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Biology, Physiology; obesity; plant secondary compound; Clinacanthus nutans; gene expression
Online: 24 April 2018 (10:04:11 CEST)
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Obesity is a universal health concern that can lead to serious diseases. The side effects of synthetic anti-obesity drugs necessitate the finding of suitable natural/herbal alternatives. Mother nature offers a wide range of plants with medicinal properties that include crude extracts and isolated compounds which are effective for controlling and reducing weight gain. Obesity was induced in 60, 3-week-old male ICR mice, using high-fat diet (60% dietary energy from fat) for 16-week. The mice were divided at random into six groups with 10 mice: mice fed with high-fat diet (HFD) only, mice fed normal diet only (NC), and orlistat at 15.9 mg/kg (HFD+Orlistat), and mice in three other high-fat diet groups treated with methanolic leaf extract of Clinacanthus nutans (MECN) at 500, 1000 and 1500 mg/kg. After 21-day of the treatment, MECN significantly reduced (P<0.05) the body weight, visceral fat and muscle saturated fatty acid compositions. There was also significant downregulation of HSL, PPAR α and PPAR γ and SCD genes expressions in the obese mice treated with 1500 mg/kg MECN compared to the HFD group. Therefore, MECN is a potentially useful natural supplement for alleviating obesity and obesity-mediated metabolic diseases.
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Biology, Ecology; wilderness study areas; light pollution; noise pollution; wildness; protected areas
Online: 24 April 2018 (06:25:12 CEST)
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Wildlands are increasingly lost to human development. Conservation scientists repeatedly call for protecting the remaining wildlands and expanding the land area protected in reserves. Despite these calls, conservation reserves can be eliminated through legislation that demotes their conservation status. For example, legislation introduced to the Congress of the United States recently would demote 29 Wilderness Study Areas (WSAs) from the protections afforded by their existing status. The legislation suggests that the 29 areas are not suitable for a promotion and future inclusion in the National Wilderness Preservation System based on decades-old local evaluations. Local evaluations, notwithstanding, it may be important to consider the value of lands from a national perspective. Without a national perspective, local evaluations alone may overlook the national significance of lands. With this in mind, I used five qualities of wildland value (wildness, light pollution, noise pollution, intactness of mammals, and intactness mammal carnivores of conservation concern) to compare the 29 WSAs to all national parks and wilderness areas located within the contiguous United States. The pool of 29 WSAs were similar to the pool of national parks and wilderness with respect to the five qualities assessed, and some of the WSAs were characterized by higher values than most of national parks and wilderness areas. This analysis demonstrates the national significance of the WSAs targeted for conservation status demotion. Such an approach could be used in future land management legislation and planning to ensure that a national perspective on conservation value is brought to bear on decisions facing federally-managed lands.
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Biology, Other; maximum entropy production; mass action kinetics; statistical thermodynamics; metabolism
Online: 23 April 2018 (10:53:06 CEST)
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We report the application of a recently proposed approach for modeling biological systems using a maximum entropy production rate principle in lieu of having in vivo rate constants. The method is applied in four steps: (1) a new ODE-based optimization approach based on Marcelin’s 1910 mass action equation is used to obtain the maximum entropy distribution, (2) the predicted metabolite concentrations are compared to those generally expected from experiment using a loss function from which post-translational regulation of enzymes is inferred, (3) the system is re-optimized with the inferred regulation from which rate constants are determined from the metabolite concentrations and reaction fluxes, and finally (4) a full ODE-based, mass action simulation with rate parameters and allosteric regulation is obtained. From the last step, the power characteristics and resistance of each reaction can be determined. The method is applied to the central metabolism of Neurospora crassa and the flow of material through the three competing pathways of upper glycolysis, the non-oxidative pentose phosphate pathway, and the oxidative pentose phosphate pathway are evaluated as a function of the NADP/NADPH ratio. It is predicted that regulation of phosphofructokinase (PFK) and flow through the pentose phosphate pathway are essential for preventing an extreme level of fructose 1, 6-bisphophate accumulation. Such an extreme level of fructose 1,6-bisphophate would otherwise result in a glassy cytoplasm with limited diffusion, dramatically decreasing the entropy and energy production rate and, consequently, biological competitiveness.
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Biology, Other; Fitness, Natural selection
Online: 20 April 2018 (14:51:02 CEST)
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A review of the concept of "fitness" as it is used in evolutionary theory.
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Biology, Plant Sciences; gas exchange; leaf canopy temperature; life forms; thermography; woody vines
Online: 20 April 2018 (11:55:08 CEST)
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Leaf temperature (Tleaf) influences photosynthesis and respiration. Currently, there is a growing interest on including lianas in productivity models due to their increasing abundance, and their detrimental effects on net primary productivity in tropical environments. Therefore, understanding the differences of Tleaf between lianas and trees is important for future of forest on whole ecosystem productivity. Here we determined the displayed leaf temperature (Td= Tleaf – ambient temperature) of several species of lianas and their host trees during ENSO and non-ENSO years to evaluate if the presence of lianas affects the Td of their host trees, and if leaves of lianas and their host trees exhibit differences in Td. Our results suggest that close to midday, the presence of lianas does not affect the Td of their host trees; however, lianas tend to have higher values of Td than their hosts across seasons, in both ENSO and non-ENSO years. Although lianas and trees tend to have similar physiological-temperature responses, differences in Td could lead to significant differences in rates of photosynthesis and respiration based temperature response curves. Future models should thus consider differences in leaf temperature between these life forms to achieve robust predictions of productivity.
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Biology, Anatomy & Morphology; molecular profile; extracellular matrix; osmotic pressure; depth articular cartilage; spheroidal organoid; cartilage regeneration
Online: 18 April 2018 (08:48:06 CEST)
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Articular chondrocytes are surrounded by chondroitin sulfate proteoglycan, which attracts an abundant volume of interstitial water. The articular cartilage is compressed with joint-loading and weight-bearing stresses, followed by a bulging of the tissue during times of off-loading. Thus, osmotic pressure in articular cartilage is higher than in other tissues due to the fixed charged density and altered between loading and off-loading due to change in water content. Another unique characteristic of the articular cartilage is that it has longitudinal depth: surface, middle, and deep zones. Since each zone composes unique components of extracellular matrices, each zone has a various level of the osmotic pressure. It was unclear how changes in osmotic pressure affected chondrocyte homeostasis and matrix accumulation in specific longitudinal zone. We hypothesized that change in extrinsic osmotic pressure alters metabolic functions and histogenesis of extracellular matrix by zone-specific chondrocytes. We compared the gene expression of matrix related typical anabolic and catabolic molecules produced by zone specific articular chondrocytes and the immunohistology of these corresponding genes. Since the newly synthesized matrix needed a space to accumulate, we used a chondrocyte-spheroid model formed by longitudinal depth zone-derived cells and altered extrinsic osmotic pressure by changing media containing different osmotic pressures. Anabolic molecules upregulated continuously at high osmotic pressure and transiently by switching back the osmotic pressure from high to low. Each zone derived chondrocytes showed zone specific level of the gene expression. The spheroids once exposed to the high osmotic pressure accumulated extracellular matrices with empty spaces.
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Biology, Ecology; multilevel factors; sit-and-wait foraging; active foraging
Online: 12 April 2018 (06:19:14 CEST)
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Pheidole oxyops Forel, 1908 is a generalist ant, which forages actively for plant debris to dead arthropods. In addition, its nest has an entrance that allows the ants gather resources passively by capturing falling preys into the nest. Our objective was to verify if different day periods, temperature and residual soil accumulation (ground pile in the side of nest entrance) could influence the patterns of foraging activity. Foraging activities were registered in the morning, afternoon and twilight. We measured direction and vector of trails, air temperature and humidity during foraging events. Our results showed that foraging routes are independent of residual soil accumulation and other nearby nests. However, air temperature and the time daily period are significant factors to foragers’ exits. Higher air temperatures influenced negatively the exits. In the period of the afternoon, the ants do not show any preference for routes, different from the morning and twilight. In addition, foraging activities were significantly more frequent during twilight period. Leaving the nest at twilight could allow ants foraging in an environment with less exposition to potential predators and competitors. Moreover, it may be also related to opportunism to hunt other nocturnal insects.
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Biology, Ecology; species richness; latitudinal gradients; water-energy; habitat; animal richness
Online: 11 April 2018 (11:24:46 CEST)
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Species data of 249 National Nature Reserves in China was used to identify potential underlying drivers of latitudinal gradients in plant diversity. We used generalized linear models (GLMs) to assess the correlations between predictor and response variables. We also used SAM (Spatial Analysis in Macroecology) to eliminate autocorrelation along each of the 249 studied locations. We used the Akaike information criterion (AICc; Montoya et al. 2007) to select the independent variables were those included in the best models from different combinations of climate, habitat and animal variables. Variance partitioning was used to decompose the variation in plant richness across different taxonomic levels among the three groups of predictors. We found that: Total plant species, gymnosperms, angiosperms and ferns showed significant latitudinal trends in richness (p < 0.001). Water-energy and habitat variables generally explained more variation in richness across different plant groups than did animal richness. Annual precipitation was selected as the best water-energy variable across different taxonomic plants groups, soil PH and elevation range were selected as the best habitat variables across different taxonomic plant groups. The independent effects of habitatvariables were higher than that of water-energy and animal variables across different taxonomic plants groups. Water-energy, habitat heterogeneity, and animal variables explain 48.8% of the variation in total species richness, 28.2% in gymnosperm richness, 44.2% in angiosperm richness, and 38.9% in fern richness.Plants showed significant latitudinal trends in richness (p < 0.001). Water-energy and habitat variables generally explained more variation in richness across different taxonomic plants groups than did animal variables. The independent effects of habitat variables were higher than those of water-energy and animal variables across different taxonomic plants groups.
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Biology, Plant Sciences; bacterial artificial chromosomes; RNAseq; genetic map; transposable element; gene density
Online: 10 April 2018 (10:49:41 CEST)
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Many dioecious plants have sex chromosomes that are cytologically heteromorphic, but about half of species lack cytological differences between males and females and are thus homomorphic. Very little is known about the size and content of the non-recombining sex-determining region (SDR) in these species. Here, we assess the size and content of the SDR of the diploid dioecious herb Mercurialis annua, which has homomorphic sex chromosomes and shows signatures of mild Y-chromosome degeneration. We used RNAseq to identify new Y-linked markers for M. annua. Twelve of 24 transcripts with male-specific and male-biased expression could only be PCR-amplified from males and are thus Y-linked. We found a further six Y-linked sequences that were present in males but not females using genome capture data from multiple populations. We used the Y-linked sequences to identify and sequence 17 sex-linked bacterial artificial chromosomes (BACs), which form 11 groups of non-overlapping sequence, covering a total sequence length of about 1.5 Mb. Content analysis of this region suggests it is enriched for repeats, has a low gene density and contains few candidate sex-determining genes. The BACs map to a subset of the sex-linked region of the genetic map, which is estimated to be at least 14.5 Mb. This is substantially larger than estimates for other dioecious plants with homomorphic sex chromosomes, especially given the small genome size of M. annua. Our data provide a rare, high-resolution view of the homomorphic Y chromosome of a dioecious plant.
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Biology, Agricultural Sciences & Agronomy; conservation agriculture; soil greenhouse gas (GHG) fluxes; soil tillage
Online: 10 April 2018 (10:02:25 CEST)
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Conservation Agriculture (CA) alters soil properties and microbial processes compared to conventional agriculture. These changes can affect soil-atmosphere greenhouse gas (GHG) fluxes. In this overview, we summarized the results of global literature and the gaps in measuring and understanding of GHG fluxes in CA systems and conventional agriculture. Some studies compared soil carbon sequestration and soil respiration in conservation agriculture and no-tillage system with conventional agriculture and the results were not consistent in all experiments. Interactions between CA pillars and soil factors such as soil moisture, temperature, texture can determine the rate of respiration rate and soil-atmosphere CO2 fluxes. The majority of studies reported larger N2O emissions in no-tillage treatment compared with conventional tillage while some other studies reported no difference between no-tillage and conventional tillage systems. In the majority of CA studies, there is lack of required information which is necessary to understand the mechanisms and processes that affect soil GHG fluxes. Determining factors like climate, amount of plant residues, soil type, crop types included in crop rotation and cover crops and duration of the study are not considered. Static chamber method was used for measuring soil-atmosphere GHG fluxes in the majority of studies. Spatial and temporal changes in GHG flux rates are high and missing part of highly episodic events by using static chamber method may result over- or under-estimation in flux balance calculation. Applying standard techniques for measuring continuous fluxes can help to calculating accurate GHG balance.
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Saeed Karbin,
Hossein Ali Alikhani,
Pramod Sahu,
Bharat Mogare,
Bhaskar Mitra,
Sandeep Viswakarma,
Jitendra Singh,
RamKrishna Mahajan,
Sunil Malviya,
Pankaj Badole,
Naveen Patidar,
Amir Kassam
Biology, Agricultural Sciences & Agronomy; conservation agriculture; greenhouse gases; soil health
Online: 10 April 2018 (06:30:15 CEST)
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Conservation Agriculture (CA) is capable of improving soil health and ecosystem functions. Soil carbon sequestration is one of the ecosystem processes that is of importance in sustainable land management involving reduction in greenhouse gas emissions and adaptation to climate change. In this study, we wanted to determine, during the first year of the process of establishing a CA cropping system in rain-fed areas in Madhya Pradesh state of India, which soil health indicators show measurable signs of improvement. Four field trials were selected, each comprising two neighboring plots. One plot (15×15 m) was managed conventionally under farmer practice and was tilled before sowing seeds, and in the adjacent plot Conservation Agriculture practices were applied. No mineral fertilizers or pesticides were applied in both treatments. Soil health indicators of soil aggregate stability, soil-atmosphere CO2 fluxes, water infiltration, soil moisture, potentially mineralizable nitrogen, soil organic content and bulk density were measured. Results demonstrate that soil CO2 emissions in CA soils decreased and soil aggregates stability improved in the first year. Generally, in CA soils, there were measurable improvements in all soil health indicators but only some of them were statistically significant.
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Biology, Plant Sciences; Hippophae rhamnoides L.; dioecious; sex determination; RAPD; SCAR
Online: 9 April 2018 (10:48:47 CEST)
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The dioecious property of sea buckthorn (Hippophae rhamnoides L.) prevents sex recognition via traditional observation at the juvenile stage, thus impeding breeding and economic cropping; RAPD and SCAR markers were used to identify the sexes. A total of 45 random decamer primers were used to screen genomic DNA pools of staminate and pistillate genotypes for genetic polymorphisms. One female sex-linked marker was identified. D15 (5′-CATCCGTGCT-3′) amplified a particular band of 885 bp, which showed polymorphism among staminate and pistillate genotype plants. The SCAR marker Hrcx-15 was obtained by sequencing the fragment. The alleles of 140 pistillate genotypes were examined but not of the 140 staminate genotypes discerned via taxonomy. Staminate and pistillate genotypes of sea buckthorn plants can be distinguished, using Hrcx-15 as a genetic marker for sex identification and for expediting cultivation for commercial applications.
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Biology, Plant Sciences; Clematis; chloroplast genome; rearrangement; inversion; IR expansion; synonymous substitution rate
Online: 9 April 2018 (10:34:28 CEST)
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Genus Clematis is one of the largest within Ranunculaceae. Here we report the chloroplast genome of two Clematis species, C. brachyura and C. trichotoma endemic to Korea. The chloroplast genome lengths of C. brachyura and C. trichotoma are 159,532 bp and 159,170 bp, respectively. Gene contents in the complete chloroplast genomes of these two Clematis species are identical to that of most Ranunculaceae and other angiosperms. However, our data results demonstrated that genus Clematis has inversion and rearrangement events concerning gene rps4 gene, rps16 to trnH region, and trnL to ndhC region, and IR regions expansion. Comparison of IR regions among Ranunculaceae species revealed that Clematis species contained six protein coding genes (infA, rps8, rpl14, rpl16, rps3, and rpl22) usually found in the long single copy (LSC) region of other species. Phylogenetic analysis demonstrated that genus Clematis is closely related to genus Ranunculus. Differences in repeat structure, substitution rates, and IR expansion in genera Clematis and Ranunculus, explained their relationship. Clematis species showed slightly higher tandem repeats content than Ranunculus species. The six protein-coding genes showed lower synonymous substitution rates in the IR of Clematis species than in the LSC of Ranunculus species. Overall, the chloroplast genomes and results presented here provide important information on the evolution of Ranunculaceae.
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Biology, Entomology; immune response; lectin; Mirabilis jalapa; phagocytic activity; phenoloxidase; Spodoptera litura
Online: 8 April 2018 (09:39:35 CEST)
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Biological control provides a safer alternative to reduce the population of agricultural pest. Mirabilis jalapa is one of biopesticides containing chemical substances that have a feeding deterrent property against Spodoptera litura as folifagus insect pest. This study aimed to analyze the humoral and cellular immunes responses of S. litura after exposure to biopesticide extracted from M. jalapa. The measured indicator immune responses were activity of hemocyte, lectin, phenoloxidase (PO), and phagocytic activity. The results showed that the average total hemocyte was different significantly depending on the treatment. Exposure to 0.1% and 0.2% (w/v) of M. jalapa extract increased the total number of hemocytes as much as 38.08% and 64.15%, respectively. Lectin was quickly formed at 0.1% and 0.2% (w/v) concentrations. The amount of PO enzymes was significantly different at sublethal concentrations compared with control samples (P < 0.05). The highest increase in PO activity occurred at 2 h post-treatment and at M. jalapa extract concentrations of 0.2% (592.33 IU/mg) and 0.1% (521.33 IU/mg), whereas the highest concentration of the extract (0.8% w/v) caused a decrease in lectin and PO activities. In terms of phagocytic activity, the proportion of phagocytosis cells were 47.62% in control group, and decreased significanlty in both concentrations exposure.
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Biology, Animal Sciences & Zoology; Mongolian oak cups; ethanol crude extract (ECE); ellagic acid- and kaempferol-derivatives; alloxan-induced rats; type 1 diabetes; hypoglycemic effect
Online: 8 April 2018 (08:45:39 CEST)
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Our previous in vitro reports showed that crude extract prepared with 50% ethanol (ethanol crude extract, ECE) from Mongolian oak cups possessed excellent antioxidant capacities as well as inhibitory activities against α-glucosidase, α-amylase and protein glycation caused by its enrichment in phenolics, including mainly ellagic acid, kaempferol and their derivatives. Nevertheless, few in vivo studies on antidiabetic activities of these phenolics were conducted. The present study investigated hypoglycemic effects with normal and diabetic rats being administrated orally without or with ECE at 200 and 800 mg/kg for 15 days. In normal rats, no significant differences were exhibited after ECE administration in body weight, fasting blood glucose level, levels of chelesterol, triglyceride, LDL and AST in serum, organ indexes, and levels of GSH and MDA in organs. In diabetic rats, the fasting blood glucose level, indexes of heart and liver, and levels of chelesterol and triglyceride in serum and MDA in heart tissue were significantly decreased. Moreover, HDL levels in serum and SOD activities in the four organs of diabetic rats were significantly improved after ECE administration at 800 mg/kg. Thus, in addition to inhibiting α-glucosidase, α-amylase and protein glycation reported previously, oak cups might contain novel dietary phytonutrients in preventing abnormal changes in blood glucose and lipid profile and attenuating oxidant stress in vivo. The results also implied that it is ellagic acid, kaempferol and their derivatives enriched in ECE that might play vital roles in managing type 1 as well as type 2 diabetes.
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Biology, Other; BLAST; DNA, open source; phylogenetics; R; sequence orthology.
Online: 4 April 2018 (06:00:40 CEST)
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The exceptional increase in molecular DNA sequence data in open repositories is mirrored by an ever-growing interest among evolutionary biologists to harvest and use those data for phylogenetic inference. Many quality issues, however, are known and the sheer amount and complexity of data available can pose considerable barriers to their usefulness. A key issue in this domain is the high frequency of sequence mislabelling encountered when searching for suitable sequences for phylogenetic analysis. These issues include the incorrect identification of sequenced species, non-standardised and ambiguous sequence annotation, and the inadvertent addition of paralogous sequences by users, among others. Taken together, these issues likely add considerable noise, error or bias to phylogenetic inference, a risk that is likely to increase with the size of phylogenies or the molecular datasets used to generate them. Here we present a software package, phylotaR, that bypasses the above issues by using instead an alignment search tool to identify orthologous sequences. Our package builds on the framework of its predecessor, PhyLoTa, by providing a modular pipeline for identifying overlapping sequence clusters using up-to-date GenBank data and providing new features, improvements and tools. We demonstrate our pipeline’s effectiveness by presenting trees generated from phylotaR clusters for two large taxonomic clades: palms and primates. Given the versatility of this package, we hope that it will become a standard tool for any research aiming to use GenBank data for phylogenetic analysis.
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Biology, Animal Sciences & Zoology; galectins; goats; periparturient
Online: 3 April 2018 (06:03:13 CEST)
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Galectins constitute an evolutionarily conserved family of β-galactoside-binding proteins. They regulate innate and adaptive immunity and homeostasis. Expression of Galectins may regulate periparturient immune suppression. Galectin gene expression was studied in goat blood during the periparturient period. Body weight, body condition and FAMACHA scores, and fecal and blood samples were collected from Five BoerXSpanish goats at 14 days and 7 days after parturition. Fecal samples were used to assess parasite load. Total RNA was isolated from blood using Trizol and converted to cDNA for real-time PCR using specific primers for goat LGALs-1, -2, -3, -4, -7, -8, -9, -11, -12, -14, -15, -16, and ligand Gal3bp, T-cell immunoglobulin domain, and mucin domain 3(TIM-3). Beta-actin and GAPDH housekeeping genes were used as internal controls. Fold changes in transcript abundance were compared to non-pregnant goats and calculated using the Livak method. Secretion of GALS-1, -3 and -9 in plasma was detected using ELISA. Data were analyzed using SAS 9.4 and Pearson correlations (p<0.05). Galectins were expressed and correlated to changes in leukocytes and fecal egg counts. Secreted GALS-1 decreased and GALS-3 and -9 increased (p<0.05) postpartum. Differential expression of Gal may have functional implications in animal health and homeostasis and needs further study.
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Biology, Other; thymidylate synthase (TYMS); dimer; octamer; biochemical reconstitution; overexpression and purification
Online: 2 April 2018 (09:37:29 CEST)
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Thymidylate synthase (TYMS) is an essential enzyme for the de novo synthesis of dTMP and has been a primary target for cancer chemotherapy. Although the physical structure of TYMS and the molecular mechanisms of TYMS catalyzing the conversion of dUMP to dTMP have been conducted thorough studies, oligomeric structure remains unclear. Here, we show that human TYMS not only exists in dimer but also octamer by intermolecular Cys43-disulfide formation. We optimize the expression condition of recombinant human TYMS using Escherichia coli system. Using HPLC-MS/MS, we show that purified TYMS has catalytic activity for producing dTMP. In the absence of reductant β-mercaptoethanol, SDS-PAGE and size exclusion chromatography (SEC) showed size of TYMS protein is about 35 KDa, 70 KDa, and 280 KDa. While the Cys43 was mutated to Gly, the band of ~280 KDa and the peak of octamer disappeared. Therefore, TYMS was determined to form octamer, dependent on the presence of Cys43-disulfide. By measuring Steady-State Parameters for monomer, dimer and octamer, we found the kcat of octamer is increased slightly than monomer. On the basis of these findings, we suggest that octamer in the active state might have a potential influence on the design of new drug targets.
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Biology, Animal Sciences & Zoology; feline immunodeficiency virus; FIV; human immunodeficiency virus; HIV; animal models, opportunistic disease, lentiviral pathogenesis; molecular biology
Online: 2 April 2018 (07:54:28 CEST)
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Feline immunodeficiency virus (FIV) is a naturally-occurring retrovirus that infects domestic and non-domestic feline species, producing progressive immune depletion that results in an acquired immunodeficiency syndrome (AIDS). Much has been learned about FIV since it was first described in 1987, particularly in regard to its application as a model to study the closely related lentivirus, human immunodeficiency virus (HIV). In particular, FIV and HIV share remarkable structure and sequence organization, utilize parallel modes of receptor-mediated entry, and result in a similar spectrum of immunodeficiency-related diseases due to analogous modes of immune dysfunction. This review summarizes current knowledge of FIV infection kinetics and mechanisms of immune dysfunction in relation to opportunistic disease, specifically in regard to studying HIV pathogenesis. Furthermore, we present data which highlight changes in the oral microbiota and oral immune system during FIV infection, and outline the potential for the feline model of oral AIDS manifestations to elucidate pathogenic mechanisms of HIV-induced oral disease. Finally, we discuss advances in molecular biology, vaccine development, neurologic dysfunction, and the ability to apply pharmacologic interventions and sophisticated imaging technologies to study experimental and naturally occurring FIV, which provide an excellent, but often overlooked resource for advancing therapies and management of HIV/AIDS.
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Biology, Plant Sciences; Idaeovirus; Blackcurrant leaf chlorosis associated virus; next-generation sequencing (NGS); bridge reads; abutting primers; RNase R digestion; circular RNA; concatenated RNA
Online: 30 March 2018 (11:40:46 CEST)
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Blackcurrant leaf chlorosis associated virus (BCLCaV) was detected recently by next-generation sequencing (NGS) and proposed as a new and distinct species in the genus Idaeovirus. Genomic components of BCLCaV that were detected and confirmed include: 1) RNA-1 that is monocistronic and encodes the replicase complex; 2) a bicistronic RNA-2 that encodes a movement protein (MP) and the coat protein (CP) of the virus, with open reading frames (ORF) that overlap by a single adenine (A) nucleotide (nt) representing the third position of an opal stop codon of the MP ORF2a and the first position of the start codon of the CP ORF2b; 3) a subgenomic form of RNA-2 (RNA-3) that contains ORF2b; and 4) a concatenated form of RNA-2 that consists of a complementary and inverted RNA-3 conjoined to the full-length RNA-2. Analysis of NGS-derived paired-end reads revealed the existence of bridge reads encompassing the 3’-terminus and 5’-terminus of RNA-2 or RNA-3 of BCLCaV. The full RNA-2 or RNA-3 could be amplified using outward facing or abutting primers; also RNA-2/RNA-3 could be detected even after three consecutive RNase R enzyme treatments with denaturation at 95 oC preceding each digestion. Evidence was obtained indicating that there are circular forms of BCLCaV RNA-2 and RNA-3.
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Biology, Physiology; TMEM16A, CLCA1, Cl- channels, Ca2+, Ca2+-activated Cl- channels, Epithelium
Online: 30 March 2018 (11:04:55 CEST)
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Calcium-activated chloride secretion in epithelial tissues described for many years. However, the molecular identity of the channel responsible for the Ca2+-activated Cl− secretion in epithelial tissues has remained a mystery. More recently, TMEM16A has been identified as a new putative Ca2 -activated Cl- channel (CaCC),. The primary goal of this article will be to review the characterization of TMEM16A, as it relates to the physical structure of the channel, as well as, important residues that confer voltage and Ca2+-sensitivity of the channel. This review will also discuss the role of TMEM16A in epithelial physiology and potential associated-pathophysiology. This will include discussion of developed knockout models that have provided much needed insight on the functional localization of TMEM16A in several epithelial tissues. Finally, this review will examine the implications of the identification of TMEM16A as it pertains to potential novel therapies in several pathologies.
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Biology, Entomology; Curculionidae; Cossoninae; Rhyncolini; Rhyncolina; taxonomy; new species; mature larva; morphology; host plant; Cape Verde; biogeography; microclimate; species competition
Online: 29 March 2018 (14:53:47 CEST)
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The genus Aphanommata in the Old World is reviewed. Aphanommata kuscheli sp. nov. from São Nicolau and A. strakai sp. nov. from Fogo (both Cape Verde islands) are described. Aphanommata euphorbiarum (Wollaston, 1867) from Santo Antão in the Cape Verde islands is redescribed and its lectotype is designated. All three Aphanommata species from the Cape Verde islands as well as A. filum (Mulsant & Rey, 1859) from Old World are diagnosed, illustrated, and keyed. Mature larva of A. kuscheli sp. nov. is described, larval morphology is discussed and the current state of knowledge about immature stages of Cossoninae is summarized. Vertical and inter-insular distributional pattern of Cape Verde Aphanommata and Pselactus is reviewed and discussed.
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Biology, Plant Sciences; Keywords: TMV, plant vaccine, génital herpes, HSV-2, gD, VP16, GFP, mouse model genital herpes
Online: 28 March 2018 (09:18:30 CEST)
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A B S T R A C T Genital herpes disease is caused mainly by herpes simplex virus type 2 (HSV-2), which is sexually transmitted with a high prevalence in both developed and developing countries. No vaccine is currently available against genital herpes. In this study, we introduced and expressed two genes encoding HSV-2 glycoprotein D (gD) and VP16 protein and a GFP marker gene (control) in tobacco seedlings. Positive plant infection was assessed through characteristic tobacco mosaic virus disease symptoms on leaves and by monitoring the fluorescence emitted by the expressed GFP protein. Expression of the HSV-gD2 and VP16 antigens was verified by RT-PCR, ELISA and Western blot. As a proof of concept, the immunogenicity and the protection ability of the plant produced gD antigen was tested in a mouse model of genital herpes and compared to gD antigen produced in a mammalian expression system. This showed that the plant-gD preparation, when used in combination with a CpG oligodeoxynucleotide as adjuvant, was highly immunogenic and capable of inducing complete immunity to lethal vaginal HSV-2 challenge in mice. Thus, the data presented here may have implications for the development of a production system for highly immunogenic plant-based HSV-2 vaccine antigens.
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Biology, Agricultural Sciences & Agronomy; wild chili pepper; domestication; seed germination; capsaicinoids content; halopriming; gibberellic acid
Online: 26 March 2018 (08:51:45 CEST)
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The effects of different priming techniques were evaluated to improve the dormancy and germination of wild seeds of “Piquín” chili pepper. Three experiments were designed for pre-sowing treatment of seeds: a) chemical seeds digestion; b) halopriming (with K+ or NH4+ of NO3-, SO42- or Cl-) at different priming times (24, 48 or 72 h) and osmotic potential (-5, -10 or -15 atm) and c) previously selected halopriming (KNO3 and NH4NO3) + Gibberellic acid (GA3, at 100 or 200 ppm) were tested. Digestion treatments did show a negative effect on seed germination. Recommended values of osmotic potential (Ψs), to improve Piquín chili seed germination, must be between -10 and -15 atm (-1.0 and -1.5 MPa) and the priming time must be between 48 and 72 hours. Priming techniques can considerably reduce Capsaicinoids content on seeds, improve dormancy, seed germination performance, and increase the rate and uniformity of seedling establishment. KNO3 and secondly GA3 treatments may improve rapid and uniform germination and seedling emergence. The results provide basic information to develop guidelines for commercial establishment of Piquín pepper crops.
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Biology, Ecology; above-ground carbon stock; below-ground carbon stock; soil nutrients; exclosure
Online: 26 March 2018 (08:17:48 CEST)
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Exclosures are used to regenerate native vegetation as a way to reduce soil erosion, increase rain water infiltration and provide fodder and woody biomass in degraded grazing lands. Therefore, this study assessed the impact of grazing exclosure on vegetation biomass, carbon sequestration and soil nutrients under five and ten years of grazing exclosures and freely grazed areas in Tigray, northern Ethiopia. Vegetation biomass, carbon stocks and soil nutrients increased with increasing grazing exclusion. However, open grazing lands and five years of grazing exclosure did not differ in aboveground biomass, above-and-belowground carbon stocks. Moreover, ten years of grazing exclosure had a higher (P<0.01) grass, herb and litter carbon stocks compared to five years exclosure and open grazing lands. The total carbon stock was higher for ten years exclosure (193.3 t C ha-1) than the five years exclosure (154.0 t C ha-1) and in open grazing areas (146.6 t C ha-1). Grazing lands closed for ten years had a higher SOC, organic matter, total N, available P, and exchangeable K+ and Na+ compared to five year’s exclosure and open grazing lands. Therefore, establishment of grazing exclosures had a positive effect in restoring degraded grazing lands, thus improving vegetation biomass, carbon sequestration potentials and soil nutrients under the changing climate and global warming.
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Biology, Anatomy & Morphology; Gilbertella persicaria; Pilobolus crystallinus; mucoralean fungi; phylogeny; morphology; undiscovered taxa
Online: 26 March 2018 (05:37:04 CEST)
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The order Mucorales, the largest in number of species within the Mucoromycotina, comprises typically fast-growing saprotrophic fungi. During a study of the fungal diversity of undiscovered taxa in Korea, two mucoralean strains, CNUFC-GWD3-9 and CNUFC-EGF1-4, were isolated from specific habitats including freshwater and fecal samples, respectively, in Korea. The strains were analyzed both for morphology and phylogeny based on the internal transcribed spacer (ITS) and large subunit (LSU) of 28S ribosomal DNA regions. On the basis of their morphological characteristics and sequence analyses, isolates CNUFC-GWD3-9 and CNUFC-EGF1-4 were confirmed to be Gilbertella persicaria and Pilobolus crystallinus, respectively.To the best of our knowledge, there are no published literature records of these two genera in Korea.
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Biology, Animal Sciences & Zoology; cyclophosphamide; cytoprotective; hepatotoxicity; hematotoxicity; Hypericum triquetrifolium turra.; myelotoxicity; rat
Online: 19 March 2018 (08:53:25 CET)
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The aim of this study was to investigate in-vitro antioxidant properties and in-vivo protective effects of different concentrations of Hypericum triquetrifolium Turra. (HT) seed methanol extracts against acute hepatotoxicity, myelotoxicity and hematotoxicity in rats exposed to overdose of cyclophosphamide (CP). HT seed methanol extracts were tested in view of its in-vitro antioxidant activities as total phenolic contents and DPPH free radical-scavenging activity. To investigate in-vivo protective effects of HT seed methanol extracts on rat tissues; tested animals were divided into nine groups. Three groups only were treated with HT extracts (25, 50 and 100 mg/kg HT) for 6 days. Three groups were pre-treated with the extract of HT (25, 50 and 100 mg/kg HT) for 6 days and on the last day they were injected with single dose of CP (150-mg/kg body weight). Two groups were used as control groups and one group was only treated with CP (150 mg/kg) on the 6th day. The toxic effects of CP and protective effects of HT extracts on the nucleated cells which were produced by bone marrow and serum alanine transaminase (ALT), alkaline phosphatase (ALP), lactate dehydrogenase (LDH), oxidative stress index (OSI) levels were investigated biochemically. Additionally, liver tissue samples were examined histopathologically. Our results show that HT seed methanol extract has high total phenolic content and antioxidant activity. Over dose CP administration caused hepatotoxicity, myelotoxicity and hematotoxicity on rat. Whereas, 25, 50 and 100 mg/kg HT plus CP administered groups showed significant protective effects on nucleated cells. And 25, 50, 100 mg/kg HT plus CP treated groups showed an important decrease on serum ALT, ALP, LDH and OSI levels when compared with CP treated group. Our results showed that the administration of different HT doses with high doses of CP significantly reduced hepatotoxicity, myelotoxicity and hematoxicity on rats.
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Biology, Physiology; syntrophic acetate oxidation; energy conservation; methane production; hydrogen production; anaerobic digestion process
Online: 19 March 2018 (07:23:17 CET)
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Syntrophic acetate oxidation operates close to the thermodynamic equilibrium and very little is known about the participating organisms and their metabolism. Clostridium ultunense is one of the most abundant syntrophic acetate-oxidising bacteria (SAOB) found in engineered biogas processes operating with high ammonia concentrations. It has been proven to oxidise acetate in cooperation with hydrogenotrophic methanogens. There is evidence that the Wood-Ljungdahl (WL) pathway plays an important role in acetate oxidation. In this study we analysed the physiological and metabolic capacities of C. ultunense on genome scale and conducted a comparative study of all known characterised SAOB, namely Syntrophaceticus schinkii, Thermacetogenium phaeum, Tepidanaerobacter acetatoxydans and Pseudothermotoga lettingae. The results clearly indicated physiological robustness beneficial for anaerobic digestion environments and revealed unexpected metabolic diversity with respect to acetate oxidation and energy conservation systems., Unlike S. schinkii and Th. phaeum, C. ultunense clearly does not employ the oxidative WL pathway for acetate oxidation, as its genome (and that of P. lettingae) lack important key genes. In both those species, a proton motive force is likely formed by chemical protons involving putative electron-bifurcating [Fe-Fe] hydrogenases rather than proton pumps. No genes encoding a respiratory Ech hydrogenase, as involved in energy conservation in Th. phaeum and S. schinkii, were identified in C. ultunense and P. lettingae. Moreover, two respiratory complexes sharing similarities to the proton-translocating ferredoxin:NAD+ oxidoreductase (Rnf) and the Na+ pumping NADH:quinone hydrogenase (NQR) were predicted. These might form a respiratory chain involved in reduction of electron acceptors other than protons. However, involvement of these complexes in acetate oxidation in C. ultunense and P. lettingae needs further study. This genome-based comparison provides a solid platform for future meta-proteomics and meta-transcriptomics studies and for metabolic engineering, control and monitoring of SAOB.
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Biology, Entomology; pesticides; native bee; persistency; biomonitoring
Online: 16 March 2018 (06:56:09 CET)
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In this paper we show the results of investigating the presence of organochlorine pesticides in honey and pollen samples from managed colonies of the honey bee, Apis mellifera L. and of the stingless bee Scaptotrigona Mexicana Guérin. We found that 88.44% and 93.33% of honey samples, and 22.22% and 100% of pollen samples of S. mexicana and A. mellifera, respectively, resulted positive to at least one organochlorine. The most abundant pesticides were DDE, DDT, Endrin and heptaclor. Despite the low foraging range of S. mexicana the number of pesticides detected in the honey samples was similar to that of A. mellifera. Paradoxically we a found a small number of organochlorines in pollen samples of S. mexicana, perhaps indicating a rapid turnover of this material as compared to A. mellifera.
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Biology, Other; Oryza sativa; genetic diversity; tidal swamp; breeding and conservation programs
Online: 15 March 2018 (06:50:32 CET)
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Tidal swamp rice has long been cultivated by the local people of the South Kalimantan, Indonesia. This germplasm possess some important traits for adapted to a wide range of abiotic and biotic stresses. In this study, a total of sixteen cultivars of this germplasm, consisting of fifteen of the South Kalimantan Province and one of Sumatera Island, Indonesia (an outgroup) were analyzed, phylogenetically based on the chloroplast trnL-F and nuclear intergenic spacer region (IGS). The results showed that this germplasm has a relatively more extraordinary genetic diversity than other local rice germplasm. In a nucleotide level, this germplasm showed a genetic diversity of 0.61 for nuclear IGS and 0.58 for trnL-F. The phylogenetic reconstruction also exhibited that this germplasm has the unique illustration of phylogenetic trees, particularly for the combined sequence datasets. Thus, the results of our study would provide useful information for further understanding of evolutionary relationships of this germplasm and facilitate the efficient utilization of valuable genes for genetic improvement, particularly in the tidal swamp areas.
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Biology, Physiology; high-intensity functional training; work capacity; performance
Online: 12 March 2018 (05:33:23 CET)
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High-Intensity Functional Training (HIFT) is a novel exercise intervention that may test body systems in a balanced and integrated fashion by challenging individuals’ abilities to complete mechanical work. However, research has not previously determined if physical work capacity is unique to traditional physiologic measures of fitness. Twenty-five healthy men and women completed a six-week HIFT intervention with physical work capacity and various physiologic measures of fitness assessed pre- and post-intervention. At baseline, these physiologic measures of fitness (e.g., aerobic capacity) were significantly associated with physical work capacity and this relationship was even stronger at post-intervention assessment. Further, there were significant improvements across these physiologic measures in response to the delivered intervention. However, the change in these physiologic measures failed to predict the change in physical work capacity induced via HIFT. These findings point to the potential utility of HIFT as a unique challenge to individuals’ physiology beyond traditional resistance or aerobic training. Elucidating the translational impact of increasing work capacity via HIFT may be of great interest to health and fitness practitioners ranging from strength/conditioning coaches to physical therapists.
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Biology, Entomology; Aedes aegypti; insecticide resistance; pyrethroid; permethrin; VGSC gene
Online: 9 March 2018 (05:27:12 CET)
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Aedes aegypti mosquito is a vector that could transmit various pathogens, such as viruses, bacteria, and parasites. Several human diseases transmitted by Ae. aegypti mosquito are dengue fever (DHF), Chikungunya, Yellow Fever and Zika. The occurance of resistance to various insecticides, including pyrethroid, is a current problem faced by various countries. In this research, a WHO bioassay test on Palembang and Jakarta Ae. aegypti was conducted using 0.25% permethrin pyrethroid insecticide. VGSC gene fragments associated with pyrethroid resistance (L982, S989, I1011, L1014, V1016 and F1534) of resistant and sensitive strains were amplified and analyzed. The test showed the presence of resistance in Ae. aegypti isolates from Palembang and Jakarta. From the results of VGSC gene fragment analyses, it was known that there were mutations (S989P and/or V1016G) on isolates from Palembang and (S989P and/or V1016G) on resistant isolates from Jakarta.
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Biology, Anatomy & Morphology; mouse node; Kupffer’s vesicle; primary cilium; asymmetry; symmetry breaking; bilateral symmetry; cell chirality; centriole; centrosome
Online: 6 March 2018 (04:57:46 CET)
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In zebrafish inner ear, hair cell orientation in anterior and posterior maculae of the embryonic otic vesicle is different (about 30–40 degrees): this is rather unusual in planar polarity mechanism of action, instead suggests that kinocilia may be rotationally polarized. In mice node, the innermost monociliated cells generate a left-ward fluid flow sensed by the immotile primary cilia of Left peri-nodal cells: the Nodal signaling pathway is then expressed asymmetrically, in the Left lateral plate mesoderm, breaking symmetry in visceral organs (situs solitus); however, Right peri-nodal cells also, if artificially excited by a right-ward flow, break symmetry and activate the Nodal cascade, though inverting visceral organ asymmetry (situs inversus); surprisingly, peri-nodal cells prove to be adept at distinguishing flow directionality. Recently, in the Kupffer vesicle (the zebrafish laterality organ), chiral primary cilia orientation has been described: primary cilia, in the left and right side, are symmetrically oriented, showing a mirror average divergence of about 15–20 degrees from the midline. This finding, taken together with the mirror behavior of mouse perinodal cells and zebrafish hair cells, champions the idea of primary cilia enantiomerism.
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Biology, Other; gene flow; sympatry; parapatry; simulation model; population genomics; Heliconius;coupling; nonlinear transitions
Online: 1 March 2018 (15:23:13 CET)
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During speciation-with-gene-flow, a transition from single-locus to multi-locus processes can occur, as strong coupling of multiple loci creates a barrier to gene flow. Testing predictions about such transitions with empirical data requires building upon past theoretical work and the continued development of quantitative approaches. We simulated genomes under different evolutionary scenarios of gene flow and divergent selection, extending previous work with the additions of neutral sites and coupling statistics, allowing us to investigate if and how selected and neutral sites differ in the conditions they require for transitions during speciation. As the per-locus strength of selection grew and/or migration decreased, it became easier for selected sites to show divergence – and thus to rise in linkage disequilibrium (LD) with each other as a statistical consequence – farther in advance of the conditions under which neutral sites could diverge. Indeed, even very low rates of gene flow were sufficient to prevent differentiation at neutral sites. However, once strong enough, coupling among selected sites eventually reduced gene flow at neutral sites as well. To explore whether similar transitions might be detectable in empirical data, we used published genome resequencing data from three taxa of Heliconius butterflies. We found that allele-frequency outliers and F ST outliers exhibited stronger patterns of LD than the genomic background, as expected. The statistical characteristics of LD – likely indicative of the strength of coupling of barrier loci – varied between chromosomes and taxonomic comparisons. Broad qualitative agreement between the patterns we observed in the empirical data and our simulations suggests that selection drives rapid genome-wide transitions to multi-locus coupling, illustrating how divergence and gene flow interact along the speciation continuum.
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Biology, Plant Sciences; color tests; thin layer chromatography; chemotaxonomy; secondary metabolites; solvent system
Online: 24 February 2018 (08:28:11 CET)
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Presence and identity of secondary metabolites are two of the main components of lichen taxonomy. Aromatic compounds formed via the acetyl-polymalonate pathway are the most studied lichen substances. In addition, compounds derived from the mevalonic acid pathway (e.g., terpenes and steroids) are sometimes detected in the medulla. However, their identity and value as diagnostic characters in the genus Usnea are yet poorly understood despite the fact that they were mentioned in several taxonomical papers. We conclude that i) aside from the previously recognized polyphenolic compounds, carbohydrates and steroids are also detected in the medulla of some Usnea species; ii) the use of sulfuric anisaldehyde reagent greatly improves the detection of terpenes, carbohydrates and steroids compared with the sulfuric acid reagent routinely used in thin layer chromatography; iii) among carbohydrates, we detected arabitol and sucrose in the medulla; iv) steroids and terpenes remain unidentified and deserve further investigations.
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Biology, Ecology; Pinus albicaulis; whitebark pine; blister rust; national park; subalpine; Cascades; mountain pine beetle
Online: 23 February 2018 (11:08:42 CET)
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Whitebark pine (Pinus albicaulis Engelm.) is a key component of subalpine and alpine ecosystems in the northern Cascades. The species survival is threatened by white pine blister rust, mountain pine beetles, fire exclusion, and climate change. Trees were monitored in permanent plots in two national parks three times between 2004 and 2016. The proportion of trees showing signs of blister rust infection increased in North Cascades National Park Service Complex from 32% in 2004 to 51% in 2016 and from 18% to 38% in Mount Rainier National Park. Mortality increased from 7% to 21% in North Cascades National Park Service Complex and 38% to 44% in Mount Rainier National Park. Annual mortality rates were calculated for three time periods: 2004-2009, 2009-2015/2016, and 2004-2015/2016. Mortality rates, annualized across the entire study period, were 1.47% in Mount Rainier National Park and 2.27% in North Cascades National Park Service Complex; these rates decreased between the first time period and the second, which could reflect blister rust resistance. Signs of mountain pine beetle were rare and limited to a few trees in individual plots. Although reproductive trees were found in most stands, densities were low and regeneration was dominated by subalpine fir.
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Biology, Other; myeloperoxidase, leukocytes, inflammation, oxidative stress, chronic diseases, disease biomarker
Online: 15 February 2018 (16:54:25 CET)
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Myeloperoxidase (MPO) belong to the family of heme containing peroxidases, produced mostly from polymorphonuclear neutrophils. The active enzyme (150 kD) is the product of MPO gene located on long arm of chromosome 17. The primary gene product undergoes several modifications like removal of introns and signal peptide and leads to the formation of enzymatically inactive glycosylated apoproMPO which complexes with chaperons, producing active proMPO by the insertion of heme moiety. The active enzyme is a homodimer of heavy and light chain protomers. This enzyme is released into extracellular fluid after oxidative stress and different inflammatory responses. MPO is the only type of peroxidase using H2O2 to oxidize several halides and pseudohalides to form different hypohalous acids. So the antibacterial activities of MPO involve the production of reactive oxygen and reactive nitrogen species. Controlled MPO release at the site of infection is of prime importance for its efficient activities. Any uncontrolled degranulation exaggerates the inflammation that can also lead to tissue damage even in absence of inflammation. Several types of tissue injuries and pathogenesis of several other major chronic diseases like rheumatoid arthritis, cardiovascular diseases, liver diseases, diabetes and cancer have been reported to be linked with myeloperoxidase derived oxidants. So the enhanced level of MPO activity is one of the best diagnostic tool of inflammatory and oxidative stress biomarkers among these commonly occurring diseases.
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Sergei Kliver,
Mike Rayko,
Alexey Komissarov,
Evgeny Bakin,
Daria Zhernakova,
Kasavajhala V. S. K. Prasad,
Catherine Rushworth,
R. Baskar,
Dmitry Smetanin,
Jeremy Schmutz,
Daniel S. Rokhsar,
Thomas Mitchell-Olds,
Ueli Grossniklaus,
Vladimir Brukhin
Biology, Plant Sciences; Boechera; Brassicaceae; genome; assembly; annotation; apomixis
Online: 14 February 2018 (07:29:29 CET)
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Closely related to the model plant Arabidopsis thaliana, the genus Boechera is known to contain both sexual and apomictic species or accessions. Boechera retrofracta is a diploid sexually reproducing species and is thought to be an ancestral parent species of the apomictic species Boechera divaricarpa. Here we report the de novo assembly of the B. retrofracta genome using short Illumina and Roche reads from 1 paired-end and 3 mate pair libraries. The distribution of 23-mers from the paired end library has indicated a low level of heterozygosity and the presence of detectable duplications and triplications. The genome size was estimated to be equal 227 Mb. N50 of the assembled scaffolds was 2.3 Mb. 27048 protein-coding genes were predicted using a hybrid approach that combines homology-based and de novo methods. Also repeats, tRNA and rRNA genes were annotated. Finally, genes of B. retrofracta and 6 other Brassicaceae species were used for phylogenetic tree reconstruction. Also, a detailed analysis of evolution of the APOLLO apomixis-associated locus was performed. An assembled genome of B. retrofracta will help in the challenging assembly of the highly heterozygous genomes of hybrid apomictic species such as B. divaricarpa.
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Huili Yan,
Wenxiu Xu,
Jianyin Xie,
Yiwei Gao,
Lulu Wu,
Liang Sun,
Xu Chen,
Tian Zhang,
Changhua Dai,
Xiuni Lin,
Lu Feng,
Xueqiang Wang,
Fengmei Li,
Xiaoyang Zhu,
Jinjie Li,
Zichao Li,
Caiyan Chen,
Mi Ma,
Hongliang Zhang,
Zhenyan He
Biology, Plant Sciences; OsCd1; Cadmium accumulation; rice grain; indica; japonica; GWAS
Online: 9 February 2018 (07:13:17 CET)
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Cadmium accumulation in rice grain poses a serious threat to people’s health. Understanding the genetic basis on grain cadmium accumulation facilitates efforts to reduce it. Here, we show that OsCd1 is involved in Cd uptake and contributes to grain accumulation in rice. Natural variation in OsCd1 with a missense mutation Val449Asp is responsible for the divergence of rice grain cadmium accumulation between japonica and indica. Notably, near-isogenic line tests confirmed that the indica variety carrying the OsCd1V449 allele could reduce the grain cadmium accumulation. The favorable allele OsCd1V449 may be an important genetic resource to reduce grain cadmium accumulation for indica.
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Biology, Anatomy & Morphology; Aging, Nutrition, Diet, Muscle atrophy, Body wasting, Food choice
Online: 5 February 2018 (23:43:16 CET)
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Inadequate protein intake can impair protein balance and lead to skeletal muscle atrophy, impaired body growth, and functional decline. Foods provide both non-essential (NEAAs) and essential amino acids (EAAs) that may convey different metabolic stimuli to specific organs and tissues. In this study, we sought to evaluate the impact of six diets with various EAA/NEAA blends on body composition and the risk of developing tissue wasting in late middle-aged male mice. Mice consuming NEAA-based diets, although showing increased food and calorie intake, suffered the most severe weight loss. Interestingly, even moderate NEAAs prevalence was able to induce inflammatory catabolic stimuli, generalized body wasting and systemic metabolic alterations. Complete depletion of retroperitoneal white adipose tissue and a severe loss (>75%) of brown adipose tissue were observed together with muscle wasting. Conversely, EAA-based diets induced significant decreases in weight by reducing primarily fat reserves, but improved clinical parameters. Tissue wasting was caused by altered AA quality, independent of reduced nitrogen or caloric intake. Our results indicate that an optimized balance of AA composition is necessary for preserving overall bodily energy status. These findings are particularly relevant in the context of aging and may be exploited for contrasting its negative correlates including body wasting.
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Biology, Plant Sciences; protease; plant; pathogen; defence; substrate; immunity; hypersensitive response; recognition; signalling; priming
Online: 5 February 2018 (04:11:42 CET)
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Proteases are integral enzymes of the plant immune system. Multiple aspects of defence are regulated by proteases, including the hypersensitive response, pathogen recognition, priming and peptide hormone release. These processes are regulated by unrelated proteases residing at different subcellular locations. In this review we discuss ten prominent plant proteases contributing to the plant immune system, highlighting the diversity of roles they perform in plant defence.
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Biology, Animal Sciences & Zoology; relinquishment; dog; cat; online; Australia
Online: 2 February 2018 (07:27:47 CET)
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While traditionally people relinquish their pets to an animal shelter or pound, the internet provides a newer method to re-home. We analysed advertisements (ads) on the largest website in Australia for trading dogs and cats, gumtree.com.au. Data was collected in 2016. Dogs were sampled on February 7, 16 and 24, 2016 and cats on February 9, 19 and 26, 2016 with 2640 ads for relinquished dogs, and 2093 ads for relinquished cats. It was estimated >31,000 puppies/dogs and >24,000 kittens/cats are relinquished on gumtree.com.au per year. The median age of dogs was 1.42 and cats 0.9 years of age. There were 23% of dog ads and 62% of cat ads for free animals. Compared to the human population there were proportionately more ads in Queensland and fewer ads in Victoria. A total of 15 people were surveyed who had relinquished a dog or cat using gumtree.com.au. The dog owners used gumtree.com.au because they believed the shelters were full (n = 4), and; they wanted to see/interview the new owner (n = 2). For cat owners it was because they had originally got the cat on gumtree.com.au (n = 2); they use gumtree.com.au for other things, and it works (n = 2), and; they wanted to see/interview the new owner (n = 2). The data collected will be valuable for implementation of policy and interventions to protect the welfare of un-wanted dogs and cats.
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Biology, Entomology; volatile fatty acids; Alphitobius diaperinus; locomotor activity; repellency
Online: 30 January 2018 (14:46:51 CET)
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Volatile fatty acids (VFAs) are a group of common metabolites with a potential of universal infochemicals dedicated to transferring of information between higher organisms and bacteria either from microbiome or external environment. VFAs are common substances among various insect orders, there are numerous studies exploring their influence on the behavior of different insect species. In relation to papers published by J. E. McFarlane, we assess the effects of formic, acetic, propionic, butyric, valeric acids on spatial preference of common stored food grain products, and poultry industry pest – lesser mealworm (Alphitobius diaperinus). We present novel method of continuous, simultaneous assessment of site preference as well as travelled distance in constant-flow olfactometer. All tested VFAs except valeric had a significant repellent effect with formic acid being effective in the lowest concentration. Additionally, VFAs significantly altered distance travelled by insects. Obtained results indicate a potential role of VFAs in the olfactory guided behavior of A. diaperinus, we speculate that reaction to the presence if VFAs may deviate form specificity of species’ original habitat.
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Biology, Plant Sciences; cold stress; heat stress; stress recovery; mitochondria; proteomics; respiration; Brassica; angiosperms
Online: 30 January 2018 (10:31:07 CET)
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Complex proteomic and physiological approaches to study cold and heat stress responses in plant mitochondria are still limited. Variations in the mitochondrial proteome of cauliflower (Brassica oleracea var. botrytis) curds after cold and heat and after stress recovery were assayed by 2D PAGE in relation to respiratory parameters. Quantitative analysis of the mitochondrial proteome revealed numerous stress-affected protein spots. In cold alternative oxidase isoforms were extensively upregulated; major downregulations in the level of photorespiratory enzymes, porine isoforms, oxidative phosphorylation (OXPHOS) and some low-abundant proteins were observed. On the contrary, distinct proteins, including carbohydrate metabolism enzymes, heat-shock proteins, translation, protein import, and OXPHOS components were involved in heat response and recovery. Few metabolic regulations were suggested. Cauliflower plants appeared less susceptible to heat; closed stomata in heat stress resulted in moderate photosynthetic, but only minor respiratory impairments, however photosystem II performance was unaffected. Decreased photorespiration corresponded with proteomic alterations in cold. Our results show that cold and heat stress not only operate in diverse mode (exemplified by cold-specific accumulation of some heat shock proteins), but exert some associations on molecular and physiological levels. This implies more complex model of action of investigated stresses on plant mitochondria.
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Biology, Plant Sciences; dehydrins; 2D PAGE; drought; mitochondrial biogenesis; mitochondrial proteome; plant transcriptome
Online: 30 January 2018 (04:17:44 CET)
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The early generative phase of cauliflower (Brassica oleracea var. botrytis) curd ripening is sensitive to the water deficit. Mitochondrial responses under drought within Brassica genus are poorly understood. The main goal of this study was to investigate the mitochondrial biogenesis of three cauliflower cultivars varying with drought tolerance. Diverse quantitative changes (down-regulations mostly) in the mitochondrial proteome were assayed by 2D PAGE coupled with LC-MS/MS. Respiratory (e.g. CII, CIV and ATP synthase subunits), transporter (including diverse porin isoforms) and matrix multifunctional proteins (e.g. components of RNA editing machinery) appeared diversely affected in their abundance under two drought levels. Western immunoassays showed also cultivar-specific responses of selected mitochondrial proteins. Dehydrin-related tryptic peptides found in few 2D spots that appeared immunopositive with dehydrin-specific antisera highlighted the relevance of mitochondrial dehydrin-like proteins for the drought response. The level of selected messengers participating in drought response was also determined. We conclude that the mitochondrial biogenesis was strongly, but diversely affected in various cauliflower cultivars and associated with drought tolerance on the proteomic and functional levels. However, transcriptomic and proteomic regulations were largely uncoordinated due to the suggested altered availability of messengers for translation, mRNA/ribosome interactions and/or miRNA impact on transcript abundance and translation.
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Biology, Other; Mangrove, Avicennia marina, Size Index, Sediment, Urban Development, Human Impacts.
Online: 26 January 2018 (16:27:11 CET)
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Significant changes have occurred at Arabian Gulf Coast of Saudi Arabia over the last three decades. The area of mangrove was reduced by about 55%. Thus the economic, social, and environmental value of mangroves must be assessed over short -to long-term scales and employ these assessments for the awareness rising at local communities. This study provides a preliminary assessment of the risks on mangrove vegetation; it will provide database to mitigate the tremendous pressures due to coastal development and urban activities. The effects of human development on the mangrove plant cover in Eastern Region of KSA were recognised, during 2013 to 2016. The mean variations of physio-chemical characteristics in water and sediment were recorded. With regard to water analyses including; nitrogen, phosphorus, TSS, TDS, BOD, and turbidity were evaluated. On the other hand, for sediment: TDS, nitrogen, phosphorus, sulphate and total organic carbon were assessed. Moreover, the growth parameters: plant height, and size index, of Avicennia marina were recorded and estimated. It is concluded that human impact and urban developments have exerted drastic effects on the coastal ecosystems and its environments.
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Biology, Ecology; microbiomes; next generation sequencing, plant yield; rhizobacteria; rhizosphere; sustainable agriculture
Online: 25 January 2018 (17:41:19 CET)
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Rhizosphere microbiomes which have been implicated to enhance plant growth and yield are modulated or influenced by a couple of environmental factors such as soil type, plant cultivar, climate change and anthropogenic activities. In particular, anthropogenic activity such as the use of nitrogen-based chemical fertilizers is associated with environmental destruction and this call for a more ecofriendly strategy to increase nitrogen level of agricultural land. This feat is attainable by harnessing nitrogen-fixing endophytic and free-living rhizobacteria. Rhizobium, Pseudomonas, Azospirillum and Bacillus have been found to have positive impacts on crops by enhancing both above and belowground biomass and could therefore play positive roles in achieving sustainable agriculture. Thus, it is needful to study these rhizosphere microbiomes with more sophisticated culture-independent technologies such as next generation sequencing (NGS) with the prospect of discovering novel bacteria with plant growth promoting traits. This review is therefore aimed at discussing factors that can modulate rhizosphere microbiomes with focus on the contributions of nitrogen fixing bacteria towards sustainable agricultural development and the techniques that can be used for their study.
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Biology, Other; epoxyqinomicin; DHMEQ; metastasis; invasion; adhesion; 3D cell culture
Online: 25 January 2018 (10:27:11 CET)
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We previously designed and synthesized dehydroxyepoxyquinomicin (DHMEQ) as an inhibitor of NF-κB based on the structure of microbial secondary metabolite epoxyquinomicin C. DHMEQ showed anti-inflammatory and anticancer activity in various in vivo disease models without toxicity. Cell detachment from the primary tumor and subsequent invasion are considered to be early phase of metastasis, while tumor cell attachment to the tissue and secondary tumor formation the late phase. The assay system for late phase was set up with intra-portal-vein injection of pancreatic cancer cells. Administration of DHMEQ was found to inhibit the liver metastasis possibly by decreasing the expression of MMP-9 and IL-8. Also when the pancreatic cancer cells treated with DHMEQ was inoculated into the peritoneal cavity of mice, the metastatic foci formation was inhibited. These results indicate that DHMEQ is likely to inhibit the late phase of metastasis. Meanwhile, we have recently employed three-dimensional (3D) culture of breast cancer cells for the model of early phase metastasis. DHMEQ inhibited the 3D invasion of breast cancer cells without toxicity. In this way, DHMEQ was shown to inhibit the late and early phases of metastasis. Thus, DHMEQ is likely to be useful for the suppression of cancer metastasis.
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Biology, Other; small non-coding RNAs; gene regulation; archaea; stress response; regulatory networks
Online: 25 January 2018 (03:57:55 CET)
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Small non-coding RNAs (sRNAs) are ubiquitously found in the three domains of life playing large-scale roles in gene regulation, transposable element silencing, and defense against foreign elements. While a substantial body of experimental work has been done to uncover function of sRNAs in Bacteria and Eukarya, the functional roles of sRNAs in Archaea are still poorly understood. Recently, high throughput studies using RNA-sequencing revealed that sRNAs are broadly expressed in the Archaea, comprising thousands of transcripts within the transcriptome during non-challenged and stressed conditions. Antisense sRNAs, which overlap a portion of a gene on the opposite strand (cis-acting), are the most abundantly expressed non-coding RNAs and they can be classified based on their binding patterns to mRNAs (3’ UTR, 5’ UTR, CDS-binding). These antisense sRNAs target many genes and pathways, suggesting extensive roles in gene regulation. Intergenic sRNAs are less abundantly expressed and their targets are difficult to find because of a lack of complete overlap between sRNAs and target mRNAs (trans-acting). While many sRNAs have been validated experimentally, a regulatory role has only been reported for very few of them. Further work is needed to elucidate sRNA-RNA binding mechanisms, the molecular determinants of sRNA-mediated regulation, whether protein components are involved, and how sRNAs integrate with complex regulatory networks.
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Biology, Agricultural Sciences & Agronomy; abiotic stress; antioxidant defense; enzyme regulations; oxidative stress; plant nutrients; reactive oxygen species; soil fertility
Online: 24 January 2018 (07:01:05 CET)
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Among the plant nutrients potassium (K) is one of the vital elements required for plant growth and physiology. Potassium is not only a constituent of plant structure but also plays regulatory function in several biochemical processes related to protein synthesis, carbohydrate metabolism, enzyme activation. There are several physiological processes like stomatal regulation and photosynthesis are dependent on K. In the recent decades K was found to provide abiotic stress tolerance. Under salt stress, K helps in maintaining ion homeostasis and regulation of osmotic balance. Under drought stress condition K regulates the stomatal opening and makes the plants adaptive to water deficit. Many reports provided the notion that K enhances the antioxidant defense in plants and therefore, protects the plants from oxidative stress under various environmental adversities. Also, it provides some cellular signaling alone or in association with other signaling molecules and phytohormones. Although a considerable progress in understanding K-induced abiotic stress tolerance in plants has been achieved the exact molecular mechanisms of such protections are still under research. In this review, we summarized the recent literature on the biological functions of K, its uptake, and translocation and its role in plant abiotic stress tolerance.
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Biology, Plant Sciences; CO2; adaptation; photosynthesis; growth; weeds; carboxylation efficiency
Online: 22 January 2018 (17:44:14 CET)
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Seeds of three C3 and one C4 annual weedy species were collected from agricultural fields in Beltsville, Maryland in 1966 and 2006, when atmospheric CO2 concentrations averaged about 320 and 380 mmol mol-1, respectively. Plants from each collection year were grown over a range of CO2 concentrations to test for adaptation of these weedy species to recent changes in atmospheric CO2. In all three of the C3 species, the increase in CO2 concentration from 320 to 380 mmol mol-1 increased total dry mass at 24 days in plants from seeds collected in 2006, but not in plants from seeds collected in 1966. Shoot and seed dry mass at maturity was greater at the higher growth CO2 in plants collected in 2006 than in 1966 in two of the species. Down regulation of photosynthetic carboxylation capacity during growth at high CO2 was less in the newer seed lots than in the older in two of the species. Overall, the results indicate that adaptation to recent changes in atmospheric CO2 has occurred in some of these weedy species.
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Biology, Forestry; Forest rehabilitation, humic acid fertilizer, relative height growth rate, soil chemical properties
Online: 22 January 2018 (17:34:43 CET)
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Field experiments were carried out during 2011-2014 at the Research and Experimental Center to Combating Desertification located in the Elsen Tasarkhai station of central Mongolia. The study was aimed to identify the effects of oxidized brown coal humic acid fertilizer on the relative growth rate of several trees for forest rehabilitation. The trees used were Populus sibirica, Salix ledebouriana and Acer tataricum. The experiment was carried out with the concentrations of 2,000, 10,000 and 20,000 mg L-1 of humic acid fertilization treatments. The measurement of relative height growth rate (RHGR) was conducted for a period of 4 years. The treatments showed significant differences within humic fertilizer concentrations which differed depending on the species. Compared to the monthly RHGR over the study, the treatment of fertilizers were significantly better for tree growth. P. sibirica in the 10,000 and 20,000 mg L-1 humic acid fertilizers had significant height growth rates. In addition, when the humic acid treatments were compared to control, A. tataricum decreased over the years which were statistically significant for high growth rate and a positive effect of humic acid fertilization treatments was observed. Furthermore, results showed that oxidized brown coal humic acid fertilizers as organic fertilizer can have a positive effect for the growth of A. tataricum during the study years. The results showed that the soil chemical properties EC, CO2, NO3, and K2O were significant among all the treatments compared to the control. The effect on P2O5 statistically significantly increased among all the treatments. However, pH and Mg were not significant effect among all the treatments. Combining the results obtained from the oxidized brown coal humic acid fertilization with sustainable land management practices can help improve soil organics for environmental issues in degraded sandy soil regions.
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Biology, Animal Sciences & Zoology; Indian ocean; livestock; Extended-Spectrum β-Lactamase producing Enterobacteriaceae; risk factors; CTX-M; enzymes
Online: 22 January 2018 (12:02:53 CET)
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In South Western Indian ocean (IO), Extended-Spectrum β-Lactamase producing Enterobacteriaceae (ESBL) are a main public health issue. In livestock, ESBL burden was unknown. The aim of this study was estimating the prevalence of ESBL on commercial farms in Reunion, Mayotte and Madagascar and genes involved. Secondly, risk factors of ESBL occurrence in broiler, beef cattle and pig farms were explored. In 2016-2017, commercial farms were sampled using boot swabs and samples stored at 4°C before microbiological analysis for phenotypical ESBL and gene characterization. A semi-directive questionnaire was performed. Prevalences observed in all production types and territories were elevated, except for beef cattle in Reunion which differed significantly. The most common ESBL gene was the CTX-M-1 subtype. Generalized linear models explaining ESBL occurrence varied between livestock production sectors and allowed identifying main protective (e.g., water quality control and detergent use for cleaning) and risk factors (e.g., recent antibiotic use, other farmers visiting the exploitation, pet presence). This study is the first to explore tools for antibiotic resistance management in IO farms. It provides interesting hypothesis to explore about antibiotic use in IO and ESBL transmission between pig, beef cattle and humans in Madagascar.
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Biology, Ecology; current; filtration rate; freshwater bivalve; mussel size; response surface methodology; Sinanodonta woodiana
Online: 19 January 2018 (06:41:05 CET)
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In this study, we applied a central composite design to estimate independent variables and establish optimal conditions of filtration rate and feces production that enhance filtration of suspended organic matter by the freshwater mussels Sinanodonta woodiana. The results indicated that statistical design methodology offers an efficient and feasible approach for high filtration and low feces production condition optimization. The proposed model equation takes into account the quantitative effect of variables and also the influence of interactions among variables on mussel filtration rate. Under the optimal experimental conditions (mussel size, 13.0 ± 0.2 cm; water current, 17.5 L/h), the experimental filtration rate of 4.47 ± 1.82 L/mussel/h showed a degree of correspondence with the predicted value of 8.4 L/mussel/h, which verified the practicability of this optimum strategy.
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Biology, Other; Dunaliella salina; new isolates; characterization; light intensity; β-carotene; carotenoids; correlations; lutein; classification
Online: 17 January 2018 (12:04:11 CET)
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The halotolerant microalga Dunaliella salina has been widely studied for natural β-carotene production. This work shows biochemical characterization of three newly isolated Dunaliella salina strains DF15, DF17 and DF40 compared with D. salina CCAP 19/30 (confirmed to be D. tertiolecta) and D. salina UTEX 2538 (also known as D. bardawil). Although all three new strains have been genetically characterized as Dunaliella salina strains, their ability to accumulate carotenoids and their capacity for photoprotection against high light stress are different. DF15 and UTEX 2538 reveal great potential for producing large amount of β-carotene and maintained a high rate of photosynthesis under light of high intensity; however, DF17, DF40 and CCAP 19/30 showed increasing photoinhibition with increasing light intensity, and reduced contents of carotenoids, in particular b-carotene, suggesting that the capacity of photoprotection is dependent on the cellular content of carotenoids, in particular β-carotene. Strong positive correlations were found between the cellular content of each of all-trans β-carotene, 9-cis β-carotene, all-trans α-carotene and zeaxanthin but not lutein in the D. salina strains. Lutein was strongly correlated with respiration in photosynthetic cells and strongly related to photosynthesis, chlorophyll and respiration, suggesting an important and not hitherto identified role for lutein in co-ordinated control of the cellular functions of photosynthesis and respiration in response to changes in light conditions, which is broadly conserved in Dunaliella strains. Statistical analysis based on biochemical data revealed a different grouping strategy from the genetic classification of the strains. The significance of these data for strain selection for commercial carotenoid production is discussed.
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Biology, Ecology; lead pollution; alpine environments; Alticola argentatus; Microtus gregalis; atmospheric deposition; heavy metals
Online: 17 January 2018 (11:37:36 CET)
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High mountain areas are an appropriate indicator of anthropogenic lead (Pb), which can reach the remote mountain ranges through long distance atmospheric transport. We compared the content of Pb in ecologically equivalent rodent species from Tian-Shan with European mountain ranges Tatra, Vitosha and Rila mountains. We used bone tissues from terminal tail vertebrae of small rodents for detection of Pb levels by using electrothermal atomic absorption spectroscopy (AAS). The tail bones of Tian-Shan rodents had significantly lower Pb levels than snow voles from Tatra mountains, but there was no significant difference in comparison with Vitosha and Rila mountains. We can conclude that Tian-Shan shows lower pollution by Pb than Tatra mountains, what may be a reason of longer lasting industrialization of north-western Europe and strongly prevailing west winds in Tatra mountains.
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Biology, Other; MMP-1, EGFR-TKI resistance, lung adenocarcinoma, mTOR
Online: 16 January 2018 (13:57:04 CET)
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Lung adenocarcinoma with EGFR-TKI (epidermal growth factor receptor-tyrosine kinase inhibitor) resistance was reported to harbor higher ability of invasion and migration than those sensitive to EGFR-TKI, but the function of MMPs (matrix metalloproteinases) has not been explored in EGFR-TKI resistant lung adenocarcinoma. In this study, the correlation between immunohistochemical status of MMP-1 and clinicopathological factors were analyzed in 89 lung adenocarcinoma. We performed microarray, migration assay and invasion assay using EGFR-TKI sensitive cell lines and EGFR-TKI resistant cell lines. To clarify the mechanism of MMP-1 induction, we treated lung adenocarcinoma cells with EGF and rapamycin, performed phosphorylation antibody array and analyzed the correlation between MMP-1 expression and EGFR or mTOR (mammalian target of rapamycin) pathway. As a result, we firstly demonstrated that MMP-1 played an important role in migration and invasion abilities of EGFR-TKI resistant lung adenocarcinoma, and that mTOR pathway could be associated with an induction of MMP-1. We demonstrated the significant positive correlation between MMP-1 status in lung adenocarcinoma cells and the history of smoking, and the subtype of invasive mucinous adenocarcinoma. In conclusion, This study provides insights into the development of a possible alternative therapy manipulating MMP-1 and mTOR signaling pathway in EGFR-TKI resistant lung adenocarcinoma.
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Biology, Plant Sciences; somaclones; micropropagation; cactus; Cactaceae; microsatellite.
Online: 15 January 2018 (17:07:19 CET)
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Somaclones with typical and atypical shoots were regenerated from a callus culture in the same culture medium and in equal culture conditions. Since the genetic relationship among regenerated somaclones has not been investigated, current study employed heterologous microsatellite primers to examine the molecular diversity within and among somaclones, showing typical and atypical phenotypes with high morphological divergence. Nei identity value calculated between the somaclones was high (I = 0.929) and AMOVA showed higher genetic variation within (96%) than among (4%) the samples of somaclones. The polymorphism in the microsatellite loci indicated high levels of mean observed and expected heterozygosity in atypical somaclones, presumably with high adaptive potential and as source of genotypes for generation of new varieties of ornamental cacti. Low molecular divergence between typical and atypical morphologies of somaclones is a promising perspective for use of the atypical somaclones as source of chemical compounds of commercial and industrial interest. The somaclonal variations occurring in vitro callus culture has generated phenotypically differentiated subpopulations with low molecular divergence, however with high genetic variability, enough to be recommended as a source of genotypes to generate new varieties of ornamental cacti and of plants with new traits, necessary for breeding programs.
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Biology, Physiology; carbonic anhydrases; CA gene family; Chlamydomonas reinhardtii; model alga; metabolic role; photosynthesis
Online: 12 January 2018 (07:21:25 CET)
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Carbonic anhydrases (CAs) are metalloenzymes that are omnipresent in nature. The CAs catalyze the basic reaction of reversible hydration of CO2 to HCO3− and H+ in all living organisms. Photosynthetic organisms contain six evolutionarily different classes of CAs, namely, α-CAs, β-CAs, γ-CAs, δ-CAs, ζ-CAs, and θ-CAs. Many of the photosynthetic organisms contain multiple isoforms of each CA family. Model alga, Chlamydomonas reinhardtii contains fifteen CAs belonging to three different CA gene families. Out of the fifteen CAs, three belong to α-CA gene family, nine to β-CA gene family, and three are γ-CAs. The multiple copies of the CAs in each gene family may be due to gene duplications within the particular CA gene family. The CAs of Chlamydomonas reinhardtii are localized in different subcellular compartments of this unicellular alga. The presence of a large number of CAs and their diverse subcellular localization within a single cell suggests the importance of these enzymes in metabolic and biochemical roles they perform in this unicellular alga. In the present review, we update the information on molecular biology of all the fifteen CAs and their metabolic and biochemical roles in Chlamydomonas reinhardtii. We also present a hypothetical model showing the known functions of CAs and predicting the functions of CAs for which precise metabolic roles are yet to be discovered.
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Biology, Other; Tuberculosis; Type 2; diabetes mellitus PM2.5; air pollution; inflammation
Online: 11 January 2018 (01:45:36 CET)
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Rapid urbanization, increasing population and increased industrialization to cater to demands of the growing population has imposed upon us a huge environmental cost. The significantly deteriorated air quality across the globe is associated with a direct and indirect impact on public health. While associated disorders such as chronic obstructive pulmonary diseases, heart failures are well documented, less is known about the biological basis of the process. We hypothesize that the worsening air quality may likely impact common systemic inflammatory processes, thus driving communicable and non-communicable diseases alike.Receptor mediated entry of particulate matter (PM2.5) results in activation of signaling cascades which culminate in production of inflammatory chemokine and cytokine responses, traversing through the blood mediating impacting not only on other organs but also dysbiosis of microflora. For the purpose of the review we choose tuberculosis (TB) as a model for communicable infectious disease and type 2 diabetes mellitus (T2DM) as a marker for non-communicable disorder. The increasing prevalence of these co-morbidities and the burdening of public health systems justifies this example. However the hypothesis may be applicable to other inflammation driven disorders also.
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Biology, Anatomy & Morphology; octacalcium phosphate; bone matrix gelatin; osteogenesis
Online: 9 January 2018 (03:14:28 CET)
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Objective: Regeneration of bone defects remains a challenge for maxillofacial and reparative surgeons. The purpose of this histological study was to assess the osteogenic potential of octacalcium phosphate (OCP) and bone matrix gelatin (BMG) alone and in combination in artificially created mandibular bone defects in rats. The quality of the newly formed bone was also evaluated. Methods: Thirty-six male Sprague Dawley rats (6-8 weeks old with 120-150 g weight) were randomly divided into four groups. Defects (3 mm in diameter and 2 mm in depth) were created in the mandible of rats and filled with 6 mg of OCP, BMG or a combination of both (1/4 ratio), respectively. Defects were left unfilled in the control group. To assess osteoinduction and bone regeneration and determine the quality of the newly formed bone, tissue specimens were harvested at seven, 14, and 21 days post-implantation. The specimens were processed, stained with hematoxylin and eosin (H&E) and histologically analyzed under light microscopy. Results: In the experimental groups, new bone formation was initiated at the margins of defects from seventh day after implantation. At the end of the study period, the amount of the newly formed bone increased and the bone was relatively mature. Osteoinduction and new bone formation were greater in OCP/BMG group. In the control group, slight amount of new bone had been formed at the defect margins (next to host bone) on day 21. Conclusion: Combination of OCP/BMG may serve as an optimal biomaterial for treatment of mandibular bone defects.
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Biology, Animal Sciences & Zoology; prevalence; soil transmitted helminth; Nkpor; Mgbodohia
Online: 2 January 2018 (12:25:01 CET)
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Soil transmitted helminthic infections (STHIs) are common public health concern among children in Sub saharan Africa. A study to determine the prevalence of these infections among pupils in two primary schools in Nkpor and Mgbodohia communities, Obio/Akpor Local Government Area, Rivers State, Nigeria was conducted. The formo-ether concentration technique was used to concentrate and separate the eggs and cysts from the faeces. Out of 107 pupils investigated, 81 (75.7 %) were positive for at least one helminthic infection. Although more females (54.3%) were infected than males (45.7%), there was no significant (P>0.05) difference in the prevalence of Soil transmitted helminthic infections in relation to sex. There was a significant difference (P>0.5) in infection among two major age groups (5-10years-45% and 11-15years-41.9%). Children within the age group of 16-20years had the least infection (9.9%). Out of the 81 children positive for STH, 47 (43.9 %,), 23 (21.5%), 11 (10.3%) and 5(4.7%) had Ascaris lumbricoide, Hookworm, Trichirus trichiura and mixed infection (A.lumbricoide + T. trichiura) respectively. Ascaris lumbricoide (43.9%) was significantly (P<0.05) higher in prevalence than other parasites. Soil transmited helminthic infections are a public health among children concern in the study area. Provision of portable water, toilet facilities and good education on the epidemiology of STHIs in addition to regular de-worming will enhance control measures.
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Biology, Forestry; plant nutrition; chemical fertilization; nutrient diagnosis; forest plantation; foliar nutrients
Online: 2 January 2018 (10:25:46 CET)
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Pinus patula is one of the most planted wood conifer species worldwide; however, no foliar nutrient standards exist for this species up to date. The objective of the present study was to generate and verify two sets of foliar nutrient standards for nearly ten-year-old P. patula trees: critical nutrient concentrations and DRIS norms. Nutrients studied were N, P, K, Ca, Mg, Fe, Cu, Zn, Mn, and B. The reference standards were verified experimentally by installing two fertilization trials; one of them located in Huayacocotla, state of Veracruz and the other one in Aquixtla, state of Puebla, Mexico. Nutrient status of each fertilization trial was correctly predicted by critical nutrient values and DRIS as well. Both standards were able to detect the secondary growth-limiting nutrient deficiency in the Huayacocotla trial, where the primary limitation for growth was scarcity of solar radiation within tree crowns. The limiting nutrient in both experimental trials was K.
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Biology, Animal Sciences & Zoology; polycyclic aromatic hydrocarbons; petroleum; Clarias gariepinus
Online: 2 January 2018 (09:56:53 CET)
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One hundred and twenty (120) fingerlings of Clarias gariepinus (mean weight: 0.96 ± 0.1g) were randomly exposed to 4 experimental treatments of petroleum, based on LC50 values (6.4mg/L of crude oil, 8.7mg/L of petrol, 8.0mg/L of kerosene and 7.8mg/L of diesel oil) and replicated thrice, to determine polycyclic aromatic hydrocarbons (PAH) in exposed fish for 96 h. There was no significant difference (P > 0.05) in total (PAHs) between crude oil (97.1 ng/uL) and diesel (97.2 ng/uL) exposed fish and also between petrol (53.2 ng/uL) and kerosene (49.6 ng/uL) exposed fish, but there was a significant difference (P < 0.05) in PAH levels of the crude oil/diesel exposed -groups of fish compared to petrol/kerosene exposed -groups of fish (97.1/97.2 and 53.2/49.6 ng/uL). Naphthalene correlated positively to benzo a anthracene (r=0.672, (P < 0.05), benzo b fluoranthene (r=0.681, P < 0.05) and chrysene (r=0.615, P < 0.05) but did not correlate to fluorene. Benzo a anthracene correlated positively to benzo a pyrene (r=0.578, P < 0.05), phenathrene (r=0.685, P < 0.05) but did not correlate to acenaphthene. Fluorene correlated positively to benzo a pyrene (r=0.695, P < 0.05) but did not correlate to chrysene. Chrysene correlated positively to dibenzo a,h, pyrene (r=0.658, P < 0.05) to phenathrene and benzo b fluoranthene (r=0.659, P< 0.05). Indeno 123 cd- pyrene and fluranthene however did not correlate to other PAHs except naphthanene, acenaphthene and acenaphthylene. The level of PAH in fish may translate to the toxicity effect since crude oil and diesel with lower LC50 (6.4 and 7.8 mg/L) deposited greater PAH than kerosene and petrol with higher LC50 (8.7 and 8.0 mg/L) in fingerlings of C. gariepinus. High risk to cancer disorders may occur in exposed fish to petroleum with high incidence of fluorene , anthracene, pyrene and benz a anthracene which correlated positively to benzo a pyrene which provide some basis for predicting impact of oil spills on fingerling population.
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Biology, Plant Sciences; Actinidia deliciosa; ethylene; fruit ripening; mass spectrometry; post-harvest; proteomics
Online: 29 December 2017 (09:01:57 CET)
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An understanding of the mechanism underlying fruit ripening is critical for fruit quality improvement. Although post-harvest ethylene application is known to enhance the onset of fruit ripening, exact mechanisms remain unclear. To characterize the fruit ripening process and mechanism, we investigated the effects of exposing kiwifruit cultivars ‘Hayward’ and ‘Gamrok’ to exogenous ethylene treatment post-harvest using comprehensive proteomic analyses. Comparative two-dimensional gel electrophoresis showed that most of the proteins aggregated in ethylene-treated samples compared to the control (non-treated). We observed that among all ethylene treatments, 95 proteins from ‘Hayward’ and 106 from ‘Gamrok’ were differentially expressed. Interestingly, among the elicited protein successfully identified by matrix-assisted laser desorption/ionization tandem time-of-flight mass spectrometry, 50% from “Hayward’ and 60% from ‘Gamrok’ are associated with fruit ripening. Furthermore, 18% and 10% of proteins, respectively, are associated with defense response, whereas other major proteins are related to protein biosynthesis and photosynthesis/Calvin cycle. Interactions between identified proteins were demonstrated by bioinformatic analysis, providing insights into biological pathways and molecular functions in post-harvest kiwifruit ripening elicited by ethylene application. The present proteomic study in accordance with physiological analysis provides a quantitative evaluation of fruit ripening in response to exogenous ethylene in post-harvest kiwifruit.
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Biology, Animal Sciences & Zoology; local perceptions; chimpanzees; conservation; natural resources; human-chimpanzees conflict; traditional beliefs
Online: 29 December 2017 (08:00:35 CET)
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The objective is to study the local perceptions on the conservation of wild chimpanzees (Pan troglodytes verus) in the Réserve Naturelle Communautaire de Dindéfélo (RNCD), southeast of Senegal, to design specific actions to improve conservation management. We conducted 338 semi-structured interviews in three main villages of RNCD. Three-fourths of the population were farmers. Of those interviewed, 29% received elementary education. Two of the three villages participated in a project to plant trees as fences. On average, 66% of the respondents were animists. Of the respondents who were afraid to see a chimpanzee, 68% answered because they attack. Seventy-seven percent washed their clothes in the forest river because there was more water than in the village wells. Of the interviewees who threw the old clothes into the forest, 50% did it due to tradition. Ninety-six percent of respondents stated that chimpanzees do not feed from their crops. The main problems of the locals with the Reserve were lack of water and basic resources and not been allow to cut trees in protected areas. There were significant relationships between education (1 relationship), environmental project (4 relationships) and animism (11 relationships) with local perceptions. The 93% of the respondents who had the traditional belief that “if the old clothes were burnt, children would become sick” feel fear of chimpanzees, while those who did not have this animistic belief the 6% are afraid (χ2 = 1.57, P < 0.02). These local perceptions allow us to design specific course of action to improve chimpanzee conservation and sustainable coexistence in this complex period of the Anthropocene.
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Petr Maděra,
Hana Habrová,
Martin Šenfeldr,
Irena Kholová,
Samuel Lvončík,
Lenka Ehrenbergerová,
Matěj Róth,
Nadezhda Nadezhdina,
Petr Němec,
Jonathan Rosenthal,
Jindřich Pavliš
Biology, Forestry; afforestation; browsing; dragon's blood tree; regeneration; semi-arid tropical zone; Soqotra
Online: 25 December 2017 (07:47:00 CET)
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Dragon's blood tree, a flagship endemic species of Socotra, is threatened with extinction due to lack of natural regeneration, likely because of goat herbivory and/or climatic factors. Loss of dragon's blood tree would result in loss of other native flora, heightening the importance of formulating a conservation strategy for it. Although artificial afforestation might be used to offset the lack of natural regeneration, it would have to overcome the same threats faced by naturally occurring seedlings. Moreover, there is no published information on the growth dynamics of seedlings in plantations in situ on Socotra. To fill this information gap, we compared seedling growth over an 8-year period after planting at three sites that differed in the degree to which goats were excluded and in whether they were watered regularly over the period. In addition to developing a new classification of the growth stages, which will enable better tracking of population dynamics, we found that continuous goat exclusion was necessary to prevent seedling mortality. Also, although seedling growth overall was slow, growth parameters of regularly irrigated seedlings ranged from 156 % to 446 % of those not regularly watered, suggesting that this treatment can speed seedlings’ escape from goat browsing.
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Biology, Plant Sciences; pre-harvest; ripeness; image analysis; machine learning; fruit phenotyping
Online: 20 December 2017 (09:35:36 CET)
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Global food security for the increasing world population not only requires increased sustainable production of food but a significant reduction in pre- and post-harvest waste. The timing of when a fruit is harvested is critical for reducing waste along the supply chain and increasing fruit quality for consumers. The early in field assessment of fruit ripeness and prediction of the harvest date and yield by non-destructive technologies have the potential to revolutionize farming practices and enable the consumer to eat the tastiest and freshest fruit possible. A variety of non-destructive techniques have been applied to estimate the ripeness or maturity but not all of them are applicable for in situ (field or glasshouse) assessment. This review focuses on the non-destructive methods which are promising, or have already been, applied to the pre-harvest in field measurement including colorimetry, visible imaging, spectroscopy and spectroscopic imaging. Machine learning and regression models used in assessing ripeness are also discussed.
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Biology, Agricultural Sciences & Agronomy; data needs; empirical models; integrated models; process-based models; review
Online: 15 December 2017 (07:13:40 CET)
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There is increasing evidence that the impact of climate change on the productivity of grasslands will at least partly depend on their biodiversity. A high level of biodiversity may confer stability to grassland ecosystems against environmental change, but there are also direct effects of biodiversity on the quantity and quality of grassland productivity. To explain the manifold interactions, and to predict future climatic responses, models may be used. However, models designed for studying the interaction between biodiversity and productivity tend to be structurally different from models for studying the effects of climatic impacts. Here we review the literature on the impacts of climate change on biodiversity and productivity of grasslands. We first discuss the availability of data for model development. Then we analyse strengths and weaknesses of three types of model: ecological, process-based and integrated. We discuss the merits of this model diversity and the scope for merging different model types.
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Biology, Other; cell programming; stress resistance; gene overexpression; radiation; oxidative stress; chemical genotoxins; malignant transformation; diversity of mechanisms
Online: 9 December 2017 (13:26:14 CET)
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Different organisms, cell types, and even similar cell lines can dramatically differ in resistance to genotoxic stress. This testifies to the wide opportunities for genetic and epigenetic regulation of stress resistance. These opportunities could be used to increas the effectiveness of cancer therapy, develop new varieties of plants and animals, and search for new pharmacological targets to enhance human radioresistance, for example, for -manned deep space expeditions. Based on the comparison of transcriptomic studies in cancer cells, in this review we propose that there is a high diversity of genetic mechanisms of development of genotoxic stress resistance. This review focused onpossibilities and limitations of the proposed regulation of the resistance of normal cells whole organisms to genotoxic and oxidative stress by overexpressing of stress-response genes. Moreover, the existing experimental data on the effect of such overexpression on the resistance of cells and organisms to various genotoxic agents has been analyzed and systematized. We suggest that the recent advances in the development of multiplex and highly customizable gene overexpression technology that utilizes the mutant Cas9 protein and the wealth of available data on gene functions and their signal networks open new opportunities for research in this field.
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Biology, Horticulture; Grafting; Pecan; Transcriptome; Graft union; Hormone
Online: 7 December 2017 (17:21:15 CET)
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Pecan (Carya illinoinensis), as a popular nut tree, is widely planted in China in recent years. Grafting is an important technique for its cultivation. For a successful grafting, graft union development generally involves the formation of callus and vascular bundles at the graft union. To explore the molecular mechanism of graft union development, we applied high through-put RNA sequencing to investigate transcriptomic profiles of graft union at four time points (0d, 8d, 15d, and 30d) during pecan grafting process. We identified a total of 12,180 differentially expressed genes. In addition, we found that the content of auxin, cytokinin and gibberellin were accumulated at the graft unions during the grafting process. Correspondingly, genes involved in those hormone signaling were found to be differentially expressed. Interestingly, we found that most genes associated with cell division were up-regulated at callus formative stages, while genes related to cell elongation, secondary cell wall deposition, and programmed cell death were generally up-regulated at vascular bundle formative stages. In the meantime, genes responsible for reactive oxygen species were highly up-regulated across the graft union developmental process. These results will aid in our understanding of successful grafting in the future.
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Biology, Other; proteolysis; site-directed mutagenesis; complementation; mutants; morphology
Online: 3 December 2017 (06:23:08 CET)
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Viruses with spindle or lemon-shaped virions are rare in the world of viruses, but are common in viruses of archaeal extremophiles, possibly due to the extreme conditions in which they thrive. However, the structural and genetic basis for the unique spindle shape is unknown. The best-studied spindle-shaped virus, SSV1, is composed mostly of the major capsid protein VP1. Similar to many other viruses, proteolytic cleavage of VP1 is thought to be critical for virion formation. Unlike half of the genes in SSV1, including the minor capsid protein gene vp3, the vp1 gene does not tolerate deletion or transposon insertion. In order determine the role of the vp1 gene and its proteolysis for virus function, we developed techniques for site-directed mutagenesis of the SSV1 genome and complemented deletion mutants with vp1 genes from other SSVs. By analyzing these mutants we demonstrate that the N-terminus of the VP1 protein is required, but the N-terminus, or entire SSV1 VP1 protein, can be exchanged with VP1s from other SSVs. However, the conserved glutamate at the cleavage site is not essential for infectivity. Interestingly, viruses containing point mutations at this position generate mostly abnormal virions.
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Biology, Ecology; affordance; umwelt; agency; active inference; allostasis; immune cognition; situated Darwinism; information; entropy; free energy principle
Online: 30 November 2017 (09:02:17 CET)
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The relationship of the animal with its environment has been of longstanding interest in philosophy and science. Here I provide a brief introduction to concepts that place an emphasis on mutualism as the basis of organism - environment interaction, in contrast to the long standing view that the environment exerts an instrumental role in shaping the organism. Two influential theories have been von Uexküll’s theory of umwelt and Gibson’s theory of affordances. The former envisioned the animal as immersed in its surroundings (umwelt) to form a functional unit. In a similar manner, the latter theory describes a unity between 1) environmental information that provides the animal with opportunities for action (affordances) and 2) the ability of the animal to perceive and engage with those affordances. These views have influenced more recent ecological models of the organism as the functional unit of biology and have also influenced models of immune function. In ecological models, agency is seen as the ability of the organism to predict and control its engagement with the environment in order to maintain its integrity. The predominant contemporary model of neural function in which perception and action are understood to operate through Bayes-like active inference complements the concept of agency as proposed by the mutualism models. However, it is suggested that rather than a constant mutualism, encounters between organism and environment range over a dynamic spectrum from dualism to mutualism. It is also suggested that along this spectrum, agency emerges when the balance of instrumentality shifts from the environment to the organism, and that the balance of this relationship can further progress towards a felicitous mutualism. Meaning emerges between environmental information and an agent as opportunity for action. Implications for opportunities to foster agency in animals within our care is noted.
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Biology, Agricultural Sciences & Agronomy; carbohydrate starvation; non-structural carbohydrate; photosynthesis; photosynthesis inhibition; respiration; relative growth rate; structure; diurnal variation
Online: 30 November 2017 (08:48:58 CET)
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Predicting the growth response of seedlings from the environmental responses of photosynthesis and metabolism may be improved by considering the dynamics of non-structural carbohydrate, NSC, over a diurnal cycle. Attenuation of growth metabolism when NSC content is low could explain why some NSC is conserved through the night. A dynamic model, incorporating diurnal variation in NSC, was developed to simulate growth of seedlings hour-by-hour. I compared predictions of this model to published growth and NSC data for seedlings that varied according to temperature, light, day length, or CO2. Prolonged-darkness experiments showed a temperature dependent upper limit on the respiration capacity. Respiration was attenuated as NSC was depleted. Furthermore, when NSC was high at dawn, inhibition of photosynthesis could attenuate the accumulation of NSC under low temperature, or high light, or high CO2. These concepts were used to simulate plant metabolism and growth rates and diurnal variation of NSC in tomato seedlings under two light levels and various temperatures. Comparison of other results using the same model parameters showed the dynamic model could predict results for starch and starch-less plants, and when growth was affected by CO2 enrichment and day length.
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Biology, Anatomy & Morphology; Dutch Konik; Metacarpal; Metatarsal; primitive horse; splint bones; Tarpan
Online: 29 November 2017 (07:01:17 CET)
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The Dutch Konik is valued from a genetic conservation perspective and also for its role in preservation of natural landscapes. The primary management objective for the captive breeding of this primitive horse is to maintain its genetic purity, whilst also maintaining the nature reserves on which they graze. Breeding selection has traditionally been based on phenotypic characteristics consistent with the breed description, and the selection of animals for removal from the breeding program is problematic at times due to high uniformity within the breed. With the objective of identifying an additional non-invasive selection criterion with potential uniqueness to the Dutch Konik, this study investigates the anatomic parameters of the distal equine limb, with a specific focus on the relative lengths of the individual splint bones. Post-mortem dissections performed on distal limbs of Dutch Konik (n = 47) and modern domesticated horses (n = 120) revealed significant differences in relation to the length and symmetry of the 2nd and 4th Metacarpals and Metatarsals. Distal limb characteristics with apparent uniqueness to the Dutch Konik are described which could be an important tool in the selection and preservation of the breed.
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Biology, Other; RpoS; crystal structure; Legionella pneumophila; intracellular pathogen; regulatory factor
Online: 29 November 2017 (05:04:33 CET)
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Legionella pneumophila RpoS (LpRpoS) is an alternative sigma factor of RNA polymerase (RNAP) essential for virulence and stress resistance. To investigate the mechanism of RpoS in the intracellular pathogen L. pneumophila, we determined the high-resolution crystal structure of the LpRpoS (residues 95-194) containing a partial region 1.2 and region 2. The structure of LpRpoS (residues 95-194) reveals that the conserved residues are critical for promoter melting, DNA and core RNAP binding. The differences in regulatory factor binding site between Escherichia coli RpoS and LpRpoS suggest that LpRpoS may employ a distinct mechanism to recruit alternative regulatory factors controlling transcription initiation.
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Biology, Anatomy & Morphology; radiation; skin barrier; sebaceous gland; transepidermal water loss; skin pH
Online: 23 November 2017 (08:33:29 CET)
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Abstract: Radiation-induced skin injury can be a serious cutaneous damage and have specific characteristics. Asymptomatic periods are classified as the latent stage. The skin barrier plays a critical role in the modulation of skin permeability and hydration and protects the body against a harsh external environment. However, an analysis on the skin barrier dysfunction against radiation exposure in the latent stage has not been conducted. Thus, we investigated whether skin barrier is impaired by irradiation in the latent stage and aimed to identify the molecules involved in skin barrier dysfunction. We analyzed skin barrier function and its components in SKH-1 mice that received 20 and 40 Gy local irradiation. Increased transepidermal water loss and skin pH were observed in the latent stage of the irradiated skin. Skin barrier components, such as structural proteins and lipid synthesis enzymes in keratinocyte, increased in the irradiated group. Interestingly, we noted sebaceous gland atrophy and increased serine protease and inflammatory cytokines in the irradiated skin during the latent period. This finding indicates that the main factor of skin barrier dysfunction in the latent stage of radiation-induced skin injury is sebaceous gland deficiency, which could be an intervention target for skin barrier impairment.
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Biology, Other; Suya (Barbecued meat); biochemical analysis; total aerobic bacteria count; Baze University, Lugbe; Kubwa; Maitama
Online: 22 November 2017 (17:05:24 CET)
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Barbecued meat, popularly known as ‘Suya’ in Nigeria, is eaten by most Nigerians. However, the raw meat is sometimes prepared in unhygienic environments. This study examines the possibility of contracting infectious food and water borne diseases as a result of eating microbial contaminated barbecued meat. Meat samples were collected from four locations- Baze University, Kubwa, Lugbe and Maitama within FCT, Abuja, Nigeria. Microbial analysis of the samples showed bacterial contamination of all the barbecued meat sampled from the different locations. These meat samples were contaminated with indicator bacteria such as Escherichia coli, Staphylococcus aureus, Providencia spp, Bacillus spp, and Pseudomonas aeroginosa.Comparative analysis of the total aerobic bacterial count revealed a significantly higher concentration of bacteria in the barbecued meat compared to the raw meat samples. The specific bacteria were on average about 1.5 – 5.9 times higher in the barbecued meat relative to the raw meat samples. This alarming trend was observed in all selected locations.In addition, the bacterial contamination of the barbecued meat sampled from Baze University was significantly lower (6.0 x 105 CFU/g) in comparison to the barbecued meat from the other locations: Lugbe - 31.2 x105 CFU/g, Kubwa - 34.0 x 105 CFU/g and Maitama - 42.6 x 105 CFU/g, with the latter being the most contaminated. The implications of this result in relation to human health and hygiene are discussed.
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Biology, Other; bacteria isolates; bacteria; water sources; physicochemical parameters; bacteriological parameters
Online: 22 November 2017 (09:23:39 CET)
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Diseases caused by contaminated water consumption and poor hygiene are among the leading cause of death in children, the elderly and people with compromised immune system. The present study aims to assess the drinking water quality of some selected drinking water sources in the chosen study area using water quality index (WQI). Samples of drinking waters were collected from four different sources—river, sachet (packaged), borehole and well in Jabi, Abuja, Nigeria for physicochemical and bacteriological analyses using standard methods. With the exception of pH, river water had the highest content of all the physicochemical parameters examined. Some of the physicochemical parameters such as temperature and pH determined in this study were mostly within the World Health Organization (WHO) standard. The bacteriological analyses revealed that the highest total viable counts of 1.54 (0.12) × 102 (cfu/mL) were obtained in the river sample while the least values of 0.03 (0.00) × 102 (cfu/mL) were obtained in the sachet water. Three bacterial isolates of Escherichia coli, Pseudomonas spp and Aeromonas spp were isolated from well water while Pseudomonas spp and Proteus spp were isolated from borehole water. All other bacteria were isolated from the river. The study demonstrates that the safest drinking water source in Idu district, Jabi, Abuja is the sachet/packaged water while the least safe is the river water due to the presence of significant opportunistic pathogens. The results of this study are beneficial for water quality management and could be used for low-cost effective water quality assessment in Jabi.
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Biology, Ecology; statistical mechanics; resource partitioning; stochastic processes; population dynamics
Online: 22 November 2017 (06:31:17 CET)
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Many species of plants are found in regions to which they are alien. Their global distributions are characterised by a family of exponential functions of the kind that arise in elementary statistical mechanics (an example in ecology is MacArthur's broken stick). We show here that all these functions are quantitatively reproduced by a model containing a single parameter – some global resource partitioned at random on the two axes of species number and site number. A dynamical model generating this equilibrium is a two fold stochastic process and suggests a curious and interesting biological interpretation in terms of niche structures fluctuating with time and productivity; with sites and species highly idiosyncratic. Idiosyncrasy implies that attempts to identify a priori those species likely to become naturalized are unlikely to be successful. Although this paper is primarily concerned with a particular problem in population biology, the two fold stochastic process may be of more general interest.
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Biology, Agricultural Sciences & Agronomy; carbon response curve; light response curve; photosynthesis; pigment determination; sago palm.
Online: 20 November 2017 (07:36:39 CET)
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Photosynthetic activities of the sago palm (Metroxylon sagu Rottb.) were studied to find out its sensitivity to changes in ambient air temperature. The minimum ambient air temperature designed for the experiment was 25–29⁰C, while the higher end was 29–33⁰C. Several photosynthetic parameters were studied to support our analysis in sago photosynthetic activity, including diurnal leaf gas exchange, assimilation rate vs. CO2 concentration, leaf greenness, leaf chlorophyll content, and photosynthetic rate vs. irradiance. We found that sago palm photosynthetic activity tends to be more sensitive to minimum than to maximum ambient air temperature. The plants exposed to higher air temperatures had dark green leaf color associated with higher rates of diurnal photosynthesis, chlorophyll content, and rubisco limited photosynthetic activity. They also exhibited higher trend in optimum irradiance absorption level. Consequently, maximum light energy dissipation occurred at higher temperatures.
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Mehdi Sharifi-Rad,
Elena Maria Varoni,
Bahare Salehi,
Javad Sharifi-Rad,
Karl R. Matthews,
Seyed Abdulmajid Ayatollahi,
Farzad Kobarfard,
Salam A. Ibrahim,
Dima Mnayer,
Zainul Amiruddin Zakaria,
Majid Sharifi-Rad,
Zubaida Yousaf,
Marcello Iriti,
Adriana Basile,
Daniela Rigano
Biology, Plant Sciences; Zingiber; ginger; essential oil; rhizome; herbal remedies; traditional healing systems; food preservatives
Online: 16 November 2017 (04:38:52 CET)
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Plants of the genus Zingiber (Family Zingiberaceae) are widely used throughout the world as food and medicinal plants. They represent very popular herbal remedies in various traditional healing systems; in particular, rhizome of Zingiber spp. plants has a long history of ethnobotanical uses because of a plethora of curative properties. Antimicrobial activity of rhizome essential oil has been extensively confirmed in vitro and attributed to its chemical components, mainly consisting in monoterpene and sesquiterpene hydrocarbons such as α-zingiberene, ar-curcumene, β-bisabolene and β-sesquiphellandrene. In addition, gingerols have been identified as the major active components in the fresh rhizome, whereas shogaols, dehydrated gingerol derivatives, are the predominant pungent constituents in dried rhizome. Zingiber spp. may thus represent a promising and innovative source of natural alternatives to chemical food preservatives. This approach would meet the increasing concern of consumers aware of the potential health risks associated with the conventional antimicrobial agents in food. This narrative review aims providing a literature overview on Zingiber spp. plants, their cultivation, traditional uses, phytochemical constituents and biological activities.
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Biology, Other; Hedgehog signaling; skin; epidermis; hair follicle; development; homeostasis; basal cell carcinoma; signaling crosstalk
Online: 15 November 2017 (07:11:15 CET)
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The epidermis is the outermost layer of skin and provides a protective barrier against environmental insults. It is a rapidly renewing tissue undergoing constant regeneration, maintained by several types of stem cells. Hedgehog (HH) ligands activate one of the fundamental signaling pathways that contribute to epidermal development, homeostasis and repair. The HH pathway interacts with other signal transduction pathways such as those activated by Wnt and bone morphogenetic protein. Furthermore, aberrant activation of HH signaling is associated with various tumors, including basal cell carcinoma. Therefore, an understanding of the regulatory mechanisms of the HH signaling pathway is important to elucidate fundamental mechanisms underlying both organogenesis and carcinogenesis. In this review, we discuss the role of the HH signaling pathway in skin development, homeostasis and basal cell carcinoma formation, providing an update of current knowledge in this field.
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Biology, Entomology; DNA barcoding; genetic diversity; hymenopteran parasitoids; Nephotettix spp.; Nilaparvata lugens; rice
Online: 13 November 2017 (17:06:38 CET)
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On-going intensification of rice production systems in Southeast Asia is causing devastating yield losses each year due to rice hoppers. Continuing development of immunity to resistant rice varieties and pesticide application further complicate this problem. Hence, there is a high demand for biological control agents. Egg parasitoid wasps are among the most important natural enemies of rice hoppers such as Nilaparvata lugens and Nephotettix spp. However, our knowledge on their diversity is still very limited due to their small size and the lack of available morphological information. Classifying these parasitoids is the first step to properly understand their role in the rice agroecosystem. We used traditional morphological identification as well as DNA sequencing of COI and 28S genes to investigate the diversity of four important hopper egg parasitoid genera in the Philippines. Parasitoids of the genera Anagrus spp., Oligosita spp., Gonatocerus spp. and Paracentrobia spp. were collected in eight study landscapes located in Luzon. We found discrepancies between the morphological and the molecular analysis. Morphological and molecular results were only valid for Paracentrobia spp. Anagrus spp. and Gonatocerus spp. showed more genetic diversity, than expected after the morphological analysis, indicating cryptic species. The sequences for Oligosita spp. revealed less variation than expected. This is the first study on molecular diversity of rice parasitoids in the Philippines. More research combining morphological, behavioural and genetic methods as well as the establishment of a comprehensive DNA database is urgently needed to assess the performance and suitability of these organisms as biocontrol agents.
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Biology, Animal Sciences & Zoology; microRNA; pig; biomarker; xenotransplantation
Online: 7 November 2017 (10:53:19 CET)
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The pig is an important source of meat production and provides a valuable model for certain human diseases. MicroRNA (miRNA), which is non-coding RNA and regulates gene expression at the posttranscriptional level, plays a critical role in various biological processes. Studies on identification and function of mature miRNAs in multiple pig tissues are increasing, yet the literature is limited. Therefore, we reviewed current research to determine the miRNAs expressed in specific pig tissues that are involved in carcass values (including muscle and adipocytes), reproduction (including pituitary, testis, and ovary), and development of some solid organs (e.g., brain, lung, kidney, and liver). We also discuss the possible regulating mechanisms of miRNA. Finally, as pig organs are suitable candidates for xenotransplantation, biomarkers of their miRNA in xenotransplantation were evaluated.
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Biology, Agricultural Sciences & Agronomy; adoption; land-use; degradation; ethnobotany; networking; agroforestry; dry semi-deciduous
Online: 7 November 2017 (04:06:23 CET)
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Bamboo agroforestry is currently being promoted as a viable land use option to reduce dependence on natural forest for wood fuels in Ghana. To align the design and introduction of bamboo agroforestry in conformity with farmers’ needs, perceptions, skills and local cultural practices, information on its acceptability and adoption potential among farmers is necessary. It is therefore the objective of this study to (1) describe bamboo ethnobotany and (2) assess socioeconomic factors that affect the acceptability and adoption of bamboo and its integration into farming practices. Accordingly, information has been collected from 200 farmers in the dry semi-deciduous forest zone of Ghana. The study identified the socioeconomic risks and uncertainties as well as biophysical factors that are likely to influence the potential adoption of bamboo agroforestry in the study region. Gender, age, farmers’ known uses of bamboo, the practice of leaving trees on farmlands, farmers’ networking and access to extension services, land availability and ownership by farmers were identified as suitable predictor variables for the adoption of bamboo agroforestry. It is envisaged that bamboo agroforestry is a good bet in the DSFZ though there is the need to explore domestic energy (fuelwood) provision and substitution potential in order to have a broader picture of the technology.
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Biology, Other; parboiled rice; medium-grain white rice; medium-grain brown rice; sensory evaluation; consumer acceptability
Online: 6 November 2017 (07:07:41 CET)
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Background: Previous in vitro and in vivo studies have demonstrated that storage of cooked rice at 4 °C for 24 h and reheating to 65 °C significantly reduced starch digestibility and postprandial glycaemic responses. Moreover, the effect was greater for parboiled rice compared to other rice varieties commonly consumed in New Zealand. This study aimed to evaluate consumer preferences of related sensory attributes and consumer acceptability of several rice varieties freshly cooked or reheated. Method: Sixty-four consumers volunteered and recorded on Visual Analoge Scales their preference and acceptability of freshly prepared or cold-stored and reheated medium grain white, medium grain brown and parboiled rice. Results: All six rice samples were accepted by participants (average 54%). Reheated parboiled rice and reheated medium grain brown rice were both accepted by participants as a preferred staple meal compared to other rice samples. Among all rice samples, the sweetness and the flavour of freshly cooked warm medium-grain white rice were less preferred (scored 42.1% and 45.0% respectively) compared with other samples (P = 0.05). Participants who prepared and consumed brown rice at home regularly (more than 10 times per month), preferred the reheated brown rice (73.8% (67.4, 80.2)) and reheated parboiled rice (74.3% (67.9, 80.7)) (P < 0.001). Conclusions: It is suggested that reheated parboiled rice, with the lowest starch digestibility and glycaemic impact (both in vitro glucose release and in vivo glucose response) could be accepted as a healthier alternative for the daily staple meal.
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Biology, Agricultural Sciences & Agronomy; Expired Plant Variety Protection (ex-PVP); maize; nitrogen stress; Nitrogen Use Efficiency (NUE); U.S. Corn Belt Germplasm
Online: 4 November 2017 (07:39:11 CET)
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Nitrogen use efficiency (NUE) in maize (Zea mays L.) is an important trait to maximize yield with minimal input of nitrogen (N) fertilizer. Expired Plant Variety Protection (ex-PVP) Act-certified germplasm may be an important genetic resource for public breeding sectors. The objectives of this research were to evaluate the genetic variation of N-use traits and to characterize maize ex-PVP inbreds adapted to the U.S. Corn Belt for NUE performance. Eighty-nine ex-PVP inbreds [36 stiff stalk synthetic (SSS), and 53 non-stiff stalk synthetic (NSSS)] were genotyped using 26,769 single-nucleotide polymorphisms, then 263 single-cross maize hybrids derived from these inbreds were grown in eight environments from 2011 to 2015 at two N fertilizer rates (0 and 252 kg N ha−1) and three replications. Genetic utilization and the yield response to N fertilizer were stable across environments and were highly correlated with yield under low and high N conditions, respectively. Cluster analysis identified inbreds with desirable NUE performance. However, only one inbred (PHK56) was ranked in the top 10% for yield under both N-stress and high N conditions. Broad-sense heritability across 12 different N-use traits ranged from 0.11 to 0.77, but was not associated with breeding value accuracy. Nitrogen-stress tolerance was negatively correlated with the yield increase from N fertilizer.
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Biology, Plant Sciences; RGSV; movement proteins; gene silencing; transgenic mechanism; virus-induced small interfering RNA; RNA silencing pathway; antiviral plant defenses
Online: 2 November 2017 (03:05:04 CET)
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Rice grassy stunt virus (RGSV) a member of Tenuivirus family, is very potent and destructive which effects rice crop in many countries, particularly China. Non coding RNAs have important functions in development and epigenetic regulation of gene expression in numerous organsisms. There is three type of small non coding RNAs have been found in eukaryotes, which are small interferring RNAs (siRNAs), microRNAs (miRNAs) and piwi interacting RNAs (piRNAs). Small RNAs (sRNAs) origination is from the infecting virus which is known as virus-derived small interfering RNAs (vsiRNAs), has responsibility for RNA silencing in plants. Virus-induced gene silencing (VIGS) is mainly dependent on RNA silencing (RNAi). Interestingly, RNA silencing happens in plants during viral infections. RNAi technique showed significant results in Nephotettix cincticeps. RNAi technique demonstrated the gene silencing of planthopper Nilaparvata lugens. The proteins P5, pcf4, Dnj, psn5, and pn6 act as potential movement proteins and serve as silencing suppressors for RGSV. VsiRNAs originate from dsRNA molecules which require Dicer-like (DCL) proteins, RNA dependent RNA polymerase (RdRP) proteins, and Argonaute (AGO) proteins. RdRP uses ssRNA for perfect RNA amplification process and can also be used for DCL dependent secondary vsiRNA formation. VSRs interfere with the movement of signals during silencing mechanism. Moreover, intercellular movement of viruses is facilitated by virus-encoded movement protein. RNAi is found in many eukaryotes which are related to transcriptional or post-transcriptional regulation by gene suppression. Transcription is bidirectional in ssDNA viruses which are originated from dsRNA molecules. In this review, we highlighted the biology of Rice grassy stunt virus and its insect vector and its silencing suppressors. This work will be helpful for plant virologists to understand the whole biogenesis mechanism for rice viruses especially RGSV.
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Biology, Agricultural Sciences & Agronomy; Fusarium oxysporum f. sp. Niveum; p-isopropyl benzoic acid; Biofungicide; Disease management
Online: 30 October 2017 (15:46:36 CET)
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Watermelon fusarium wilt caused by Fusarium oxysporum f.sp. niveum (FON) is a destructive soil-borne disease throughout the world leading to serious economic losses and limit watermelon production. Cuminic acid, extracted from the seed of Cuminum cyminum L., belongs to benzoic acid analogues. In this study, the median effective concentration (EC50) values for cuminic acid in inhibiting mycelial growth of FON was 22.53μg/mL. After treatment with cuminic acid, mycelial morphology was seriously influenced; cell membrane permeability and glycerol content were increased markedly, but pigment and mycotoxin (mainly fusaric acid) were significantly decreased. Synthesis genes of bikaverin and fusaric acid both were down regulated compared with the control confirmed by quantitative RT-PCR. In greenhouse experiments, cuminic acid at all concentrations displayed significant bioactivities against FON. Importantly, significant enhancement of activities of SOD, POD, CAT and decrease of MDA content after cuminic acid treatment in watermelon leaves were observed in vivo. These indicated that cuminic acid not only showed high antifungal activity, but also could enhance the self-defense system of the host plant. Above all, cuminic acid showed the potential as a biofungicide to control FON.
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Biology, Ecology; Arbuscular mycorrhiza; Chrysanthemum morifolium; N acquisition; Salt stress
Online: 30 October 2017 (15:32:49 CET)
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The study aimed to investigate the effects of colonization with two arbuscular mycorrhizal (AM) fungi, Funneliformis mosseae , Diversispora versiformis , alone and in combination on the growth and nutrient acquisition of NaCl-stressed Chrysanthemum morifolium (Hangbaiju) plants in the greenhouse experiment. Mycorrhizal and non-mycorrhizal Hangbaiju plants were grown under different salinity levels imposed by 0, 50 and 200 mM NaCl for five months, following 6 weeks of non-saline pre-treatment. The results showed that root length, shoot and root dry weight, total dry weight, shoot and root N concentration were higher in mycorrhizal than in non-mycorrhizal plants under moderate saline conditions especially with D. versiformis colonization. As salinity increased, the mycorrhizal colonization, the mycorrhizal dependence (MD) decreased. Enhancement of tissue N acquisition is probably the main mechanism underlying salt tolerance in AM plants. It is suggested that the symbiotic associations between D. versiformis fungus and C. morifolium plants may be taken as a biotechnological practice in culture.
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Biology, Animal Sciences & Zoology; refinement; mouse welfare; mouse husbandry; mouse aggression; male mice; social organisation; group housing; single housing; animal husbandry; animal welfare; animal management
Online: 24 October 2017 (03:29:02 CEST)
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It is widely recommended to group house male laboratory mice because they are ‘social animals’, but male mice do not naturally share territories and aggression can be a serious welfare problem. Even without aggression, not all animals within a group will be in a state of positive welfare. Rather, many male mice may be negatively affected by the stress of repeated social defeat and subordination, raising concerns about welfare and also research validity. However, individual housing may not be an appropriate solution, given the welfare implications associated with no social contact. An essential question is whether it is in the best welfare interests of male mice to be group- or singly-housed. This review explores the likely impacts, positive and negative, of both housing conditions, presents results of a survey of current practice and awareness of mouse behaviour, and includes recommendations for good practice and future research. We conclude that whether group- or single-housing is better (or less worse) in any situation is highly context-dependent according to several factors including strain, age, social position, life experiences, and housing and husbandry protocols. It is important to recognise this and evaluate what is preferable from animal welfare and ethical perspectives in each case.
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Biology, Plant Sciences; common bean; soybean; Argonaute5; legume-rhizobia symbiosis
Online: 18 October 2017 (03:20:37 CEST)
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The establishment of the symbiosis between legumes and nitrogen-fixing rhizobia is finely regulated at the transcriptional, posttranscriptional and posttranslational levels. Argonaute5 (AGO5), a protein involved in RNA silencing, is able to bind both viral RNAs and microRNAs to control plant-microbe interactions and plant physiology. For instance, AGO5 regulates the systemic resistance of Arabidopsis against Potato Virus X as well as the pigmentation of soybean (Glycine max) seeds. Here, we show that AGO5 is also playing a central role in legume nodulation based on its preferential expression in common bean (Phaseolus vulgaris) and soybean roots and nodules. We also report that the expression of AGO5 is induced after 1 hour of inoculation with rhizobia. Down-regulation of AGO5 gene in P. vulgaris and G. max causes diminished root hair curling, reduces nodule formation and interferes with the induction of three critical symbiotic genes: NUCLEAR FACTOR Y-B (NF-YB), NODULE INCEPTION (NIN) and FLOTILIN2 (FLOT2). Our findings provide evidence that the common bean and soybean AGO5 genes play an essential role in the establishment of the symbiosis with rhizobia in determinate legumes.
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Biology, Other; microbial communities; host-microbe interactions; mathematical modelling; diatoms; synthetic ecology; algal biotechnology
Online: 17 October 2017 (17:37:49 CEST)
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The pennate diatom Phaeodactylum tricornutum is a model organism able to synthesize industrially-relevant molecules. Commercial-scale cultivation currently requires large monocultures, prone to bio-contamination. However, little is known about the identity of the invading organisms. To reduce the complexity of natural systems, we systematically investigated the microbiome of non-axenic P. tricornutum cultures from a culture collection in reproducible experiments. The results revealed a dynamic bacterial community that developed differently in “complete” and “minimal” media conditions. In complete media, we observed an accelerated “culture crash”, indicating a more stable culture in minimal media. The identification of only four bacterial families as major players within the microbiome suggests specific roles depending on environmental conditions. From our results we propose a network of putative interactions between P. tricornutum and these main bacterial factions. We demonstrate that, even with rather sparse data, a mathematical model can be reconstructed that qualitatively reproduces the observed population dynamics, thus indicating that our hypotheses regarding the molecular interactions are in agreement with experimental data. Whereas the model in its current state is only qualitative, we argue that it serves as a starting point to develop quantitative and predictive mathematical models, which may guide experimental efforts to synthetically construct and monitor stable communities required for robust upscaling strategies.
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Biology, Forestry; fuel reduction; slash pile; grinding operation; grapple excavator; horizontal grinder; simulation; Sierra Nevada; California; wildfire
Online: 12 October 2017 (11:45:44 CEST)
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The processing of woody biomass waste piles for use as fuel instead of burning them was investigated. At each landing slash pile location, a 132 kW grapple excavator was used to transfer the waste piles into a 522 kW horizontal grinder. Economies of scale could be expected when grinding a larger pile, although the efficiency of the loading operation might be diminished. Here, three piles were ground and the operations were time-studied: Small (20 m long × 15 m wide × 4 m high), Medium (30 × 24 × 4 m), and Large (35 × 30 × 4 m) piles. Grinding the Medium pile was found to be the most productive at 30.65 bone dry tons per productive machine hour without delay (BDT/PMH0), thereby suggesting that there might be an optimum size of slash pile for a grinding operation. We also examined modeling of the excavator and grinder operations, and we observed that the constructed simulation model well-replicated the actual operations. Based on the modeling, we estimated that the productivity of grinding at a landing area of 710 m2 of slash pile location was 31.24 BDT/PMH0, which was the most productive rate.
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Biology, Agricultural Sciences & Agronomy; geometric morphometrics; morphology; paramere; Macrolophus pygmaeus; Macrolophus melanotoma; Macrolophus costalis
Online: 12 October 2017 (03:31:43 CEST)
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Within the genus Macrolophus (Heteroptera: Miridae), the species M. costalis (Fieber), M. melanotoma (Costa) and M. pygmaeus (Rambur) are present in the Mediterranean region on a wide variety of plant species. While M. costalis can easily be separated from the other two by the black tip at the scutellum, M. pygmaeus and M. melanotoma are cryptic species, extremely similar to one another in external traits, which have resulted in misidentifications. M. pygmaeus is an efficient biological control agent, both in greenhouse and field crops. The misidentification of these cryptic species could limit the effectiveness of biological control programs. Although morphology of the left paramere of the male genitalia has been used as a character for identification of these two cryptic species, there is controversy on the reliability of this character as a taxonomic tool for these species. Using geometric morphometric techniques, which are a powerful approach in detecting slight shape variations, the left parameres from these three Macrolophus species were compared. The paramere of M. costalis was larger and had a different shape than that of M. melanotoma and M. pygmaeus; however, no differences in size or shape were found between the left paramere of M. melanotoma and that of M. pygmaeus. Therefore, our results confirm that this character is too similar and it cannot be used to discriminate between these two cryptic species.
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Biology, Agricultural Sciences & Agronomy; wastewater irrigation; soil characteristics; agriculture; pollution; China
Online: 9 October 2017 (10:09:42 CEST)
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Fresh water is valuable nonrenewable resource and plays an important role of maintaining economic and social development. Condisering its large population and consumption potential, water resources deficit will certainly impede basic industries sustainable development of China in the near future. Application of sewage irrigation, to some extent, was regarded as an alternative way to solve the problem of agricultural irrigation water shortage in some areas (such as North China). However, accompanied with extensive implementation of sewage irrigation, some problems on sewage irrigation in agriculture are gradually obvious, especially serious pollution and destruction for farmland. In this paper, the effects of sewage irrigation on soil physical (soil bulk density, soil resistance to penetration and field capacity), chemical (pH, soil organic matter, nitrogen, phosphrous, patassium, heavy metal and organic pollutants) and biological characteristics (soil microorganism and enzyme activities) of farmland in China were systematically reviewed on the base of the current utilization status of China’s farmland sewage irrigation and some feasible suggestions were put forward to the development prospect for the future. This review will be beneficial for promoting healthy development of sewage irrigation and providing theoretical support for reclamation and high efficiency of effluents in China.
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Biology, Forestry; forest stand parameters; SPOT-5 satellite image; textural and spectral features; topographic information; estimation model
Online: 3 October 2017 (16:33:25 CEST)
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In recent years, remote sensing technology has been widely used to predict forest stand parameters. In order to compare the effects of different features of remote sensing images and topographic information on the prediction of forest stand parameters, multivariate stepwise regression analysis method was used to build estimation models for important forest stand parameters by using textural and spectral features as well as topographic information of SPOT-5 satellite images in northeastern Heilongjiang Province in China as independent variables. The study results show that the optimal window to predict forest stand parameters using textural features of SPOT-5 satellite image is 9×9; the ability of textural features was better than that of spectral features in terms of predicting forest stand parameters; with the inclusion of topographic information, the accuracy of prediction of all models was improved, of which elevation has the most significant effect. The highest accuracy was achieved when predicting the stand volume (SV) (R2adj=0.820), followed by basal area (BA) (R2adj =0.778), accuracy of both above models exceeded 75%. The results show that models combined use of textural, spectral features and topographic information of SPOT-5 images have a good application prospect in predicting forest stand parameters.
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Biology, Forestry; Pine pitch canker; Galicia; spore trap; air sampling; qPCR; seasonal dynamics
Online: 2 October 2017 (16:00:11 CEST)
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The airborne inoculum of Fusarium circinatum, the fungal pathogen causing Pine Pitch Canker (PPC), is one of the main means of spread of the disease in forest stands and forest nurseries. Since this world-wide known pathogen was introduced in Europe, its biology in this newly infected area still remains scarcely known. To shed more light on this topic, we set an experiment on a naturally PPC infected forest of Monterey pine in Galicia (NW Spain) with the following two goals: (i) to describe the seasonal spore dispersal pattern during one year of regular sampling and (ii) to assess the spatial spore dispersal pattern around the infested plot. Portable rotating arm spore traps were used and complemented with meteorological measurements. The abundance of F. circinatum spores in the samples was evaluated by quantitative PCR (qPCR) with hydrolysis probe. The results showed almost permanent occurrence of the air inoculum throughout the whole year, being detected in 27 of the 30 samplings. No clear temporal trends were observed, but higher air inoculum was favoured by previous lower air temperatures and lower leaf wetness. Conversely, neither rainfall nor air humidity seemed to have any significant importance. The spatial spread of the inoculum was noted to be successful up to a distance of 1000 m in the wind direction, even with winds of just 5 m s-1. Our study shows that rotating arm spore traps combined with qPCR may be an efficient tool for F. circinatum detection.
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Biology, Anatomy & Morphology; Cyprinidae; Luciobarbus barbulus; Luciobarbus, Iran; taxonomy
Online: 1 October 2017 (06:30:03 CEST)
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Western Iran barb species are scientifically, environmentally, and economically important. Some of them are the largest riverine freshwater species, which will grow in size and weight to 170 cm, and 120 kg respectively. There is little information on taxonomy or environmental status of these species Luciobarbus barbulus is one of the important large species. During the resent year since 2013, in order to find the new record of large barb species, sampling program carried out in western Iran,. Luciobarbus barbulus briefly described by Heckel (1849) but during the time, have been synonymized with other related species or vice versa, other similar species miss-identically have been known as this species. Also the synonymy of Luciobarbus barbulus with L. pectoralis remains uncertain. The possible syntypes of L. barbulus in Vienna Museum (NMW 53957 and NMW 6596) are in too poor condition to be of any value, being mostly bones, and are dried, and. The fleshy lip of NMW 6596, (measures 119.3 mm standard length) fold of the original description could not be discerned, teeth are missing and the dorsal fin is broken off short. In 1997 this was the only syntype recognized. The catalog in Vienna lists only 1 fish, while Heckel's description refers to several fishes!. So designing of Lecotype and re-description of L. barbulus is essential. In this paper the details of description and differences between these species are given.