were fed 1kg of pellet/head/day for 10 weeks. Feed intake, final LWT, average daily gain (ADG), body conformation and carcass characteristics of lambs in the supplemented groups were all greater than for the control group. SO lambs had the lowest ADG of 190.3 g/day. RBO and CO treatments had the lowest feed cost per unit gain of AU$ 3.0/kg. Supplemented lambs had similar over the hooks (OTH) incomes that were all higher than that of the control group. This empirical evidence-based data demonstrated that supplementation of lambs with RBO and CO had comparatively lower feed costs without compromising ADG, carcass characteristics and OTH income.
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Biology, Plant Sciences; Wheat, emmer; domestication; genome assembly; QTL, meta-QTL; grain weight; GRF4
Online: 2 November 2018 (15:16:48 CET)
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The domestication and subsequent genetic improvement of wheat led to the development of large-seeded cultivated wheat species relative to their smaller-seeded wild progenitors. While increased grain weight (GW) continues to be an important goal of many wheat breeding programs, few genes underlying this trait have been identified despite an abundance of studies reporting quantitative trait loci (QTLs) for GW. Here we perform a QTL analysis for GW using a population of recombinant inbred lines (RILs) derived from the cross between wild emmer wheat accession ‘Zavitan’ and durum wheat variety ‘Svevo’. Identified QTLs in this population were anchored to the recent Zavitan reference genome, along with previously published QTLs for GW in tetraploid wheat. This genome-based, meta-QTL analysis enabled the identification of a locus on chromosome 6A whose introgression from wild wheat positively affects GW. The locus was validated using an introgression line carrying the 6A GW QTL region from Zavitan in a Svevo background, resulting in >8% increase in GW compared to Svevo. Using the reference sequence for the 6A QTL region, we identified a wheat ortholog to OsGRF4, a rice gene previously associated with GW. The coding sequence of this gene (TtGRF4-A) contains four SNPs between Zavitan and Svevo, one of which reveals the Zavitan allele to be rare in a core collection of wild emmer and completely absent from the domesticated emmer genepool. Similarly, another wild emmer accession (G18-16) was found to carry a rare allele of TtGRF4-A that also positively affects GW and is characterized by a unique SNP absent from the entire core collection. These results exemplify the rich genetic diversity of wild wheat, posit TtGRF4-A as a candidate gene underlying the 6A GW QTL, and suggest that the natural Zavitan and G18-16 alleles of TtGRF4-A have potential to increase wheat yields in breeding programs.
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Biology, Animal Sciences & Zoology; practice-led, innovation, networks, laying hen
Online: 2 November 2018 (14:33:15 CET)
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The Hennovation project, an EU H2020 funded thematic network, aimed to explore the potential value of practice-led multi-actor innovation networks within the laying hen industry. The project proposed that husbandry solutions can be practice-led and effectively supported to achieve durable gains in sustainability and animal welfare. It encouraged a move away from the traditional model of science providing solutions for practice, towards a collaborative approach where expertise from science and practice were equally valued. During the 32-month project, the team facilitated 19 multi-actor networks in 5 countries through 6 critical steps in the innovation process: problem identification, generation of ideas, planning, small scale trials, implementation and sharing with others. The networks included farmers, processors, veterinarians, technical advisors, market representatives and scientists. The interaction between the farmers and the other network actors, including scientists, was essential for farmer innovation. New relationships emerged between the scientists and farmers, based on experimental learning and the co-production of knowledge for improving laying hen welfare. The project demonstrated that a practice-led approach can be a major stimulus for innovation with several networks generating novel ideas and testing them in their commercial context. The Hennovation innovation networks not only contributed to bridging the science-practice gap by application of existing scientific solutions in practice but more so by jointly finding new solutions. Successful multi-actor, practice-led innovation networks appeared to depend upon the following key factors: active participation from relevant actors, professional facilitation, moderate resource support and access to relevant expertise. Farmers and processors involved in the project were often very enthusiastic about the approach, committing significant time to the network’s activities. It is suggested that the agricultural research community and funding agencies should place greater value on practice-led multi-actor innovation networks alongside technology and advisor focused initiatives to improve animal welfare and embed best practices.
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Biology, Physiology; peripheral and meningeal lymphatics 1; blood-brain barrier 2; neurorehabilitation 3.
Online: 2 November 2018 (10:53:09 CET)
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The peripheral lymphatic system plays a crucial role in the recovery mechanisms after many pathological changes, such as infection, trauma, vascular, or metabolic diseases. The lymphatic clearance of different tissues from waste products, viruses, bacteria and toxic proteins significantly contributes to the correspondent recovery processes. However, understanding of the meningeal lymphatics functions is a challenging problem. The exploration of mechanisms of lymphatic communication with brain fluids as well as the role of the lymphatic system in the brain drainage, clearance and recovery are still in its infancy.
Here we review novel concepts on the anatomy and physiology of the lymphatics in the brain, which warrant a substantial revision of our knowledge about the role of lymphatics in the rehabilitation of the brain functions after neural pathologies. We discuss a new vision on how to recruit the meningeal lymphatics by the opening of blood-brain barrier as a trigger mechanism of activation of the meningeal lymphatic drainage. This leads to innovative strategies in neurorehabilitation therapy.
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Biology, Agricultural Sciences & Agronomy; Crop rotation; Fertilization; Maize; Microbial community structure
Online: 2 November 2018 (09:37:31 CET)
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Examining the soil microbiome structure has a great significance in exploring the mechanism behind plant growth changes due to maize (Zea mays L.) and soybean (Glycine max Merr.) crop rotation. This study explored the effects of soil microbial community structure after soybean and maize crop rotation by designing nine treatments combining three crop rotations (continuous cropping maize or soybean; and maize after soybean) with three fertility treatments (organic compound fertilizer, chemical fertilizer, or without fertilizer). Soil was sampled to 30 cm depth the second year at approximately the middle of the growing season, and was analyzed for physical, chemical, and phospholipid fatty acid (PLFA) profiles. Bacteria was found to be the predominant component of soil microorganisms, which mainly contain the PLFAs i15:0, 16:1 ω 7c, 16:0, 10Me16:0, and 18:1 ω 7c. The concentration of soil gram-negative bacteria from the soybean and maize rotation was less than in soybean continuous cropping when organic fertilizer was applied to both. Crop rotation reduced the percentage of fungi in the soil, among which the effect of organic compound fertilizer application was significantly reduced 24%. The combined crop rotation with organic fertilizer can reduce maximum the percentage of fungi/bacteria. In addition, the content of soil aggregate and organic matter had great influence on gram-positive bacteria and actinomyces, and soil pH had a greater impact on other fungi.
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Biology, Other; connectomics; synapses; calcium imaging; optpgenetics; sonogenetics
Online: 2 November 2018 (09:17:37 CET)
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The complete structure and connectivity of the Caenorhabditis elegans nervous system was first published in 1986. The ‘mind of a worm’ was the first organism to have its nervous system to be reconstructed at the level of synapses, and represented a critical milestone considering today it remains the only organism to be mapped to that level of connection. Recently, the extrasynaptic connectome of neuropeptides and monoamines has been described. This review discusses recent technological advances used to perturb whole-organism neuronal function, such as: whole brain imaging, optogenetics, sonogenetics and mutant analysis, which have allowed for interrogations of both local and global neural circuits, leading to different behaviors. A better understanding of a whole organism requires combining experimental datasets with biophysical neuronal modelling, and behavioral quantification. Combining these approaches will provide a complete understanding of the worm nervous system and shed light into how networks function and interact with the synaptic network to modulate information processing and behavioral output.
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Biology, Animal Sciences & Zoology; mitochondria; mitochondrial dynamics; fusion; fission; pluripotency; differentiation
Online: 2 November 2018 (06:05:44 CET)
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Mitochondria are highly dynamic organelles that continuously change their shape. Their main function is ATP production; however, they are additionally involved in a variety of cellular phenomena, such as apoptosis, cell cycle, proliferation, differentiation, reprogramming, and aging. The change in mitochondrial morphology is closely related to the functionality of mitochondria. Normal mitochondrial dynamics are critical for cellular function, embryonic development, and tissue formation. Thus, defect in proteins involved in mitochondrial dynamics that control mitochondrial fusion and fission can affect cellular differentiation, proliferation, cellular reprogramming, and aging. Here we review the processes and proteins involved in mitochondrial dynamics and its various associated cellular phenomena.
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Biology, Ecology; low-cost UAV; greenness index; Pinus nigra; Pinus sylvestris; forest regeneration; flight altitude; small UAV
Online: 2 November 2018 (05:17:07 CET)
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During recent years UAVs have been increasingly used in agriculture and forestry research and application. Nevertheless, most of this work has been devoted to improving accuracy and explanatory power, often at the cost of usability and affordability. We tested a low-cost UAV and a simple workflow to apply four different greenness indices to the monitoring of pine (Pinus sylvestris and P. nigra) after-fire regeneration in a Mediterranean forest. We selected two sites and masured all pines within a pre-selected plot. Winter flights were carried out at each of the sites, at two flight altitudes (50 and 100 m). Automatically normalizing images entered an SfM based photogrammetric software for restitution and the obtained point cloud and orthomosaic processed to get a canopy height model and four different greenness indices. Sum of pine DBH was regressed on summary statistics of greenness indices and canopy height model. ExGI and GCC indices outperformed VARI and GRVI in estimating pine DBH, while canopy height model slightly improved the models. Flight altitude did not severely affect model performance. Our results show that low cost UAVs may improve forest monitoring after disturbance, even in those habitats and situations were resource limitation is an issue.
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Biology, Ecology; Iron bacteria; sulfate reduction; sulfur oxidizing bacteria; tufa; marl; manganese oxidizing bacteria
Online: 2 November 2018 (02:53:10 CET)
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Microbial populations involved in forming the distinctive precipitates of the S, Fe, Mn, and Ca cycles in the San Diego River watershed reflect an interplay between mineralogy of the rocks in the watershed, sparse rainfall, ground- and surface-water anoxia, and runoff of high sulfate, treated imported water. In the less developed headwaters, Temescal Creek tributary emerges from pyrite-bearing metamorphic rocks, and thus exhibits both an oxidized Fe and reduced S cycle. In the middle reaches, the river moves through developed land where treated, imported high sulfate Colorado River water enters from urban runoff. Mast Park surrounded by caliche-bearing sedimentary rocks is a site where marl is precipitating. Cobbles in riffles in the river are coated black with Mn oxide. When the river encounters deep-seated volcanic bedrock, it wells up to precipitate both Fe and Mn oxides at Old Mission Dam. Then, directly flowing through caliche-laced sedimentary rocks, Birchcreek tributary precipitates tufa. Further downstream, at a site that periodically receives full sunlight, a sulfuretum sets up during the summer when the river is deoxygenated. Such a rich geochemistry results in activity of iron and manganese oxidizing bacteria, sulfur oxidizers and reducers, and cyanobacteria precipitating calcareous marl and tufa.
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Biology, Plant Sciences; latent PPO; optimisation; peripheral membrane POD; total phenol content
Online: 1 November 2018 (18:00:20 CET)
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The present protocol described extraction of active polyphenol oxidase and peroxidase from a plant rich in phenolics and chlorophylls in the post-harvest browning syndrome of B. myrtifolia. Initially, general optimisation using conventional enzyme extractions was performed. However, along with membrane-bound proteins, chlorophylls and phenols were also released with Triton X (TTX). With a view to obtaining high enzymatic activity, removal of the released chlorophylls and phenols by formation of TTX-114 micelles in the detergent rich phase after high-temperature induced phase separation was tested.
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Biology, Horticulture; allelopathy; bioherbicides; corn gluten meal; essential oils; mustard seed meal; pathogens; plant extracts
Online: 31 October 2018 (07:50:29 CET)
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Over the last five decades, weed management systems have relied primarily on synthetic herbicides. Due to the concerns over the potential impact of chemicals on human health and the environment, efforts are being made to reduce the heavy reliance on synthetic herbicides. To reduce the use of synthetic herbicides, the use of natural products such as essential oils, plant extracts, allelochemicals, agricultural by-products, and some microbes are gaining attention because of their short environmental half-life and low toxicity. They are a good alternative to synthetic herbicides, especially in organic agriculture, since they focus on environmental protection, and ecological stability. Most of the commercially available natural herbicides are non-selective and require careful application in order to preserve the cash crops. Although many studies in this direction have been undertaken, the use of these natural products is still not common because of their cost the difficulties in their synthesis due to their complex structure, cost effectiveness, poor performance, and rapid degradation. When used singly, these natural herbicides do not perform as well as the chemical herbicides. An integrated approach may provide better results. Using a combination of natural herbicides may be more effective than using just one.
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Biology, Other; ncRNA; cis-encoded ncRNA; trans-encoded ncRNA; riboswitch; CRISPR.
Online: 30 October 2018 (08:48:47 CET)
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Genes encoding regulatory RNAs known as short RNAs (sRNAs) or non-coding sRNAs (ncRNAs), modulate physiological responses through different mechanisms, through RNA-RNA interaction or RNA-protein interaction. These molecules transcribed in trans and in cis relative to the target RNA. They are located between the coding regions of proteins, i.e., in the intergenic regions of the genome and show signals of promoters and termini sequences generally Rho-independent. The size of the ncRNAs genes ranges from ~ 50 to ~ 500 nucleotides and several transcripts are processed by RNase with smaller end products, which modulate physiological responses through different mechanisms, by RNA-RNA interaction or RNA-protein interactions and some interactions may be stabilized by the Hfq chaperone. The Riboswitches constitute another class of ncRNAs, located in the 5'UTR region of an mRNA that promote transcriptional regulation through their interaction with a linker molecule. Recently, in prokaryotes, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) regions have described, which repeats of sequences of palindromic bases are. Each replicate consists of short segments of "spacer DNA" from exposures prior to a bacteriophage virus or exogenous plasmid. The CRISPR system consists of an immune system of resistance to exogenous molecules.
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Biology, Animal Sciences & Zoology; diacylglycerol acyl-CoA acyltransferase (DGAT1); K232A; milk traits; milk fatty acid
Online: 30 October 2018 (08:46:38 CET)
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Milk fat production is important in the New Zealand (NZ) dairy industry. Elsewhere, an amino acid substitution (K232A) in the enzyme diacylglycerol acyl-CoA acyltransferase (DGAT1) has been reported to explain variation in some milk traits, including variation in milk fatty acid (FA) profile. In this study, associations between K232A, and milk traits including milk FA composition, were studied in wholly pasture-fed NZ Holstein-Friesian × Jersey (HF×J) cross-bred dairy cows. With a high frequency of K variant (61.9%), the KK cows produced more milk fat than the AA cows (5.41 ± 0.04 % vs 4.42 ± 0.05 %). The milk volume, fat concentration and protein concentration of AK cows were between the genotypes, AA and KK. More C16:0, CLA and C18:3 cis-9, 12, 15 FA were found in the milk of Kiwi-cross cows feed in outdoor pasture grazing system., and the influence of DGAT1 K232A, on these FAs from mid- and late lactation stages were significant. The AA cows produced (P < 0.001) more CLA and C18:3 cis-9, 12, 15, but less C16:0 (1.137 ± 0.047, 0.855 ± 0.015 and 35.170 ± 0.355) than the KK cows (0.934 ± 0.025, 0.778 ± 0.009 and 38.010 ± 0.250).
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Biology, Ecology; microplastics, sources, ecotoxicological, accumulation, freshwater
Online: 29 October 2018 (16:23:38 CET)
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Plastic production is escalating tremendously throughout the globe and the reason behind this is its durability and multipurpose utility. But there is a severe scarcity of its management. Tonnes of plastics are dumped into water bodies across the world. These plastics breakdown because of different reasons and results in the plastic debris of size <5mm termed as microplastics (MPs) which are hazardous to aquatic life. They are a potential source of toxins as they offer a large surface area to various chemicals present in the water body when these MPs are ingested by fishes it causes serious health issues leading to mortality of the fishes. Therefore, we comprehensively reviewed the sources of MPs in freshwater systems and its various types and how they get accumulated inside the body of fishes. We found that fishes ingest these particles by mistaken for food or accumulated these particles by consuming from lower trophic organisms. Some of the commonly studied MPs are PE, PS, and PVC, examined from the body of fishes. MPs can cause various ecotoxicological effects on fishes like behavioral change, cytotoxicity, neurotoxicity effects, and liver stress etc. Our review study finds that there is a paucity of information on the accumulation of MPs by freshwater fishes and there are very few studies on its effects also there is a debate whether this accumulation is subjected to the bio-magnification process which ultimately affects human life.
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Biology, Agricultural Sciences & Agronomy; chiseling depth; spring corn; canopy characteristics; photosynthesis quality
Online: 29 October 2018 (12:02:03 CET)
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Subsoil tillage loosens compacted soil for better plant growth, but promotes water loss, which is a concern in areas commonly irrigated. Therefore, our objective was to determine the physiological responses of high yield spring corn (Zea mays L.) to Subsoil tillage depth when grown in the western plain irrigation area of Inner Mongolia that leads to the best water use efficiency. The experiment during 2014 and 2015 used Zhengdan958 and Xianyu335 with three differing subsoil tillage depths (30, 40, or 50 cm) as trial factor and shallow rotary as a control. Subsoil tillage increased shoot dry matter accumulation, leading to a greater shoot/root ratio. Subsoil tillage helped retain greater leaf area index in each growth stage, increase the leaf area duration, net assimilation rate, and relative growth rate, with greater effects as tillage was deeper, effectively delaying the aging of the blade. Grain yields were increased by 0.7%–8.9% on average in subsoil tillage treatments compared to conventional soil treatment shallow rotary, Water use efficiency were increased by 1.93%–18.49% on average in subsoil tillage treatment compared to shallow rotary, resulting in net income increases by 2.24% to 6.97% compared to shallow rotary. Among the three different subsoil tillage depth treatment, the grain yield, water use efficiency, and net income is the best under the treatment of subsoil tillage depth of 50 cm.
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Karis A. Ederer,
Kelly Jin,
Sarah Bouslog,
Lu Wang,
Greg S. Gorman,
Glenn C. Rowe,
Peter Abadir,
Daniel Raftery,
Douglas Moellering,
Daniel Promislow,
Patricia Jumbo-Lucioni,
Maria De Luca
Biology, Other; aging; angiotensin-converting enzyme inhibitors; nutrient metabolism; genetic background; nutritional stress
Online: 29 October 2018 (10:33:59 CET)
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The angiotensin-converting enzyme (ACE) is a peptidase that is involved in the synthesis of Angiotensin II, the bioactive component of the renin-angiotensin system. A growing body of literature argues for a beneficial impact of ACE inhibitors (ACEi) on age-associated metabolic disorders, mediated by cellular changes in reactive oxygen species (ROS) that improve mitochondrial function. Yet, our understanding of the relationship between ACEi therapy and metabolic parameters is limited. Here, we used three genetically diverse strains of Drosophila melanogaster to show that Lisinopril treatment reduces thoracic ROS levels and mitochondrial respiration in young flies, and increases mitochondrial content in middle-aged flies. Using untargeted metabolomics analysis, we also showed that Lisinopril perturbs the thoracic metabolic network structure by affecting metabolic pathways involved in glycogen degradation, glycolysis, and mevalonate metabolism. The Lisinopril-induced effects on mitochondrial and metabolic parameters, however, are genotype-specific and likely reflect the drug’s impact on nutrient-dependent fitness traits. Accordingly, we found that Lisinopril negatively affects survival under nutrient starvation, an effect that can be blunted by genotype and age in a manner that partially mirrors the drug-induced changes in mitochondrial respiration. In conclusion, our results provide novel and important insights into the role of ACEi in cellular metabolism.
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Biology, Ecology; scorpion ecology; multivariate statistics; body size; offspring characteristics, K and r strategists
Online: 29 October 2018 (10:09:45 CET)
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There are no studies that quantitatively compare life histories among scorpion species. Statistical procedures applied to 94 scorpion species indicate that those with larger bodies do not necessarily have larger litters or longer life cycles, opposite to some theoretical predictions.
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Biology, Ecology; virus; South Scotia Ridge; viral community; diversity; Pgvv-like
Online: 29 October 2018 (09:43:50 CET)
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Viruses are the most abundant biological entities in aquatic ecosystems and harbor an enormous genetic diversity. While their great influence on the marine ecosystems is widely acknowledged, current information about their diversity remains scarce. A viral metagenomic analysis of three water samples was conducted from sites on the South Scotia Ridge (SSR) near the Antarctic Peninsula, during the austral summer 2016. The taxonomic composition and diversity of the viral communities were investigated and a functional assessment of the sequences was determined. Phylotypic analysis showed that most viruses belonging to the order Caudovirales, especially the family Podoviridae (41.92-48.7%), similar to the viromes from the Pacific Ocean. Functional analysis revealed a relatively high frequency of phage-associated and metabolism genes. Phylogenetic analyses of phage TerL and Capsid_NCLDV (nucleocytoplasmic large DNA viruses) marker genes indicated that many sequences associated with Caudovirales and NCLDV were novel and distinct from known phage genomes. High Phaeocystis globosa virus virophage (Pgvv) signatures were found in SSR area and complete and partial Pgvv-like were obtained which may have an influence on host-virus interactions. Our study expands the existing knowledge of viral communities and their diversities from the Antarctic region and provides basic data for further exploring polar microbiomes.
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Peter H. W. Biedermann,
Jean-Claude Grégoire,
Axel Gruppe,
Jonas Hagge,
Almuth Hammerbacher,
Richard Hofstetter,
Dineshkumar Kandasamy,
Miroslav Kolarik,
Martin Kostovcik,
Paal Krokene,
Jörg Müller,
Aurélien Sallé,
Diana L. Six,
Tabea Turrini,
Dan Vanderpool,
Michael Wingfield,
Claus Bässler
Biology, Ecology; European spruce bark beetle, Ips, Dendroctonus, global change, symbiosis, natural enemies, population dynamics, biotic interactions, tree killing, forest pest
Online: 26 October 2018 (16:30:11 CEST)
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Tree-killing bark beetles are the most economically important insects in conifer forests worldwide. Yet despite >200 years of research, the drivers of population eruptions or crashes are still not fully understood, precluding reliable predictions of the effects of global change on beetle population dynamics and impacts on ecosystems and humans. We critically analyze potential biotic and abiotic drivers of population dynamics of the European spruce bark beetle (Ips typographus) and present a novel ecological framework that integrates the multiple drivers governing this bark beetle system. We call for large-scale collaborative research efforts to improve our understanding of the population dynamics of this important pest; an approach that might serve as a blueprint for other eruptive forest insects.
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Biology, Plant Sciences; Chloroplast genome; H. gyantsensis; H. rhamnoides subsp. yunnanensis; Ka/ks; Optimal codons
Online: 26 October 2018 (15:40:04 CEST)
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Hippophae is a tree species with ecological, economic and social benefits. In this study, we assembled and annotated chloroplast genomes of sympatric Hippophae gyantsensis and H. rhamnoides subsp. yunnanensis. Their full-length are 155260 and 156415 bp, respectively. Each of them has 131 genes, comprising 85 protein-coding genes, 8 ribosomal RNA genes and 38 transfer RNA genes. After comparing the chloroplast genomes, we found 1302 base difference loci, and 63.29% are located in the intergenic region or intron sequences and 36.71% are located in the coding sequences. The SSC region has the highest mutation rate, followed by the LSC region; the IR regions have the lowest mutation rate. Among the protein-coding genes, three had a ratio of nonsynonymous to synonymous substitutions (Ka/Ks) >1 (but P values were non-significant) and 66 had Ka/Ks <1 (46 were significant). In general, the chloroplast protein-coding genes may be subject to purification selection. Among H. gyantsensis and H. rhamnoides subsp. yunnanensis chloroplast protein-coding genes, there are 20 and 16 optimal codons, respectively. Most of the optimal codons were ending with A or U, which indicates significant AT preference. It is an important reference for studies on the general characteristics and evolution of the Hippophae chloroplast genome.
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Biology, Other; Chalara fraxinea; Hymenoscyphus pseudoalbidus; ash dieback; Narnaviridae; evolution; invasive species; horizontal virus transmission
Online: 25 October 2018 (05:36:25 CEST)
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Hymenoscyphus albidus is a native fungus in Europe where it behaves as a harmless decomposer of leaves of common ash. Its close relative Hymenoscyphus fraxineus was introduced into Europe from Asia and currently threatens ash (Fraxinus sp.) stands all across the continent causing ash dieback. H. fraxineus isolates from Europe were previously shown to harbor a mycovirus named Hymenoscyphus fraxineus Mitovirus 1 (HfMV1). In the present study, we describe a conspecific mycovirus that we detected in H. albidus. HfMV1 was consistently identified in H. albidus isolates (mean prevalence: 49.3%) which were collected in the sampling areas before the arrival of ash dieback. HfMV1 strains in both fungal hosts contain a single ORF of identical length (717 AA) for which a mean pairwise identity of 94.5% was revealed. The occurrence of a conspecific mitovirus in H. albidus and H. fraxineus is most likely the result of parallel virus evolution in the two fungal hosts. HfMV1 sequences from H. albidus showed a higher nucleotide diversity and a higher number of mutations compared to those from H. fraxineus, probably due to a bottleneck caused by the introduction of H. fraxineus in Europe. Our data also points to multiple interspecific virus transfers from H. albidus to H. fraxineus, which could have contributed to the intraspecific virus diversity found in H. fraxineus.
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Sarina Veldman,
Seol-Jong Kim,
Tinde R. van Andel,
Maria Bello Font,
Ruth E. Bone,
Benny Bytebier,
David Chuba,
Barbara Gravendeel,
Florent Martos,
Geophat Mpatwa,
Grace Ngugi,
Royd Vinya,
Nicholas Wightman,
Kazutoma Yokoya,
Hugo J. de Boer
Biology, Plant Sciences; CITES; chikanda; conservation; DNA barcoding; orchids; species delimitation
Online: 25 October 2018 (05:10:27 CEST)
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In Zambia wild edible terrestrial orchids are used to produce a local delicacy called chikanda, which has become increasingly popular throughout the country. Commercialization puts orchid populations in Zambia and neighbouring countries at risk of overharvesting. Hitherto, no study has documented which orchid species are traded on local markets, as orchid tubers are difficult to identify morphologically. In this study, the core land-plant DNA barcoding markers rbcL and matK were used in combination with nrITS to determine which species were sold on Zambian markets. Eighty-two interviews were conducted to determine harvesting areas, as well as possible sustainability concerns. By using nrITS DNA barcoding, a total of 16 orchid species in six different genera could be identified. Both rbcL and matK proved suitable to identify the tubers up to genus- or family level. Disa robusta, Platycoryne crocea and Satyrium buchananii were identified most frequently and three previously undocumented species were encountered on the market. Few orchid species are currently listed on the global IUCN Red List. Local orchid populations and endemic species could be at risk of overharvesting due to the intensive and indiscriminate harvesting of chikanda orchids and we therefore encourage increased conservation assessment of terrestrial African orchids.
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Roberto Spogli,
Maria Bastianini,
Francesco Ragonese,
Rossana Giulietta Iannitti,
Lorenzo Monarca,
Federica Bastioli,
Irina Nakashidze,
Gabriele Brecchia,
Laura Menchetti,
Michela Codini,
Cataldo Arcuri,
Loretta Mancinelli,
Bernard Fioretti
Biology, Physiology; resveratrol; magnesium dihydroxide; solubility; bioavailability; dissolution rate; microparticles
Online: 25 October 2018 (03:53:04 CEST)
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Resveratrol, because of its low solubility in water and its high membrane permeability, is collocated in the second class of the biopharmaceutical classification system, with limited bioavailability due to its dissolution rate. Solid dispersion of resveratrol supported on magnesium dihydroxide (RESV@MDH) was evaluated to improve solubility and increase bioavailability of resveratrol. Fluorimetric microscopy and granulometric analysis display three types of microparticles with similar size: type 1 that emitted preferably fluorescence at 463 nm (λecc 358 nm), type 2 that emitted preferably fluorescence at 605 nm (λecc 550 nm) andtype 3 that are non-fluorescent. Micronized pure resveratrol display only microparticles type 1 whereas type 3 are associated to pure magnesium dihydroxide. Dissolution test in simulated gastric environment resveratrol derived from RESV@MDH in comparison to resveratrol alone displayed better solubility. According to the biopharmaceutical classification, an increase of 3 fold of resveratrol bioavailabilitywas observed after oral administration of 50 mg/Kg of resveratrol of RESV@MDH in rabbits. We hypothesize that type 2 microparticles represent magnesium dihydroxide microparticles with a resveratrol shell and that they are responsible for the improved resveratrol solubility and bioavailability of RESV@MDH.
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Biology, Forestry; ecological chemometrics; carbon cycle; nitrogen cycle; carbon and nitrogen distribution; plant leaf-litter-soil continuum
Online: 24 October 2018 (11:12:48 CEST)
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We analyzed the plant-litter-soil continuum to investigate the carbon and nitrogen distribution and ecological stoichiometry of an evergreen broad-leaved forest at Dagangshan Mountain, Jiangxi. The results showed that the average C and N contents and C:N ratios in the leaves and fine roots among 6 different tree species were 401.87g/kg, 21.41g/kg, 19.27 and 348.64g/kg, 15.73g/kg, 23.97, respectively; the average C and N contents and C:N ratios were 323.06 g/kg, 12.76 g/kg, 25.58 respectively in leaf litter, and 16.40 g/kg, 1.09 g/kg, 16.27 respectively for soil. In contrast with the C content, the total N content of the fine roots and litter had a high coefficient of variation and a high spatial heterogeneity. We ranked the six different representative tree species according to total C and N content in leaves and fine roots. The results for each species were generally consistent with each other, showing a positive correlation relationship between total C and N content in the leaves and roots. Among them, S. discolor (Champ. ex Benth.) Muell. plants displayed high carbon and nitrogen storage capacities, and on the other hand, C. fargesii Franch., C. myrsinifolia (Blume) Oersted, A. fortunei (Hemsl.) Makino, and V. fordii (Hemsl.) Airy Shaw showed a high nitrogen transfer rate. Total soil N and C decreased with depth. Soil organic carbon (SOC), soil resistant organic carbon (ROC), total N, alkali nitrogen, NH4+-N and NO3--N contents were all also negative correlated with soil depth, but the contents of the NH4+-N and NO3--N did not change significantly; The spatial distribution of soil NO3--N was significantly heterogeneous. At 0-10 cm soil depth, SOC was positively correlated with alkaline nitrogen, and at 10-20 cm soil depth, SOC was significantly positively correlated with total N. In general, when soil carbon was abundant, nitrogen supply capacity was also high.
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Biology, Other; gelatine; marine; by-products; fish; industry; extraction
Online: 24 October 2018 (09:37:38 CEST)
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In recent years, demand for consumption of marine foods, and especially fish, has substantially increased worldwide. The majority of collagen available is sourced from mammalian-derived products. Although fish derived gelatine is a viable alternative to mammalian sourced gelatine, there are some challenges related to the use of fish gelatine including odour, colour, gelling and film forming properties as well as consistency in gelatine amino acid composition. Chemicals used for pre-treatment, as well as extraction conditions such as temperature and time, can influence the length of polypeptide chains that result and the functional properties of the gelatine. Compared to mammalian sources, gelatines derived from fish show notable differences in physical and chemical properties, and great care should be paid to optimization of the production process in order to obtain a product with the best properties for intended applications. The focus of this review is to explore the feasibility of producing gelatine sourced from marine processing by-products using different pre-treatment and extraction strategies with the aim of improving the techno-functional properties of the final product and improving the clean-label status of gelatines. The bioactivities of gelatine hydrolysates are also discussed.
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Biology, Ecology; alternative states; secondary succession; tropical dry forest; Pteridium aquilinum
Online: 24 October 2018 (07:48:46 CEST)
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Understanding the role of invasive species in ecosystem functioning represents one of the main challenges in ecology. Pteridium aquilinum is a successful cosmopolitan invasive species with negative effects on the ecological mechanisms that allow secondary succession. In this study we evaluated whether P. aquilinum favours the establishment of alternative states, as well as the effect of recovery strategies on the secondary succession. A random stratified sampling was established with three treatments, each one with at least 50 year of fern invasion and with variations on the periodicity of fires and cuttings (chapeos) vs one control without fern bracken We determined the species richness and composition, as well as the relative importance value (IVI) in each treatment. We found that P. aquilinum decreases the action of the mechanisms that allow secondary succession, particularly facilitation. The recovery strategies consist in monthly cuttings and control fires allow to recover the secondary succession and eventually, the regeneration of areas invaded by P. aquilinum. Our study has relevant implications on the ecology of alternative state, and in practical strategies to maintain tropical forests, as well as for the maintenance of environmental services and sustainability.
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Biology, Agricultural Sciences & Agronomy; Cucumis sativus; nutraceutical; antioxidant; ABTS+, DPPH+
Online: 24 October 2018 (06:30:43 CEST)
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The objective of this research was to evaluate the production and phytochemical quality of cucumber fruits (Cucumis sativus), in response to the foliar application of different seaweed extracts. This study was carried out under shadow mesh conditions in the autumn - winter agricultural cycle at Instituto Tecnológico de Torreón, Torreón, Coahuila. The experimental design was completely random, using six treatments with six repetitions each. The treatments evaluated were: Macrocystis pyrifera, Bryothamnion triquetrum, Ascophyllum nodosum, Grammatophora sp., Macrocystis intergrifolia, and a control treatment with inorganic fertilization. The substrate used was a mixture of sand and vermicompost. The yield, commercial quality and phytochemical compounds of the fruit were evaluated. Results showed that yield using Steiner solution (6.75 kg m−2) was higher than that obtained with Bryothamnion triquetrum algae (6.07 kg m−2). Regarding the phenolic content, the extracts surpassed the control treatment, with Macrocystis pyrifera and Macrocystis integrifolia being statistically equal, with values of 47.37 and 43.73 mg equiv. of Ac. Gallic 100 g fresh weight, respectively. The antioxidant capacity by ABTS+ and DPPH+ methods was higher using the treatment with algae Macrocystis pyrifera with 149.4 and 454.1 μM equiv Trolox/100 g fresh base, respectively. This treatment also presented the highest value of vitamin C with 5.07 mg/100 g fresh base, being 27% greater than the control treatment. Algae extracts increased the quality of the fruits by obtaining the highest antioxidant capacity, making their use a viable option to minimize the application of conventional fertilizers, thereby attenuating the effects on the environment and improving the health of the population.
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Biology, Forestry; similarity relation neighborhoods, similarity relation decomposition, statistical analysis of within-set variability
Online: 23 October 2018 (16:12:37 CEST)
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Maximally similar sets (MSS) are sets of elements that share a neighborhood in a high-dimensional space defined by symmetric, reflexive similarity relation. Each element of the universe is employed as the kernel of a neighborhood of a given size (number of members), and elements are added to the neighborhood in order of similarity to the current members of the set until the desired neighborhood size is achieved. The set of neighborhoods is then reduced to the set of unique maximally similar sets by eliminating all sets that are permutations of an existing set. Subsequently, the within-MSS variability of attributes associated with the elements is compared to random sets of the same size to estimate the probability of obtaining variability as low as observed. Individual attributes can be compared for effect size by the ratio of within-MSS variability to random set variability, correcting for statistical power as necessary. The analyses performed identify constraints, as opposed to determinants, in the triangular distribution of pair-wise element similarity. In the example given here, the variability in spring temperature, summer temperature, and growing degree days of forest vegetation samples shows the greatest constraint on forest composition of a large set of candidate environmental variables
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Biology, Other; poor blood circulation; Ecklonia cava; phlorotannins; pyrogallol-phloroglucinol-6,6-bieckol; functional ingredients; endothelial cell death; vascular smooth muscle cell proliferation and migration; inflammation
Online: 23 October 2018 (09:39:50 CEST)
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Ecklonia cava (E.cava) can alleviate vascular dysfunction in diseases associated with poor circulation. E. cava contains various polyphenols with different functions, but few studies have compared the effects of these polyphenols. Here, we comparatively investigated four major compounds present in an ethanoic extract of E. cava. These four major compounds were isolated and their effects were examined on monocyte-associated vascular inflammation and dysfunctions. Pyrogallol-phloroglucinol-6,6-bieckol (PPB) significantly inhibited monocyte migration in vitro by reducing levels of inflammatory macrophage differentiation and of its related molecular factors. In addition, PPB protected against monocyte-associated endothelial cell death by increasing the phosphorylations of PI3K-AKT and AMPK, decreasing caspase levels, and reducing monocyte-associated vascular smooth muscle cell proliferation and migration by decreasing the phosphorylations of ERK and AKT. The results of this study show that four compounds were effective for reduction of monocyte-associated vascular inflammation and dysfunctions, but PPB might be more useful for the treatment of vascular dysfunction in diseases associated with poor circulation.
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Biology, Agricultural Sciences & Agronomy; object detection; tomato organ; K-means clustering; Soft-NMS; migration learning; convolutional neural network; deep learning
Online: 23 October 2018 (07:57:44 CEST)
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In the current natural environment, due to the complexity of the background and the high similarity of the color between immature green tomato and plant, the occlusion of the key organs (flower and fruit) by the leaves and stems will lead to low recognition rate and poor generalization of the detection model. Therefore, an improved tomato organ detection method based on convolutional neural network has been proposed in this paper. Based on the original Faster R-CNN algorithm, Resnet-50 with residual blocks was used to replace the traditional vgg16 feature extraction network, and K-means clustering method was used to adjust more appropriate anchor size than manual setting to improve detection accuracy. A variety of data augmentation techniques were used to train the network. The test results showed that compared with the traditional Faster R-CNN model, the mean average precision (mAP) of the optimal model was improved from 85.2% to 90.7%, the memory requirement decreased from 546.9MB to 115.9 MB, and the average detection time was shortened to 0.073S/sheet. As the performance greatly improved, the training model can be transplanted to the embedded system, which lays a theoretical foundation for the development of precise targeting pesticide application system and automatic picking device.
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Biology, Other; spatiotemporal neural dynamics; vision; dorsal and ventral streams; multivariate pattern analysis; representational similarity analysis; fMRI; MEG
Online: 23 October 2018 (06:41:16 CEST)
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To build a representation of what we see, the human brain recruits regions throughout the visual cortex in cascading sequence. Recently, an approach was proposed to evaluate the dynamics of visual perception in high spatiotemporal resolution at the scale of the whole brain. This method combined functional magnetic resonance imaging (fMRI) data with magnetoencephalography (MEG) data using representational similarity analysis and revealed a hierarchical progression from primary visual cortex through the dorsal and ventral streams. To assess the replicability of this method, here we present results of a visual recognition neuro-imaging fusion experiment, and compare them within and across experimental settings. We evaluated the reliability of this method by assessing the consistency of the results under similar test conditions, showing high agreement within participants. We then generalized these results to a separate group of individuals and visual input by comparing them to the fMRI-MEG fusion data of Cichy et al. (2016), revealing a highly similar temporal progression recruiting both the dorsal and ventral streams. Together these results are a testament to the reproducibility of the fMRI-MEG fusion approach and allows for the interpretation of these spatiotemporal dynamic in a broader context.
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Biology, Forestry; acacia species; allometric equation; above ground biomass; carbon stock
Online: 18 October 2018 (15:58:15 CEST)
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Allometric equations are used to estimate accurate biomass and carbon stock of forests. However, in Ethiopia only few allometric equations as compared to its floral diversity and species-specific allometric equations for Acacia species are still not developed in Ethiopia. The numbers of tree marked for sampling are Fifty-four (54) using preferential sampling. Diameter at breast height, wood density and tree height were collected as independent variables to predict species specific dry biomass of Acacia species. The new species-specific allometric models have been performed using linear regression analysis in the R software. The Above ground biomass (AGB) have been validated using quantitative statically using the pantropic model. Six candidate models have been developed for each species and four best models for each species of dry biomass was selected based on goodness-of-fit statistics and equation performance analysis of the candidate models. The best model for predicting above ground biomass for Acacia seyal is 0.20636*((DBH2)Hρ) 0.53167, for Acacia polyacantha is 7.26982((DBH)2Hρ)0.21750, for Acacia ethibcia is 29.01898*((DBH)2Hρ)0.21518 and for Acacia toritolis is 3.82427*((DBH)2Hρ)0.16748. The selected models are the best performing (P> 0.01) and higher adjusted R2 (>80%) and has lower Akaike’s Information Criteria (AIC) and residual standard error (RSE) values as comparing the rest of the model. The validation of new developed biomass model using Tukey test indicated that significant variation of mean biomass (P<0.05) between the new developed model and the generalized model. The statistics model performance analysis of Nash-Sutcliffe efficiency (NSE) value is approaching to one, indicating that the new developed model has better performance model as compared with generalized model. Moreover, the percent bias of the new developed models is close to zero which indicates that the site-specific biomass models have more accurate estimator and the generalized biomass models have overestimated biomass for the four Acacia species.
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Biology, Animal Sciences & Zoology; milk protein; amino acids; milk protein synthesis; omics; mammary gland
Online: 18 October 2018 (10:15:44 CEST)
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With deep knowledge and numerous researches about DNA in addition to recent advances in molecular biology and omics analysis methodology, manipulation of DNA transcription becomes possible that may eventually affect protein expression. Possible posttranscriptional modifications such as phosphorylation of proteins could also greatly affect protein expression. There are vast evidences showing that synthesis of milk protein is strongly regulated by several factors such as insulin, amino acids and their specific amino acid transporters as well as various energy sources through transcriptional and posttranscriptional pathways with insulin-mTOR pathway serving as the central point. Available latest data suggest the possibility of nutrigenomic interventions to manipulate milk protein synthesis by supplying amino acids and different energy sources. This could greatly contribute to major progress in understanding milk protein synthesis. With improvement of ‘omics’ tools, utilization of these tools in our future studies would help us fully understand the mechanism behind. This could lead to possible control and manipulation of milk protein synthesis in mammary gland.
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Biology, Plant Sciences; Dendrobium officinale; ITS; loop-mediated isothermal amplification; identification; rapid
Online: 18 October 2018 (06:15:37 CEST)
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Background: Dendrobium officinale is not only an ornamental plant, but also a valuable medicinal herb that is both effective and widely used in traditional Chinese medicine. However, distinguishing D. officinale from other Dendrobium species is usually a difficult task that need much time and complex technologies due to their very similar external morphologies. The aim of this study is to develop a fast, even on-spot approach to identify D. officinale. Methods: We used DNA barcode-based loop-mediated isothermal amplification (LAMP) method with species-specific LAMP primers targeting the internal transcribed spacer (ITS) region of the rDNA of D. officinale. LAMP reaction time and temperature were optimized and the specificity and sensitivity of LAMP species-specific primers were assessed. Results: This technique showed a high specificity and sensitivity to amplify the genomic DNA of D. officinale and allowed for rapid amplification (within 40 min) of the ITS region under a constant and mild temperature range of 65 °C without using thermocyclers. Besides, by using SYBR® Green I dye as the color developing agent, the color change was easily observed with naked eye. Reaction mixture containing DNA of D. officinale changed from orange to green, while the other Dendrobium species and the negative control retained original orange color. The specificity of this LAMP-based method was confirmed by testing 17 samples of D. officinale and 32 adulterant samples from other Dendrobium species. Conclusions: This LAMP-based rapid identification method does not require expensive equipment or specialized techniques and can be used in field surveys for accurate and fast on site identification.
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Biology, Agricultural Sciences & Agronomy; intercropping; microbial community; high throughput sequencing; nifH gene; sugarcane
Online: 17 October 2018 (10:20:19 CEST)
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Intercropping significantly improves land use efficiency and soil fertility. This study examines the impact of three cultivation systems (monoculture sugarcane, peanut-sugarcane and soybean-sugarcane intercropping) on soil properties and diazotrophs. Sugarcane rhizosphere soil was sampled from the farmers’ field. Soil properties and nifH gene abundance were analyzed by high throughput sequencing. Moreover, a total of 436,458 nifH gene sequences were obtained and classified into the 3201 unique operational taxonomic units (OTUs). Maximum unique OTUs resulted with soybean-sugarcane intercropping (<375). The dominant groups across all cultivation were Alpha-proteobacteria and Beta-proteobacteria. On the basis of microbial community structure, intercropping systems were more diverse than monoculture sugarcane. In the genus level, Bradyrhizobium, Burkholderia, Pelomonas, and Sphingomonas were predominant in the intercropping systems. Moreover, diazotrophic bacterial communities of these cultivation systems were positively correlated to the soil pH and soil enzyme protease. Moreover, low available P recovered from intercropping system showed a strong correlation with higher nutrient uptake activity of soil microbes. Based on the results, our investigation concluded that intercropping system caused a positive effect on the growth of diazotrophic bacterial communities and it might boost the soil fertility and this kind of study helps to develop an eco-friendly technology for sustainable sugarcane production.
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Biology, Plant Sciences; Juniperion lagunae; cross-border cooperation; landscape evolution; cluster analysis; conservation; sustainable development; territorial cohesion; Ombroedaphoxeric Index; phytosociology; SCI areas
Online: 16 October 2018 (12:33:03 CEST)
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We have studied Juniperus oxycedrus subsp. badia in the central and southern Iberian Peninsula. Here, the macrobioclimate ranges from Mediterranean-pluviseasonal-oceanic and Mediterranean-pluviseasonal-continental, thermotype from thermomediterranean and supramediterranean. The relevés were taken following the Braun-Blanquet phytosociological methodology. A statistical treatment was applied to establish a separation among Juniperus communities. To understand the presence of Juniperus communities in territories dominated by species of the genus Quercus, we applied the formula of Thornthwaite to calculate potential evapotranspiration. The general cluster analysis clearly separates two groups of plant communities and separates the different associations in each group. All plant communities growing on rocky crests and in steeply extreme sloping areas are significantly influenced by the soil. The Ombroclimatic Index does not explain the presence of plant communities influenced by substrate: so, we propose a new Ombroedaphoxeric Index which explains the presence of the Juniperus communities in territories with a thermotype ranging from the thermo to the supramediterranean belt. The areas of distribution of Juniperus species are expanding due to the spread of rocky areas: this phenomenon causes a rise in edaphoxerophilous areas and a decrease in climatophilous one. We propose four new plant associations and with this update on their structures and floristic compositions, it is possible to make an efficient form of conservation in both territories studied (Spain and Portugal) with specific cross-border-cooperation projects.
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Biology, Physiology; 4-octylphenol; male sertoli cells; reproductive toxicity; apoptosis; mitochondria
Online: 16 October 2018 (08:35:47 CEST)
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The toxic effects of 4-octylphenol (4-OP) have been studied in species such as mouse and fish; however, the toxic effects of 4-OP in male specific niche cells has not been researched. In this study, we investigated the molecular mechanism of toxicity of 4-OP in mouse TM4 Sertoli cells. TM4 cells were treated with four concentrations (0, 10, 30, and 50 µM/mL) of 4-OP at time points 24, 48, and 72 h. Cell viability and apoptosis assay was conducted following exposure. 4-OP significantly decreased cell viability in a concentration- and time-dependent manner, and increased apoptosis. Quantitative PCR analysis showed that Bad, Bax, and Bak mRNA expression levels were higher in exposed cells than in the control, but Bcl-2 expression was decreased. Western blotting revealed that 4-OP induced activities of caspase-3 and phosphorylation of Bad in a concentration- and time-dependent manner. Additionally, cytochrome C protein did not colocalize with mitochondria marker dye by 24 h. Cytochrome c protein expression increased in a time-dependent manner with 50 µM/mL. These results suggest that 4-OP induces mitochondria-mediated apoptosis by regulation of Bcl-2 family proteins and caspase-3 activation in male Sertoli cells.
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Biology, Forestry; Insects, Forest, Fungi, ITS1, metagenomics, NGS, Oomycete, Phytopathogens, Phytophthora, vectors
Online: 15 October 2018 (18:52:27 CEST)
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Understanding ecological interactions is a key in managing phytopathology. Although entomologists rely mostly on both traditional molecular methods and morphological characteristics to identify pests, next-generation sequencing is becoming the go-to avenue for scientists studying fungal and oomycete phytopathogens. These organisms sometimes infect plants together with insects. There are many relationships yet to be discovered and much to learn about how these organisms interact with one another. Considering the growing number of exotic insect introductions in Canada, a high-throughput strategy for screening those insects is already implemented by the Canadian Food Inspection Agency (CFIA). However, no plan is deployed to investigate the phytopathogenic fungal and oomycete species interacting with insects. Metagenomics analysis was performed on the preservation fluids from CFIA’s insect traps across Canada. Using the Ion Torrent PGM technology and fusion primers for multiplexing and indexing, community profiling was conducted on the different semiochemicals used in the insect traps and the various areas where these traps were placed. Internal transcribed spacer 1 (fungi and oomycetes) and adenosine triphosphate synthase subunit 9-nicotinamide adenine dinucleotide dehydrogenase subunit 9 spacer amplicons were generated. Although direct links between organisms could not be established, moderately phytopathogenic fungi (e.g., Leptographium spp. and Meria laricis) and oomycetes (mainly Peronospora spp. and Pythium spp.) unique to every type of semiochemical were discovered. The entomopathogenic yeast Candida michaelii was also detected. This project demonstrated our ability to screen for unwanted species faster and at a higher scale and throughput than traditional pathogen diagnostic techniques. Additionally, minimal modifications to this approach would allow it to be used in other phytopathology fields.
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Biology, Other; Cancer; cancer therapies; cancer recurrence; stem cells; porphine-related macrocycles, enhanced targeting; nanomedicine
Online: 12 October 2018 (14:31:03 CEST)
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Deregulation of cell growth and development lead to cancer, a severe condition that claims millions of lives worldwide. Targeted or selective approaches used during cancer treatment determine the efficacy and outcome of the therapy. In order to enhance specificity and targeting and better treatment options for cancer, novel and alternative modalities are currently under development. Photodynamic therapy has the potential to eradicate cancer and combination therapy would yield even greater outcomes. Nanomedicine-aided cancer therapy shows enhanced specificity for cancer cells and minimal side-effects coupled with effective cancer destruction both in vitro and in vivo. Nanocarriers used in drug-delivery systems are well able to penetrate cancer stem cell niche, simultaneously killing cancer cells and eradicate drug-resistant cancer stem cells, yielding therapeutic efficiency up to 100 fold against drug-resistant cancer in comparison with free drugs. Safety precautions should be considered when using Nano-mediated therapy as the effects of extended exposure to biological environments are still to be determined.
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Biology, Other; essential oils; drug resistant microorganisms; antimicrobial activity; antifungal activity; medicinal plants
Online: 11 October 2018 (11:51:16 CEST)
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Antimicrobial resistance (AMR) is a recurring global problem, which constantly demands new antimicrobial compounds to challenge the resistance. It is well known that essential oils (EOs) have been known for biological activities including antimicrobial properties. In this study, EOs from seven aromatic plants of Asir region of southwestern Saudi Arabia were tested for their antimicrobial efficacy against four drug resistant pathogenic bacterial isolates (Staphylococcus aureus, Streptococcus pyogenes, Escherichia coli and Streptococcus typhimurium) and one fungal isolate (Candida albicans). Chemical compositions of EOs were determined by Gas chromatography-Mass Spectrometry (GC-MS). The results revealed that EOs from Mentha cervina, Ocimum basilicum and Origanum vulgare proved most active against all isolates with inhibitory zone range between17 to 45 mm. The lowest minimum inhibitory concentration (MIC) of 0.025mg/ml was observed for Staph. aureus and Streptococcus pyogenes with EO of Origanum vulgare. All the three EOs showed significant anti candida activity. Together form the results the EOs from Mentha cervina, Ocimum basilicum and Origanum vulgare demonstrated a significant antimicrobial efficacy against drug resistant microorganisms.
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Biology, Agricultural Sciences & Agronomy; biochar; surface area; enzyme activity; immobilization; protein assay
Online: 11 October 2018 (07:49:15 CEST)
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Extracellular enzymes catalyze biogeochemical reactions in soil, cycling carbon and nutrients in agricultural systems. Enzymes respond quickly to soil management, including organic amendment inputs, such as biochar, a charcoal-like solid byproduct of bioenergy production. In a previous agricultural field trial, a pine biochar amendment caused an approximately 40% decrease in the enzyme activities of β-glucosidase (BG) and phosphatase (PHOS). The large surface area of the pine biochar has the potential to sorb nutrients and other organic molecules. To test if sorption caused decreased enzyme activity, we used a laboratory assay to quantify the activity of two sorbed enzymes: BG and acid PHOS, involved in the cycling of carbon and phosphorous. The enzymes were incubated with three solid phases: (1) the high surface area pine biochar, (2) the agricultural soil, and (3) a low surface area grass biochar, for an additional comparison. We quantified the sorbed enzymes at pH 6, 7, and 8, using a Bradford protein assay, and measured the immobilized enzyme activities via high-throughput fluorometric analysis. After sorption onto pine biochar, detectable BG and PHOS activity levels dropped by over 95% relative to the soil, supporting direct sorption as one mechanism that reduces enzyme activity in biochar amended soil. This laboratory assay demonstrated that sorption could account for the lack of priming of native soil organic matter and changes in soil phosphorous cycling after pine biochar addition.
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Biology, Other; Influenza virus; within-host viral dynamics; spatial spread; within-host evolution
Online: 11 October 2018 (07:36:15 CEST)
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The spread of viral pathogens both between and within hosts is inherently a spatial process. While the spatial aspects of viral spread at the epidemiological level have been increasingly well characterized, the spatial aspects of viral spread within infected hosts are still understudied. Recent experimental studies, however, have started to shed more light on the mechanisms and spatial dynamics of viral spread within hosts. Here, we review these experimental studies as well as the limited number of computational modeling efforts that have begun to integrate spatial considerations for understanding within-host viral spread. We limit our review to influenza virus to highlight key mechanisms affecting spatial aspects of viral spread for pathogens of the respiratory tract. There is considerable empirical evidence for highly spatial within-host spread of influenza virus, yet few computational modeling studies that shed light on possible factors that structure the dynamics of this spatial spread. In existing modeling studies, there is also a striking absence of theoretical expectations of how spatial dynamics may impact the dynamics of viral populations. To mitigate this, we turn to the extensive ecological and evolutionary literature to provide informed theoretical expectations for what viral and host factors may impact the spatial patterns of within-host viral dynamics and for how spatial spread will affect the genetic composition of within-host viral populations. We end by discussing current knowledge gaps related to the spatial component of within-host influenza virus spread and the potential for within-host spatial considerations to inform the development of disease control strategies.
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Biology, Entomology; dengue; Aedes mosquitoes; environmental factor
Online: 10 October 2018 (09:49:35 CEST)
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Background: Dengue incidence has grown dramatically around the world in recent years. It transmitted by Aedes mosquitoes. Many factors contributed to the vector densities such as environmental and sociological factors. Objective: This study is aimed at determining the environmental and sociological factors contributing to dengue cases. Methods: The study used questionnaire survey involving 379 respondent with dengue history. Result: The study showed that there is significant association between the time departs to work and mobility of respondents (95%CI = 2.779 and 5.594, p < 0.0001). Similarly, there is significant association between the time of arrival to work and mobility of respondents (95%CI = 1.617 and 2.155, p < 0.0001). Moreover, the type of housing and the surrounding vegetation were the environmental factors that showed significant values; p = 0.023, and p = 0.017. Conclusion: The study indicated the factors contributed are patient who lived in independent houses and the time of mobility patient.